https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=Jgrethe 2026-05-14T07:33:35Z User contributions MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=60721 2010-11-11T04:52:07Z

<p>Jgrethe: /* Attendees */</p> <hr /> <div> [[Events|Back to Events]]<br /> <br /> '''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br /> =Logistics=<br /> * When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br /> * Where: Boston SPL, 1249 Facility<br /> * Who: Engineering Core leaders and key personnel<br /> * Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, Massachusetts 02142, Phone: 1-617-494-6600<br /> <br /> =Strategy=<br /> * Slicer 3.6.x is in maintenance mode.<br /> * New development efforts are targeted at Slicer 4. <br /> * Communication with &quot;Customers&quot; is a top priority.<br /> ** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br /> ** For end-users: simplify the user interface, streamline and simplify common workflows<br /> ** Support the development of solutions<br /> ** We are '''not''' in the &quot;early adopter game&quot; for the next two years<br /> <br /> ==Short term goals==<br /> * Targeted for AHM<br /> * Assign owners for each bullet item on this list<br /> ===Slicer 3===<br /> *stabilize and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues debug Slicer 3.6]<br /> *stabilize and document extensions and the process leading to them<br /> <br /> ===Slicer 4===<br /> * Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br /> ** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br /> ** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br /> * Rons number 2: Make load/save easier to understand for new users.<br /> ** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br /> ** Plan and implement minimalist UI design for load<br /> * Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br /> * Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br /> * Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br /> * Implement and package up module templates for developers of interactive modules to get a jump on consistent UXP.(wjp)<br /> * Refine design of slice viewer's control panel to make more compact and quiet. (wjp)<br /> * [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots <br /> * Update Wiki pages:<br /> ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br /> ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br /> ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br /> * Create a XML Schema for .mrml to check if a mrml document is 'well-formed' and 'valid'. Automatic generated (error free) parser can then be used for accessing/editing mrml files.<br /> * Bug patches from Slicer 3.6 to Slicer 4<br /> <br /> === Requests from the DBPs ===<br /> ==== Utah ====<br /> ==== Iowa ====<br /> ==== UCLA ====<br /> * [http://trackvis.org/docs/?subsect=fileformat trackvis file format interoperability]<br /> * [http://www.ncbi.nlm.nih.gov/pubmed/20206274 NIfTI DWI file format interoperability] [http://mind.loni.ucla.edu/specification/overview/ LONI MiND Framework]<br /> <br /> ==== MGH ====<br /> <br /> == Longer Term Goals ==<br /> * Identify standard workflows and allow CLI modules to declare which workflows they should be run within<br /> ** Perhaps parallel's effort to associate CLI modules with Widgets<br /> * Reduce list of available modules when a user declares a field-of-interest (e.g., microscopy researchers should not be shown MRI-specific modules)<br /> * Simplify how tests are written for loadable modules<br /> * Review all Slicer modules and determine which should be distribute with Slicer and which should be switched to being downloadable<br /> ** Determine support policies for Slicer-included modules versus downloadable modules<br /> ** Determine testing, documentation, review, and platform requirements to be a Slicer-included module<br /> * DICOM read and write (local and remote) via CTK<br /> * extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br /> * Organizing multiple data sets from one subject: time series, image fusion etc.<br /> * Packaging/Superbuild fixes<br /> ** Package for linux<br /> ** Windows - clean registry on uninstall<br /> ** Mac - .dmg into application folder<br /> * Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br /> * Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br /> ** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br /> * Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br /> * Define a &quot;Core&quot; Slicer that can be distributed with InsightApplications repository of ITKv4<br /> ** Review Slicer application framework to support modularization and customization<br /> ** Two audiences:<br /> *** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...<br /> *** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br /> * Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br /> * Switch to client/server dashboards and take advantage of its benefits<br /> ** Each night binaries copied from client machines to Dashboard page/database that manages them<br /> ** Ensures Dashboards, builds, releases using common tags/svn#s<br /> ** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br /> ** Dashboard specifies what should be build on what clients (&quot;CDash@home&quot; or &quot;Client/Server CDash&quot;)<br /> * GUI Testing<br /> ** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br /> * Support scenes containing data that spans multiple scales in time and space<br /> ** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br /> * Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br /> * Guidelines and examples for GPU-based algorithms<br /> * Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br /> * Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br /> * Batch processing (IPython) examples<br /> ** includes an algorithm validation framework<br /> * Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br /> * Consider ITKv4 module management tools being developed (after they have been released as stable release)<br /> ** Documentation prior to code development<br /> ** Module-specific dashboards<br /> ** forum-style commentaries on modules<br /> * Improve support of Windows platform <br /> ** Simplify compilation of Slicer on Windows Machines <br /> ** Increase speed and stability of Slicer on Windows Machines<br /> * Change release policy: A Slicer release version must not use/depend on ITK Review. If we do not make this modification then we cannot release Slicer as Debian package anymore.<br /> * Command line module logic redesign<br /> ** DOM objects in shared memory<br /> ** WriteCLI in all mrml nodes<br /> <br /> =Agenda=<br /> *Review of current commitments and planned activities<br /> **Kitware<br /> **GE<br /> **Isomics<br /> **St. Louis<br /> **UCSD<br /> <br /> *Discussion of short term goals<br /> *Discussion of long term goals<br /> <br /> =See also=<br /> *http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br /> *http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br /> <br /> =Attendees=<br /> #Steve Pieper<br /> #Will Schroeder<br /> #Jim Miller<br /> #Ron Kikinis<br /> #Alex Yarmarkovich<br /> #Jeff Grethe (18th only - 17th @ Neuroscience/Committee meeting)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=60720 2010-11-11T04:51:40Z

<p>Jgrethe: /* Attendees */</p> <hr /> <div> [[Events|Back to Events]]<br /> <br /> '''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br /> =Logistics=<br /> * When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br /> * Where: Boston SPL, 1249 Facility<br /> * Who: Engineering Core leaders and key personnel<br /> * Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, Massachusetts 02142, Phone: 1-617-494-6600<br /> <br /> =Strategy=<br /> * Slicer 3.6.x is in maintenance mode.<br /> * New development efforts are targeted at Slicer 4. <br /> * Communication with &quot;Customers&quot; is a top priority.<br /> ** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br /> ** For end-users: simplify the user interface, streamline and simplify common workflows<br /> ** Support the development of solutions<br /> ** We are '''not''' in the &quot;early adopter game&quot; for the next two years<br /> <br /> ==Short term goals==<br /> * Targeted for AHM<br /> * Assign owners for each bullet item on this list<br /> ===Slicer 3===<br /> *stabilize and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues debug Slicer 3.6]<br /> *stabilize and document extensions and the process leading to them<br /> <br /> ===Slicer 4===<br /> * Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br /> ** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br /> ** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br /> * Rons number 2: Make load/save easier to understand for new users.<br /> ** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br /> ** Plan and implement minimalist UI design for load<br /> * Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br /> * Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br /> * Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br /> * Implement and package up module templates for developers of interactive modules to get a jump on consistent UXP.(wjp)<br /> * Refine design of slice viewer's control panel to make more compact and quiet. (wjp)<br /> * [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots <br /> * Update Wiki pages:<br /> ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br /> ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br /> ** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br /> * Create a XML Schema for .mrml to check if a mrml document is 'well-formed' and 'valid'. Automatic generated (error free) parser can then be used for accessing/editing mrml files.<br /> * Bug patches from Slicer 3.6 to Slicer 4<br /> <br /> === Requests from the DBPs ===<br /> ==== Utah ====<br /> ==== Iowa ====<br /> ==== UCLA ====<br /> * [http://trackvis.org/docs/?subsect=fileformat trackvis file format interoperability]<br /> * [http://www.ncbi.nlm.nih.gov/pubmed/20206274 NIfTI DWI file format interoperability] [http://mind.loni.ucla.edu/specification/overview/ LONI MiND Framework]<br /> <br /> ==== MGH ====<br /> <br /> == Longer Term Goals ==<br /> * Identify standard workflows and allow CLI modules to declare which workflows they should be run within<br /> ** Perhaps parallel's effort to associate CLI modules with Widgets<br /> * Reduce list of available modules when a user declares a field-of-interest (e.g., microscopy researchers should not be shown MRI-specific modules)<br /> * Simplify how tests are written for loadable modules<br /> * Review all Slicer modules and determine which should be distribute with Slicer and which should be switched to being downloadable<br /> ** Determine support policies for Slicer-included modules versus downloadable modules<br /> ** Determine testing, documentation, review, and platform requirements to be a Slicer-included module<br /> * DICOM read and write (local and remote) via CTK<br /> * extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br /> * Organizing multiple data sets from one subject: time series, image fusion etc.<br /> * Packaging/Superbuild fixes<br /> ** Package for linux<br /> ** Windows - clean registry on uninstall<br /> ** Mac - .dmg into application folder<br /> * Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br /> * Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br /> ** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br /> * Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br /> * Define a &quot;Core&quot; Slicer that can be distributed with InsightApplications repository of ITKv4<br /> ** Review Slicer application framework to support modularization and customization<br /> ** Two audiences:<br /> *** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...<br /> *** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br /> * Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br /> * Switch to client/server dashboards and take advantage of its benefits<br /> ** Each night binaries copied from client machines to Dashboard page/database that manages them<br /> ** Ensures Dashboards, builds, releases using common tags/svn#s<br /> ** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br /> ** Dashboard specifies what should be build on what clients (&quot;CDash@home&quot; or &quot;Client/Server CDash&quot;)<br /> * GUI Testing<br /> ** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br /> * Support scenes containing data that spans multiple scales in time and space<br /> ** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br /> * Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br /> * Guidelines and examples for GPU-based algorithms<br /> * Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br /> * Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br /> * Batch processing (IPython) examples<br /> ** includes an algorithm validation framework<br /> * Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br /> * Consider ITKv4 module management tools being developed (after they have been released as stable release)<br /> ** Documentation prior to code development<br /> ** Module-specific dashboards<br /> ** forum-style commentaries on modules<br /> * Improve support of Windows platform <br /> ** Simplify compilation of Slicer on Windows Machines <br /> ** Increase speed and stability of Slicer on Windows Machines<br /> * Change release policy: A Slicer release version must not use/depend on ITK Review. If we do not make this modification then we cannot release Slicer as Debian package anymore.<br /> * Command line module logic redesign<br /> ** DOM objects in shared memory<br /> ** WriteCLI in all mrml nodes<br /> <br /> =Agenda=<br /> *Review of current commitments and planned activities<br /> **Kitware<br /> **GE<br /> **Isomics<br /> **St. Louis<br /> **UCSD<br /> <br /> *Discussion of short term goals<br /> *Discussion of long term goals<br /> <br /> =See also=<br /> *http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br /> *http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br /> <br /> =Attendees=<br /> #Steve Pieper<br /> #Will Schroeder<br /> #Jim Miller<br /> #Ron Kikinis<br /> #Alex Yarmarkovich<br /> #Jeff Grethe (18th - 17th @ Neuroscience/Committee meeting)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Iowa-NA-MIC-2010-Kickoff&diff=59664 2010-10-25T17:35:06Z

<p>Jgrethe: /* Engineers */</p> <hr /> <div> [[2010-09-Leadership-Brainstroming|Back to 2010 Brainstorming]]<br /> [[Events|Back to events page]]<br /> <br /> =What=<br /> == Planning the 3-year course of the Roadmap project ==<br /> <br /> ===Engineers ===<br /> *Clement Vachet, DBP engineer, 20% at UNC, working on Iowa DBP, translating NA-MIC technology into use for PREDICT HD<br /> *Mark Scully, DBP engineer at Iowa, Mark &amp; Clement will work closely together, both will attend engineering tcons<br /> *Two major areas: DTI processing and shape analysis<br /> *Marco Ruiz, integration of XNAT with GridWizard to allow XNAT pipeline access to external computational resources<br /> <br /> === DTI Processing ===<br /> <br /> <br /> Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.<br /> <br /> Steps/Modules:<br /> * process data from raw DICOM data (enhanced DicomToNRRDConverter)<br /> * DTI noise estimation, Rician noise filtering<br /> * DTI QC and motion/eddy current correction (enhanced DTIPrep)<br /> * DTI estimation, property map generation (existing Slicer modules)<br /> * DTI atlas registration (new Slicer module)<br /> * DTI atlas based fiber analysis (new Slicer module)<br /> * Appropriate reporting of all steps<br /> * DTI processing wizard in Slicer<br /> * Longitudinal DTI analysis module<br /> * Fiber profile measurement/visualization within Slicer<br /> <br /> === Shape Analysis ===<br /> <br /> Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM &amp; particle shape analysis processing in NA-MIC within PREDICT HD. <br /> <br /> Steps/Modules:<br /> *<br /> <br /> === Data ===<br /> <br /> Is the image data already in hand?<br /> <br /> *Yes. Over 2900 scan sessions collected. We will need to identify the meaningful subset of this data, get final approval from the Predict Steering Committee for that subset,and then re-deidentify it and post to XNAT for NA-MIC purposes.<br /> <br /> == Outreach ==<br /> *Tutorial(s) on the wiki<br /> *Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2<br /> *Hands-on teaching event for the DBP scientific community for year 3<br /> <br /> =Who=<br /> *DBP: Hans Johnson, DBP engineer Mark Scully<br /> *Algo: Martin Styner, DBP engineer Clement Vachet<br /> *Eng: Dan Marcus, Jeff Grethe, Marco Ruiz<br /> <br /> * Iowa Supporting Guests: Shuhua Wu, Joy Matsui, Ben Rogers, Vince Magnotta<br /> <br /> =When=<br /> * Monday October 25th, 10:30am - 5:30pm<br /> ** 10:30-12:00 Overview of project, and background of PREDICT-HD<br /> ** 12:00- 1:00 Lunch<br /> ** 1:00- 5:30 Working meeting focused on informatics, computations and processing<br /> ** 6:30- 8:30 Dinnner @ One-Twenty-Six<br /> * Tuesday October 26th, 8:00am - 3:30pm<br /> ** 8:00-12:00 Working meeting focused on algorithmic development<br /> ** 12:00- 1:00 Lunch<br /> ** 1:00- 3:30 Finalize timelines<br /> ** 3:30- 5:30 Discuss current limitions of XNAT, and determine how to overcome them<br /> * Wednesday October 27th, 9:30am- 3:00pm<br /> ** GridWizard deployment<br /> <br /> =Where=<br /> The University of Iowa Campus, Meet in W240 Boyd Tower. The conference room is a short distance away from there in the Iowa Center for Translational Science.<br /> <br /> Take elevator BW to the second floor, and take two immediate rights. The conference room shares a wall with the BW elevator shaft.<br /> <br /> == Travel Information ==<br /> The closest airport to Iowa City is the '''Cedar Rapids / Eastern Iowa Airport (CID)'''<br /> which is about 20 minutes from the hotel. <br /> <br /> ===Airport Shuttle Services===<br /> The easiest way to get from the airport to<br /> Iowa City is via one of the shuttle services: <br /> * [http://www.crshuttle.com/ Airport Shuttle Service] (Phone: 1-800-725-8460)<br /> * [http://www.limosbyexpress.com/ Airport Express] (Phone: 319-626-5466)<br /> Both are the same price and easiest to book before travel. The cost is roughly $60 round trip.<br /> <br /> ===Rental Cars===<br /> Rental cars are also available from the Airport. The following companies have desks at the airport<br /> * Avis<br /> ** [http://www.avis.com/ Website] <br /> ** Toll-Free Phone : 1-800-331-1212<br /> ** Local Phone : (319) 366-6418<br /> * Hertz<br /> ** [http://www.hertz.com/ Website] <br /> **Toll-Free Phone : 1-800-654-3131<br /> **Local Phone : (319) 365-9184<br /> * National and Alamo<br /> ** [http://www.nationalcar.com/ Website]<br /> **Toll-Free Phone : 1-888-826-6890<br /> **Local Phone : (319) 363-0249<br /> *Enterprise<br /> **[http://www.enterprise.com/car_rental/home.do Website]<br /> **Local Phone : (319) 366-5522<br /> <br /> <br /> If you have any questions regarding travel, feel free to contact Joe Ekdahl either via e-mail(joe-ekdahl@uiowa.edu) or phone (319-384-3026).<br /> <br /> == Hotel Information ==<br /> We reserved a block of hotel rooms at Hotel Vetro at a rate of $139. The group code to get this rate is ITK. These rooms will be held at this rate until October 22.<br /> * [http://www.hotelvetro.com/ Hotel Vetro]<br /> **Phone: 800-592-0355<br /> **Address: 201 South Linn Street, Iowa City, Iowa 52240<br /> <br /> <br /> Other hotels that are close to the conference site, University of Iowa, and downtown include:<br /> *[http://www.Sheraton.com/IowaCity Sheraton hotel]<br /> **Phone: 319-337-4058<br /> **Address: 210 South Dubuque St, Iowa City, IA 52240<br /> *[http://imu.uiowa.edu/iowahouse/ Iowa House Hotel]<br /> **Phone: 319-335-3513<br /> **Address: 125 North Madison St, Iowa City, IA 52242<br /> <br /> <br /> == Meeting Room ==<br /> <br /> TBD</div>

Jgrethe https://www.na-mic.org/w/index.php?title=NA-MIC_External_Collaborations&diff=44446 2009-10-29T19:14:26Z

<p>Jgrethe: </p> <hr /> <div> Back to [[NA-MIC_Collaborations|NA-MIC Collaborations]]<br /> <br /> =Projects funded by &quot;Collaborations with NCBC PAR&quot;=<br /> <br /> This section describes external collaborations with NA-MIC that are funded by NIH under the &quot;Collaboration with NCBC&quot; PAR. (Details for this funding mechanism are provided [[Collaborator:Resources|&lt;big&gt;&lt;big&gt;here&lt;/big&gt;&lt;/big&gt;]]).<br /> <br /> {| style=&quot;text-align:left;&quot;<br /> | style=&quot;width:10%&quot; | [[Image:Cli-mesh-quality-small-062607.png|thumb|left|300px|PAR-05-063: R01EB005973 Automated FE Mesh Development]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> <br /> == [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|PAR-05-063: R01EB005973 Automated FE Mesh Development]] ==<br /> <br /> This project is funded under an NCBC collaboration grant to PIs Nicole Grosland and Vincent Magnotta at UIowa. The goal of this project is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the [[NA-MIC-Kit|NA-MIC kit]]. [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|More...]]<br /> <br /> |-<br /> <br /> | | [[Image:NhpATOCPic.jpg|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|PAR-07-249: R01AA016748 Measuring Alcohol and Stress Interaction with Structural and Perfusion MRI]]==<br /> <br /> This project is funded under an NCBC collaboration grant to PIs James Daunais, Robert Kraft, and Chris Wyatt. The goal of this project is to examine the the effects of chronic alcohol self- administration on brain structure and function the monkey brain. MRI image analysis tools from the [[NA-MIC-Kit|NA-MIC kit]] will be adapted for use with the monkey brain datasets. [[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|More...]]<br /> <br /> |-<br /> <br /> | | [[Image:LiverRFAPhantom.png|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC_NCBC_Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors|PAR-05-063: R01CA124377 An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors]]==<br /> <br /> This project is funded under an NCBC collaboration grant to PI Kevin Cleary at Georgetown University. The goal of this project is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors.[[NA-MIC_NCBC_Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors|More...]]<br /> |-<br /> <br /> | | [[Image:HammerABrain.png|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC_NCBC_Collaboration:Development and Dissemination of Robust Brain MRI Measurement Tools|PAR-07-249: R01EB006733 Development and Dissemination of Robust Brain MRI Measurement Tools]]==<br /> <br /> This project is funded under an NCBC collaboration grant to PI Dinggang Shen at UNC-Chapel Hill. The goal of this project is to develop and widely distribute a software package for robust measurement of brain structures in MR images using computational neuroanatomy methods.[[NA-MIC_NCBC_Collaboration:Development and Dissemination of Robust Brain MRI Measurement Tools|More...]]<br /> |-<br /> <br /> | | [[Image:Virtual Colonoscopy Auto Detection - Yoshida.png|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC_NCBC_Collaboration:NA-MIC virtual colonoscopy|PAR-07-249: R01CA131718 NA-MIC virtual colonoscopy]]==<br /> <br /> This project is funded under an NCBC collaboration grant to PI Hiroyuki Yoshida. The goal of this project is to [[NA-MIC_NCBC_Collaboration:NA-MIC virtual colonoscopy|More...]]<br /> |-<br /> <br /> | | [[Image:JHUCollaboration.jpg|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC_NCBC_Collaboration:3D Shape Analysis for Computational Anatomy|PAR-07-249: R01 EB008171 3D Shape Analysis for Computational Anatomy]]==<br /> <br /> This project is funded under an NCBC collaboration grant to PI Michael Miller JHU (with Joe Hennessey)<br /> |-<br /> <br /> | | [[Image:UtahCollaboration.jpg|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC_NCBC_Collaboration:The Microstructural Basis of Abnormal Connectivity in Autism|PAR-07-249: R01MH084795: The Microstructural Basis of Abnormal Connectivity in Autism]]==<br /> <br /> This project is funded under an NCBC collaboration grant to PI Janet Lainhart, MD. <br /> It will use tools developed within NAMIC for a longitudinal neuroimaging, clinical, and neuropsychological study of late neurodevelopment in autism.combining analysis of connectivity and morphometry. <br /> |-<br /> <br /> <br /> | | [[Image:JHUSkullStripping.png|300px]]<br /> | | [[Image:JHU.jpg|100px]]<br /> <br /> ==[[NA-MIC_JHU_Skull_Stripping_Collaboration | PAR-08-183: R21-EB009900 Johns Hopkins Skull Stripping]]==<br /> <br /> The group at Johns Hopkins is developing software that enables the stripping of skull, scalp, and meninges from structural MRI scans in a fully automated fashion.<br /> <br /> <br /> <br /> |}<br /> <br /> ----<br /> <br /> ----<br /> <br /> =Additional External Collaborations=<br /> <br /> This section describes external collaborations with NA-MIC that are funded by other mechanisms:<br /> <br /> {| style=&quot;text-align:left;&quot;<br /> | style=&quot;width:10%&quot; | [[Image:BRAINS.gif|thumb|left|300px]]<br /> | style=&quot;width:90%&quot; |<br /> <br /> ==[[NA-MIC Brains Collaboration| PAR-05-057: BRAINS Morphology and Image Analysis]]==<br /> <br /> This project is a funded under a Continued Development and Maintenance of Software grant to PIs Vincent Magnotta, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen at the University of Iowa. The goal of this project is to update the '''BRAINS''' image analysis software developed at the University of Iowa. [[NA-MIC Brains Collaboration|More...]]<br /> <br /> |-<br /> <br /> | | [[Image:LevelSetSegmentGUIModule_alpha.png|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC VMTK Collaboration | Vascular Modeling Toolkit Collaboration]]==<br /> <br /> Slicer as a platform for segmentation and geometric analysis of vascular segments and image-based computational fluid dynamics (CFD). [[NA-MIC VMTK Collaboration|More...]]<br /> <br /> Collaboration with [http://villacamozzi.marionegri.it/~luca/ Luca Antiga] of the [http://www.marionegri.it Mario Negri Institute].<br /> <br /> |-<br /> <br /> | | [[Image:27y-leftabdcan-T6SQ-voltage-withheart4.png |thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC Childrens Collaboration| Children's Pediatric Cardiology Collaboration with SCI/SPL/Northeastern]]==<br /> <br /> Collaboration with John Triedman, Matt Jolley, Dana Brooks, SCI.<br /> <br /> |-<br /> <br /> | | [[Image:NITRC.png|thumb|left|300px]]<br /> | |<br /> <br /> ==[[NA-MIC and NITRC| NA-MIC Collaboration with NITRC]]==<br /> <br /> The NA-MIC Project is working to make NA-MIC neuroimaging software available through the [http://www.nitrc.org/ NITRC web site]. Supplemental support is helping to create the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules Slicer3 Loadable Modules] project so that slicer plugins can be hosted on NITRC, allowing greater scalability for developers and users of Slicer.<br /> <br /> |-<br /> <br /> | | [[Image:Logo_nac.gif|thumb|left|100px|[http://nac.spl.harvard.edu NAC website]]]<br /> | |<br /> <br /> ==[[Collaboration:NAC| NA-MIC Collaboration with NAC]]==<br /> <br /> NAC, the neuroimage analysis center, is a national resource center. NAC is relying on the NA-MIC kit for its general software environment. The mission of NAC is to develop novel concepts for the analysis of images of the brain and develop and disseminate tools based on those concepts.<br /> <br /> |-<br /> <br /> | | [[Image:Ncigtlogo.gif|thumb|left|100px]]<br /> | |<br /> <br /> ==[[Collaboration:NCIGT| NA-MIC Collaboration with NCIGT]]==<br /> <br /> NCIGT is leveraging the NA-MIC kit as a platform for developing dedicated IGT capabilities.<br /> <br /> <br /> |-<br /> <br /> | | [[Image:AISTlogo.gif|thumb|left|100px]]<br /> | |<br /> <br /> ==[[Collaboration:AIST| NA-MIC Collaboration with Research and Development Project on Intelligent Surgical Instruments]]==<br /> <br /> Intelligent Surgical Instruments Projects uses Open-source software engineering tools developed by NA-MIC, and leverage it to surgical robotics.<br /> <br /> <br /> |-<br /> <br /> | | [[Image:ISML.gif|thumb|left|100px]]<br /> | |<br /> <br /> ==[[Collaboration:UWA-Perth| Real Time Computer Simulation of Human Soft Organ Deformation for Computer Assisted Surgery]]==<br /> <br /> Real Time Computer Simulation of Human Soft Organ Deformation for Computer Assisted Surgery.<br /> <br /> |-<br /> |-<br /> <br /> | | [[Image:snapshot.gif|thumb|left|300px]]<br /> | |<br /> <br /> ==[[Collaboration:College of William and Mary|Real-Time Computing for Image Guided Neurosurgery]]==<br /> <br /> Using the Tera Grid to implement mesh-based non-rigid registration for Neurosurgery.<br /> <br /> |-<br /> <br /> | | [[Image:Harvard.shield.png|thumb|left|100px]]<br /> | | <br /> ==[[Collaboration:Harvard CTSC| NA-MIC support for Harvard CTSC Translational Imaging Consortium]]==<br /> <br /> The Harvard CTSC Translational Imaging Consortium is using NA-MIC communication tools to facilitate the rapid deployment of expertise in medical imaging acquisition, analysis and visualization to clinical translational investigators. <br /> <br /> |-<br /> <br /> | | [[Image:MicroscopyTutorialSlide.jpg|thumb|left|300px]]<br /> | | <br /> <br /> ==[[Collaboration:NCMIR Microscopy|NCBC Supplement for Microscopy and Slicer]]==<br /> <br /> An NCBC Supplement to NCMIR, UCSD focused on the utilization of Slicer with microscopy data and resulted in a tutorial for use of Slicer with confocal microscopy data.<br /> <br /> |-<br /> <br /> | | [[Image:Femur Patella Tibia.jpg‎|thumb|left|300px]]<br /> | | <br /> <br /> ==[[Stanford_Simbios_group|Stanford Simbios]]==<br /> <br /> Our sister NCBC at Stanford, dedicated to biomedical simulation, is working to adapt NA-MIC image analysis routines generate simulation models directly from MRI scans.<br /> <br /> |}</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44445 2009-10-29T19:09:22Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement, funding now completed, to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work, as part of this collaboration, focused on requirements and extensions for the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Delivered Using Slicer for Microscopy Tutorial ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A slide from the Microscopy tutorial developed through this collaboration.]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the 2009 Summer Programming Week Tutorial contest (see - http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009). <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> * Mark Ellisman (mark at ncmir.ucsd.edu)<br /> * Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44444 2009-10-29T19:08:20Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work, as part of this collaboration, focused on requirements and extensions for the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Delivered Using Slicer for Microscopy Tutorial ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A slide from the Microscopy tutorial developed through this collaboration.]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the 2009 Summer Programming Week Tutorial contest (see - http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009). <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> * Mark Ellisman (mark at ncmir.ucsd.edu)<br /> * Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44443 2009-10-29T19:07:29Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work, as part of this collaboration, focused on requirements and extensions for the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Delivered Using Slicer for Microscopy Tutorial ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A slide from the Microscopy tutorial developed through this collaboration.]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the 2009 Summer Programming Week Tutorial contest (see - http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer). <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> * Mark Ellisman (mark at ncmir.ucsd.edu)<br /> * Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44442 2009-10-29T19:02:07Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Using Slicer for Microscopy ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A slide from the Microscopy tutorial developed through this collaboration.]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the 2009 Summer Programming Week Tutorial contest (see - http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer). <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> * Mark Ellisman (mark at ncmir.ucsd.edu)<br /> * Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44441 2009-10-29T19:01:54Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Using Slicer for Microscopy ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A slide from the Microscopy tutorial developed through this collaboration.]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the 2009 Summer Programming Week Tutorial contest (see - http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer). <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> ** Mark Ellisman (mark at ncmir.ucsd.edu)<br /> ** Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44440 2009-10-29T19:01:34Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Using Slicer for Microscopy ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A slide from the Microscopy tutorial developed through this collaboration.]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the 2009 Summer Programming Week Tutorial contest (see - http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer). <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> Mark Ellisman (mark at ncmir.ucsd.edu)<br /> Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44439 2009-10-29T19:00:06Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Using Slicer for Microscopy ==<br /> [[Image:MicroscopyTutorialSlide.jpg|thumb|200px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the [[http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer|2009 tutorial contest]] <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> Mark Ellisman (mark at ncmir.ucsd.edu)<br /> Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=File:MicroscopyTutorialSlide.jpg&diff=44438 2009-10-29T18:59:33Z

<p>Jgrethe: Slicer Microscopy Tutorial Slide</p> <hr /> <div>Slicer Microscopy Tutorial Slide</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44437 2009-10-29T18:58:56Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|125px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Using Slicer for Microscopy ==<br /> [[Image:Spines01.jpg|thumb|250px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the [[http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer|2009 tutorial contest]] <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> Mark Ellisman (mark at ncmir.ucsd.edu)<br /> Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44436 2009-10-29T18:58:27Z

<p>Jgrethe: </p> <hr /> <div>== Background ==<br /> <br /> [[Image:Spines01.jpg|thumb|250px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * The collaboration in regards to Microscopy was fostered through a supplement to the National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.<br /> <br /> * Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).<br /> <br /> == Using Slicer for Microscopy ==<br /> [[Image:Spines01.jpg|thumb|250px|A small fragment of a dendrite (gray) with segmented spines (color).]]<br /> <br /> * A direct result of this collaboration was the tutorial developed by UCSD for use of Slicer with confocal microscopy data: &quot;Guiding you step by step through the process of loading confocal microscopy data, working with that data, and creating a 3D model for visualization.&quot; The tutorial covers the complete use of Slicer from loading data (including the downloading of data from publicly available open-source repositories), visualization of data and basic editing with the editor module. The tutorial then covers model building using basic slicer modules and the Otsu segmentation module.<br /> <br /> * This tutorial won the [[http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009Summer|2009 tutorial contest]] <br /> <br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy Tutorial]]<br /> <br /> == Contact ==<br /> <br /> Mark Ellisman (mark at ncmir.ucsd.edu)<br /> Jeffrey Grethe (jgrethe at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Collaboration:NCMIR_Microscopy&diff=44433 2009-10-29T18:25:14Z

<p>Jgrethe: Created page with '== Background == Text... == Current Activities == Text... == Contact == Mark Ellisman (mark at ncmir.ucsd.edu)'</p> <hr /> <div>== Background ==<br /> <br /> Text...<br /> <br /> == Current Activities ==<br /> <br /> Text...<br /> <br /> == Contact ==<br /> Mark Ellisman (mark at ncmir.ucsd.edu)</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Events:TutorialContestJune2009&diff=39628 2009-06-25T13:08:03Z

<p>Jgrethe: /* Tutorials */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[2009_Summer_Project_Week]]<br /> <br /> [[Image:Arctic_Logo.png |250px|thumb|right|First Prize in the January 2009 round: [[UNC_ARCTIC_Tutorial|ARTIC Tutorial]] ]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> =Background=<br /> <br /> [http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].<br /> <br /> =Tutorial Contest Goal=<br /> The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups. <br /> <br /> There will be two categories:<br /> #'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least: <br /> #*materials about the scientific and application background and motivation, <br /> #*step-by-step guides, and <br /> #*sample data<br /> #*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]<br /> #'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:<br /> #*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment<br /> #*step-by-step guides, and<br /> #*at least two different sample data sets from two different institutions<br /> #*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]<br /> <br /> =Template=<br /> A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]<br /> *Note: The examples above predate the template.<br /> <br /> =Rules=<br /> *Tutorial must be based on a snapshot or release of Slicer 3<br /> *Tutorial must follow the guidelines specified above<br /> *If applicable, provide clear directions for downloading and installing additional modules<br /> *The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br /> *Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).<br /> <br /> =Dates=<br /> *Presentation: all tutorials will be presented by the authors on Thursday, June 25th 9-11am during the Project Week. Each tutorial presentation should be 10 minutes long. <br /> *Decisions announced: Friday June 26, 2009, 10 am &lt;br&gt;<br /> <br /> =Tutorials=<br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Events:TutorialContestJune2009&diff=39627 2009-06-25T13:07:34Z

<p>Jgrethe: /* Tutorials */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[2009_Summer_Project_Week]]<br /> <br /> [[Image:Arctic_Logo.png |250px|thumb|right|First Prize in the January 2009 round: [[UNC_ARCTIC_Tutorial|ARTIC Tutorial]] ]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> =Background=<br /> <br /> [http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].<br /> <br /> =Tutorial Contest Goal=<br /> The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups. <br /> <br /> There will be two categories:<br /> #'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least: <br /> #*materials about the scientific and application background and motivation, <br /> #*step-by-step guides, and <br /> #*sample data<br /> #*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]<br /> #'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:<br /> #*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment<br /> #*step-by-step guides, and<br /> #*at least two different sample data sets from two different institutions<br /> #*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]<br /> <br /> =Template=<br /> A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]<br /> *Note: The examples above predate the template.<br /> <br /> =Rules=<br /> *Tutorial must be based on a snapshot or release of Slicer 3<br /> *Tutorial must follow the guidelines specified above<br /> *If applicable, provide clear directions for downloading and installing additional modules<br /> *The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br /> *Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).<br /> <br /> =Dates=<br /> *Presentation: all tutorials will be presented by the authors on Thursday, June 25th 9-11am during the Project Week. Each tutorial presentation should be 10 minutes long. <br /> *Decisions announced: Friday June 26, 2009, 10 am &lt;br&gt;<br /> <br /> =Tutorials=<br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Events:TutorialContestJune2009&diff=39626 2009-06-25T13:07:09Z

<p>Jgrethe: /* Tutorials */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[2009_Summer_Project_Week]]<br /> <br /> [[Image:Arctic_Logo.png |250px|thumb|right|First Prize in the January 2009 round: [[UNC_ARCTIC_Tutorial|ARTIC Tutorial]] ]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> =Background=<br /> <br /> [http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].<br /> <br /> =Tutorial Contest Goal=<br /> The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups. <br /> <br /> There will be two categories:<br /> #'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least: <br /> #*materials about the scientific and application background and motivation, <br /> #*step-by-step guides, and <br /> #*sample data<br /> #*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]<br /> #'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:<br /> #*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment<br /> #*step-by-step guides, and<br /> #*at least two different sample data sets from two different institutions<br /> #*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]<br /> <br /> =Template=<br /> A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]<br /> *Note: The examples above predate the template.<br /> <br /> =Rules=<br /> *Tutorial must be based on a snapshot or release of Slicer 3<br /> *Tutorial must follow the guidelines specified above<br /> *If applicable, provide clear directions for downloading and installing additional modules<br /> *The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br /> *Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).<br /> <br /> =Dates=<br /> *Presentation: all tutorials will be presented by the authors on Thursday, June 25th 9-11am during the Project Week. Each tutorial presentation should be 10 minutes long. <br /> *Decisions announced: Friday June 26, 2009, 10 am &lt;br&gt;<br /> <br /> =Tutorials=<br /> * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Events:TutorialContestJune2009&diff=39625 2009-06-25T13:06:19Z

<p>Jgrethe: /* Tutorials */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[2009_Summer_Project_Week]]<br /> <br /> [[Image:Arctic_Logo.png |250px|thumb|right|First Prize in the January 2009 round: [[UNC_ARCTIC_Tutorial|ARTIC Tutorial]] ]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> =Background=<br /> <br /> [http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].<br /> <br /> =Tutorial Contest Goal=<br /> The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups. <br /> <br /> There will be two categories:<br /> #'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least: <br /> #*materials about the scientific and application background and motivation, <br /> #*step-by-step guides, and <br /> #*sample data<br /> #*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]<br /> #'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:<br /> #*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment<br /> #*step-by-step guides, and<br /> #*at least two different sample data sets from two different institutions<br /> #*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]<br /> <br /> =Template=<br /> A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]<br /> *Note: The examples above predate the template.<br /> <br /> =Rules=<br /> *Tutorial must be based on a snapshot or release of Slicer 3<br /> *Tutorial must follow the guidelines specified above<br /> *If applicable, provide clear directions for downloading and installing additional modules<br /> *The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br /> *Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).<br /> <br /> =Dates=<br /> *Presentation: all tutorials will be presented by the authors on Thursday, June 25th 9-11am during the Project Week. Each tutorial presentation should be 10 minutes long. <br /> *Decisions announced: Friday June 26, 2009, 10 am &lt;br&gt;<br /> <br /> =Tutorials=<br /> * [[Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Events:TutorialContestJune2009&diff=39624 2009-06-25T13:05:08Z

<p>Jgrethe: /* Tutorials */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[2009_Summer_Project_Week]]<br /> <br /> [[Image:Arctic_Logo.png |250px|thumb|right|First Prize in the January 2009 round: [[UNC_ARCTIC_Tutorial|ARTIC Tutorial]] ]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> =Background=<br /> <br /> [http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].<br /> <br /> =Tutorial Contest Goal=<br /> The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups. <br /> <br /> There will be two categories:<br /> #'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least: <br /> #*materials about the scientific and application background and motivation, <br /> #*step-by-step guides, and <br /> #*sample data<br /> #*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]<br /> #'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:<br /> #*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment<br /> #*step-by-step guides, and<br /> #*at least two different sample data sets from two different institutions<br /> #*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]<br /> <br /> =Template=<br /> A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]<br /> *Note: The examples above predate the template.<br /> <br /> =Rules=<br /> *Tutorial must be based on a snapshot or release of Slicer 3<br /> *Tutorial must follow the guidelines specified above<br /> *If applicable, provide clear directions for downloading and installing additional modules<br /> *The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br /> *Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).<br /> <br /> =Dates=<br /> *Presentation: all tutorials will be presented by the authors on Thursday, June 25th 9-11am during the Project Week. Each tutorial presentation should be 10 minutes long. <br /> *Decisions announced: Friday June 26, 2009, 10 am &lt;br&gt;<br /> <br /> =Tutorials=<br /> * [[Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Events:TutorialContestJune2009&diff=39623 2009-06-25T13:02:14Z

<p>Jgrethe: /* Dates */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[2009_Summer_Project_Week]]<br /> <br /> [[Image:Arctic_Logo.png |250px|thumb|right|First Prize in the January 2009 round: [[UNC_ARCTIC_Tutorial|ARTIC Tutorial]] ]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> =Background=<br /> <br /> [http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].<br /> <br /> =Tutorial Contest Goal=<br /> The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups. <br /> <br /> There will be two categories:<br /> #'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least: <br /> #*materials about the scientific and application background and motivation, <br /> #*step-by-step guides, and <br /> #*sample data<br /> #*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]<br /> #'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:<br /> #*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment<br /> #*step-by-step guides, and<br /> #*at least two different sample data sets from two different institutions<br /> #*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]<br /> <br /> =Template=<br /> A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]<br /> *Note: The examples above predate the template.<br /> <br /> =Rules=<br /> *Tutorial must be based on a snapshot or release of Slicer 3<br /> *Tutorial must follow the guidelines specified above<br /> *If applicable, provide clear directions for downloading and installing additional modules<br /> *The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br /> *Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).<br /> <br /> =Dates=<br /> *Presentation: all tutorials will be presented by the authors on Thursday, June 25th 9-11am during the Project Week. Each tutorial presentation should be 10 minutes long. <br /> *Decisions announced: Friday June 26, 2009, 10 am &lt;br&gt;<br /> <br /> =Tutorials=<br /> * [[Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=File:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf&diff=39622 2009-06-25T12:58:50Z

<p>Jgrethe: First submission of a confocal microscopy tutorial</p> <hr /> <div>First submission of a confocal microscopy tutorial</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34221 2009-01-05T16:00:23Z

<p>Jgrethe: /* GWE Information */</p> <hr /> <div>= UCSD (PI: Mark Ellisman) =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * GWE <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]<br /> <br /> * GWE Setup<br /> ** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]<br /> ** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]<br /> <br /> * Prior Presentations<br /> ** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]<br /> ** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]<br /> <br /> * Tutorials<br /> Tutorials are provided via the [[Slicer3.2:Training| Slicer Training Site]]. Links to the tutorials provided through this site are also provided below.<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=34219 2009-01-05T15:57:54Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and 3D Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] &lt;br&gt; [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;<br /> Background Materials:[[EMSegmenter| EMSegmenter History]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br /> <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]&lt;br&gt;<br /> Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] &lt;br&gt;<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] &lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]] <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.nitrc.org/frs/download.php/516/Slicer3Training_WhiteMatterLesions_1.1.ppt.pdf Detecting white matter lesions in lupus] &lt;br&gt;<br /> This tutorial consists of five MR scans of patients with lupus.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.nitrc.org/frs/download.php/512/20081114_public_lupus_data_tutorial_release.tgz Lupus-Tutorial-Data ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Lupus2.png|200px|Lesion Segmentation]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate external executable into the Slicer3 source tree. <br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''&quot;Simple region growing&quot;''' segmentation module.<br /> &lt;br&gt;Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. &lt;br&gt;<br /> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. <br /> &lt;br&gt; Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]<br /> This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat/org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''<br /> These tutorials are intended for researchers who wish to utilize distributed computational resources.<br /> * [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> * [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.gridwizardenterprise.org/ '''Grid Wizard Enterprise''']<br /> <br /> * GWE Information<br /> ** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]<br /> ** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:GWE-overview.jpg|200px|GWE Overview]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=34218 2009-01-05T15:57:03Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and 3D Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] &lt;br&gt; [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;<br /> Background Materials:[[EMSegmenter| EMSegmenter History]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br /> <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]&lt;br&gt;<br /> Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] &lt;br&gt;<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] &lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]] <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.nitrc.org/frs/download.php/516/Slicer3Training_WhiteMatterLesions_1.1.ppt.pdf Detecting white matter lesions in lupus] &lt;br&gt;<br /> This tutorial consists of five MR scans of patients with lupus.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.nitrc.org/frs/download.php/512/20081114_public_lupus_data_tutorial_release.tgz Lupus-Tutorial-Data ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Lupus2.png|200px|Lesion Segmentation]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate external executable into the Slicer3 source tree. <br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''&quot;Simple region growing&quot;''' segmentation module.<br /> &lt;br&gt;Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. &lt;br&gt;<br /> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. <br /> &lt;br&gt; Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]<br /> This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat/org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''<br /> These tutorials are intended for researchers who wish to utilize distributed computational resources.<br /> * [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> * [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.gridwizardenterprise.org/ '''Grid Wizard Enterprise''']<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]<br /> <br /> * GWE Setup<br /> ** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]<br /> ** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:GWE-overview.jpg|200px|GWE Overview]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=34217 2009-01-05T15:55:30Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and 3D Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] &lt;br&gt; [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;<br /> Background Materials:[[EMSegmenter| EMSegmenter History]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br /> <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]&lt;br&gt;<br /> Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] &lt;br&gt;<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] &lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]] <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.nitrc.org/frs/download.php/516/Slicer3Training_WhiteMatterLesions_1.1.ppt.pdf Detecting white matter lesions in lupus] &lt;br&gt;<br /> This tutorial consists of five MR scans of patients with lupus.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.nitrc.org/frs/download.php/512/20081114_public_lupus_data_tutorial_release.tgz Lupus-Tutorial-Data ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Lupus2.png|200px|Lesion Segmentation]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate external executable into the Slicer3 source tree. <br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''&quot;Simple region growing&quot;''' segmentation module.<br /> &lt;br&gt;Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. &lt;br&gt;<br /> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. <br /> &lt;br&gt; Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]<br /> This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat/org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''<br /> These tutorials are intended for researchers who wish to utilize distributed computational resources.<br /> * [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> * [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:GWE-overview.jpg|200px|GWE Overview]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=34216 2009-01-05T15:54:59Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and 3D Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] &lt;br&gt; [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;<br /> Background Materials:[[EMSegmenter| EMSegmenter History]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br /> <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]&lt;br&gt;<br /> Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] &lt;br&gt;<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] &lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]] <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.nitrc.org/frs/download.php/516/Slicer3Training_WhiteMatterLesions_1.1.ppt.pdf Detecting white matter lesions in lupus] &lt;br&gt;<br /> This tutorial consists of five MR scans of patients with lupus.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.nitrc.org/frs/download.php/512/20081114_public_lupus_data_tutorial_release.tgz Lupus-Tutorial-Data ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Lupus2.png|200px|Lesion Segmentation]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate external executable into the Slicer3 source tree. <br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''&quot;Simple region growing&quot;''' segmentation module.<br /> &lt;br&gt;Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. &lt;br&gt;<br /> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. <br /> &lt;br&gt; Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]<br /> This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat/org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''<br /> These tutorials are intended for researchers who wish to utilize distributed computational resources.<br /> * [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> * [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:GWE-Overview.jpg|200px|GWE Overview]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=File:GWE-overview.jpg&diff=34215 2009-01-05T15:54:08Z

<p>Jgrethe: </p> <hr /> <div></div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=34214 2009-01-05T15:50:15Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and 3D Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] &lt;br&gt; [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;<br /> Background Materials:[[EMSegmenter| EMSegmenter History]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br /> <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]&lt;br&gt;<br /> Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] &lt;br&gt;<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] &lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]] <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.nitrc.org/frs/download.php/516/Slicer3Training_WhiteMatterLesions_1.1.ppt.pdf Detecting white matter lesions in lupus] &lt;br&gt;<br /> This tutorial consists of five MR scans of patients with lupus.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.nitrc.org/frs/download.php/512/20081114_public_lupus_data_tutorial_release.tgz Lupus-Tutorial-Data ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Lupus2.png|200px|Lesion Segmentation]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate external executable into the Slicer3 source tree. <br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''&quot;Simple region growing&quot;''' segmentation module.<br /> &lt;br&gt;Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. &lt;br&gt;<br /> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. <br /> &lt;br&gt; Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]<br /> This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat/org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''<br /> These tutorials are intended for researchers who wish to utilize distributed computational resources.<br /> * [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> * [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> * [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| <br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=34213 2009-01-05T15:49:36Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and 3D Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] &lt;br&gt; [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;<br /> Background Materials:[[EMSegmenter| EMSegmenter History]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br /> <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]&lt;br&gt;<br /> Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] &lt;br&gt;<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] &lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]] <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.nitrc.org/frs/download.php/516/Slicer3Training_WhiteMatterLesions_1.1.ppt.pdf Detecting white matter lesions in lupus] &lt;br&gt;<br /> This tutorial consists of five MR scans of patients with lupus.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.nitrc.org/frs/download.php/512/20081114_public_lupus_data_tutorial_release.tgz Lupus-Tutorial-Data ]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Lupus2.png|200px|Lesion Segmentation]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate external executable into the Slicer3 source tree. <br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]<br /> This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''&quot;Simple region growing&quot;''' segmentation module.<br /> &lt;br&gt;Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. &lt;br&gt;<br /> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. <br /> &lt;br&gt; Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]<br /> This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat/org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.6'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system<br /> These tutorials are intended for researchers who wish to utilize distributed computational resources.<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| <br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34211 2009-01-05T15:44:58Z

<p>Jgrethe: /* UCSD */</p> <hr /> <div>= UCSD (PI: Mark Ellisman) =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * GWE <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]<br /> <br /> * GWE Setup<br /> ** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]<br /> ** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]<br /> <br /> * Prior Presentations<br /> ** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]<br /> ** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]<br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34210 2009-01-05T15:44:13Z

<p>Jgrethe: /* GWE Information */</p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * GWE <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]<br /> <br /> * GWE Setup<br /> ** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]<br /> ** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]<br /> ** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]<br /> <br /> * Prior Presentations<br /> ** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]<br /> ** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]<br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34209 2009-01-05T15:40:12Z

<p>Jgrethe: /* GWE Information */</p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * Prior Presentations<br /> ** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]<br /> ** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]<br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34208 2009-01-05T15:39:39Z

<p>Jgrethe: /* GWE Information */</p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * Prior Presentations<br /> * GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]<br /> * GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]<br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Parallel_system&diff=34207 2009-01-05T15:38:45Z

<p>Jgrethe: </p> <hr /> <div>Overview<br /> <br /> The most obvious use case for a &quot;computational grid&quot; is to run many jobs simultaneously on remote resources, specifically on multiple clusters of identical computers. Logistically, doing so is a tedious problem that is solved by so-called application schedulers that execute individual programs on behalf of the user. GridWizard is an application scheduler being developed at UCSD and differs from existing application schedulers in several key areas. We expect that this software will make many other computational tasks substantially easier, including the batch submission of large numbers of jobs from Slicer3.<br /> <br /> <br /> Background<br /> <br /> Existing application scheduler software programs fall into one of two categories: static schedulers or dynamic schedulers. Static schedulers compute the ordering and mapping of jobs onto resources prior to running any of the actual workload. Such a strategy has an obvious problem, in that any system-level failures (a compute node crashes, a disk share becomes unavailable) will affect a larger number of tasks than necessary. Dynamic schedulers, on the other hand, maintain a list of tasks (or jobs) that need to be performed and then map some task from the list to the next available compute resource. In this context, the mapping is not computed explicitly, but is computed by the end of the application's execution.<br /> <br /> Another criteria with which to classify application scheduling is their deployment architecture. For example, the APST scheduler template is a pull scheduler: it reserves time on each compute resource and employs a reverse-access shell on each resource to poll for the next available job. In push scheduling, as performed in applications like GridSAM, the application scheduler program creates a manifest of jobs to be done by a particular resource and explicitly schedules that manifest through the mechanism on each resource (e.g., via qsub on a PBS-managed batch system).<br /> <br /> Though not immediately obvious, different scheduling styles and deployment architectures are desirable at different stages of the research process. Because a significant amount of software debugging and testing is taking place in the early stages of research, a static push scheduler is often preferable even though such a strategy has been shown to result in suboptimal execution times. The increased time in program execution can be offset if debugging the application becomes substantially easier because of a static push scheduler's predictable nature---here, one frequently prefers an application scheduler that parallelizes an application in a predictable and intuitively understandable manner, rather than according to a heuristically optimal schedule that may be less predictable. However, in some contexts a dynamic pull scheduler may be more appropriate. For example, if a researcher provides (and supports) an online website for other members of the community to analyze data, it may become necessary to add new compute resources without disrupting existing application schedules; this is much easier with a dynamic scheduler, and nearly trivial with a pull-based scheduling. However, in our experience with the one available dynamic pull-based scheduler (APST), pull-based protocols can be prone to deadlock in the face of node failure leading to a stalled application.<br /> <br /> Because an application scheduler is merely another research tool to be used in the context of some larger scientific inquiry, it stands to reason that an ideal application scheduler would provide mechanisms that fit the overall research process by selecting: (a) either static or dynamic scheduling; (b) one of several scheduling algorithms, depending on the maturity of the scheduled code; (c) execution logging and restarting; (d) integration with standard data grid tools and access protocols (e.g., sftp, SRB, GSI); (e) integration with standard resource schedulers (e.g., SGE, Condor). To our knowledge, no such application has been reported in the literature, and it is this set of requirements that we try to meet with GridWizard.<br /> <br /> Status<br /> <br /> Completed: <br /> * Successful initial demo of a statically scheduled application using Sun Grid Engine and SSH<br /> * http://www.gridwizard.org website registered and created<br /> * Automated CI server: http://builds.gridwizard.org<br /> * Bug tracker: http://bugs.gridwizard.org<br /> * Code: http://svn.gridwizard.org/gridwizard (/trunk)<br /> * Documentation: http://docs.gridwizard.org<br /> * bug tracking and wiki system configured<br /> * automated build system and revision control configured<br /> <br /> In Progress: <br /> * Design of better scheduling algorithms to take advantage of data locality<br /> * Testing<br /> * Limit detection: how many jobs *can* we schedule, exactly?</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34206 2009-01-05T15:37:51Z

<p>Jgrethe: /* Monthly Progress (since July 2007) */</p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34205 2009-01-05T15:36:45Z

<p>Jgrethe: /* GWE Information */</p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34204 2009-01-05T15:35:48Z

<p>Jgrethe: </p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = GWE Information = <br /> <br /> * Tutorials<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34203 2009-01-05T15:32:05Z

<p>Jgrethe: </p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34202 2009-01-05T15:31:16Z

<p>Jgrethe: </p> <hr /> <div>= UCSD =<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. see P2EL in Section 4) or through integration with community developed biomedical applications (e.g. see Slicer in Section 5).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34201 2009-01-05T15:30:38Z

<p>Jgrethe: </p> <hr /> <div>= UCSD Progress (in preparation for SLC AHM) =<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. see P2EL in Section 4) or through integration with community developed biomedical applications (e.g. see Slicer in Section 5).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> [[Image:GWE-logo.jpg]]<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=File:GWE-logo.jpg&diff=34200 2009-01-05T15:29:59Z

<p>Jgrethe: </p> <hr /> <div></div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34199 2009-01-05T15:26:31Z

<p>Jgrethe: </p> <hr /> <div>= UCSD Progress (in preparation for SLC AHM) =<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. see P2EL in Section 4) or through integration with community developed biomedical applications (e.g. see Slicer in Section 5).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> ''' Dissemination Activities Prior to Monthly Progress Outlined Above '''<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> ''' Infrastructure Prior to Monthly Progress Outlined Above '''<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> ''' Data Sharing Prior to Monthly Progress Outlined Above '''<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34198 2009-01-05T15:25:10Z

<p>Jgrethe: </p> <hr /> <div>= UCSD Progress (in preparation for SLC AHM) =<br /> <br /> = Overview =<br /> A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a &quot;run-everywhere&quot; philosophy for algorithm developers. By adopting a standard for algorithm &quot;self-description&quot; that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment. <br /> <br /> A basic requirement for the GWE environment is that a researcher expert in a particular scientific discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:<br /> <br /> * Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.<br /> * Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. see P2EL in Section 4) or through integration with community developed biomedical applications (e.g. see Slicer in Section 5).<br /> * Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.<br /> <br /> = Grid Wizard Enterprise (GWE) Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> == Dissemination Activities Prior to Monthly Progress Outlined Above==<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> == Infrastructure Prior to Monthly Progress Outlined Above==<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> == Data Sharing Prior to Monthly Progress Outlined Above==<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34197 2009-01-05T15:18:23Z

<p>Jgrethe: </p> <hr /> <div>= UCSD Progress (in preparation for SLC AHM) =<br /> <br /> = Overview =<br /> <br /> = GWE Background =<br /> The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the fields of computational biology and medical image analysis.<br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> == Dissemination Activities Prior to Monthly Progress Outlined Above==<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> == Infrastructure Prior to Monthly Progress Outlined Above==<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> == Data Sharing Prior to Monthly Progress Outlined Above==<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3:JavaBasedChainCLMsEngine&diff=34196 2009-01-05T15:10:04Z

<p>Jgrethe: </p> <hr /> <div>= Chain CLMs Engine =<br /> <br /> == Introduction ==<br /> <br /> * Java application which behaves as a regular Slicer3 module (JVM 1.5 or higher required).<br /> * Requires as its first parameter the location of a chain descriptor.<br /> * The rest of its parameters are the usual Slicer3 modules parameters.<br /> * This java application is currently wrapped in a shell script; which would be the actual Slicer3 chain module.<br /> * As such this script has to be deployed in the Slicer's Plugins folder.<br /> * This script does pre and post processing before invoking the engine and hardcodes a chain descriptor.<br /> <br /> == Installation ==<br /> <br /> * Unbundle the [http://www.gridwizardenterprise.org/maven/org/gwe/client/0.6.3.alpha/gwe-0.6.3.alpha-client.zip chain module engine] right under your Slicer3 installation.<br /> * Set the environmental variable SLICER_HOME to point to your Slicer3 installation. For example:<br /> <br /> export SLICER_HOME=~/Slicer3.2-2008-06-02-darwin-x86<br /> <br /> * For each chain module desired create:<br /> ** A &quot;X-Chain.xml&quot; chain descriptor file to be stored under the Slicer3 &quot;Plugins&quot; directory (see &quot;Chain Descriptor&quot; section for details).<br /> ** A chain script module for &quot;X-Chain.xml&quot;; which should look like:<br /> <br /> #!/bin/sh<br /> # Chain Slicer Module<br /> <br /> export GWE_HOME=`ls -d -t $SLICER_HOME/gwe-*/ | head -1`<br /> export GWE_FAT_JAR=`ls $GWE_HOME/lib/gwe-*-fatjar.jar`<br /> rm -fdr $SLICER_HOME/chains<br /> mkdir $SLICER_HOME/chains <br /> java -Xmx512m -cp $GWE_HOME/conf:$GWE_FAT_JAR org.gwe.integration.slicer.chains.ChainCLMProxyApp $SLICER_HOME/lib/Slicer3/Plugins/X-Chain.xml $@<br /> if [ &quot;x$1&quot; != &quot;x--xml&quot; ]<br /> then<br /> chmod a+x $SLICER_HOME/chains/chain.sh<br /> $SLICER_HOME/chains/chain.sh &gt; $SLICER_HOME/chains/result.log<br /> fi<br /> <br /> == Chain Descriptor ==<br /> <br /> * This is an XML file which contains all the information necessary to deterministically proxy into CLMs and:<br /> ** Build the new XML descriptor corresponding to the composition of the modules (removing chain arguments, applying namespaces, autogenerating certain values, etc.)<br /> ** Invoke them when necessary in sequential order respecting the argument piping instructions and the corresponding arguments for each modules' (using its namespaces).<br /> * It must conform to the following schema:<br /> <br /> &lt;xs:schema xmlns:xs=&quot;http://www.w3.org/2001/XMLSchema&quot; xmlns:clm=&quot;http://www.na-mic.org/clm&quot; targetNamespace=&quot;http://www.na-mic.org/clm&quot; elementFormDefault=&quot;qualified&quot;&gt;<br /> &lt;xs:element name=&quot;modules&quot;&gt;<br /> &lt;xs:complexType&gt;<br /> &lt;xs:sequence&gt;<br /> &lt;xs:element name=&quot;module&quot; type=&quot;clm:module&quot; minOccurs=&quot;2&quot; maxOccurs=&quot;unbounded&quot;/&gt;<br /> &lt;/xs:sequence&gt;<br /> &lt;/xs:complexType&gt;<br /> &lt;/xs:element&gt;<br /> &lt;xs:complexType name=&quot;module&quot;&gt;<br /> &lt;xs:sequence&gt;<br /> &lt;xs:element name=&quot;argument&quot; type=&quot;clm:argument&quot; minOccurs=&quot;0&quot; maxOccurs=&quot;unbounded&quot;/&gt;<br /> &lt;/xs:sequence&gt;<br /> &lt;xs:attribute name=&quot;id&quot; type=&quot;xs:string&quot;/&gt;<br /> &lt;/xs:complexType&gt;<br /> &lt;xs:complexType name=&quot;argument&quot;&gt;<br /> &lt;xs:attribute name=&quot;name&quot; type=&quot;xs:string&quot;/&gt;<br /> &lt;xs:attribute name=&quot;value-ref&quot; type=&quot;xs:string&quot;/&gt;<br /> &lt;/xs:complexType&gt;<br /> &lt;/xs:schema&gt;<br /> <br /> * &quot;Chain Descriptor&quot; template example:<br /> <br /> &lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;<br /> &lt;modules xmlns=&quot;http://www.na-mic.org/clm&quot; xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot; xsi:schemaLocation=&quot;http://www.na-mic.org/schemas/chainCLM.xsd&quot;&gt;<br /> &lt;module id=&quot;Module1&quot;/&gt;<br /> &lt;module id=&quot;Module2&quot;&gt;<br /> &lt;argument name=&quot;param2A&quot; value-ref=&quot;Module1.param1A&quot; /&gt;<br /> &lt;argument name=&quot;param2B&quot; value-ref=&quot;Module1.param1B&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;module id=&quot;Module3&quot;&gt;<br /> &lt;argument name=&quot;param3C&quot; value-ref=&quot;Module1.param1C&quot; /&gt;<br /> &lt;argument name=&quot;param3D&quot; value-ref=&quot;Module2.param2D&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;/modules&gt;<br /> <br /> <br /> == Real Examples ==<br /> <br /> [[Image:ChainSamples-Menu.png]]<br /> <br /> * Chaining modules GaussianBlurImageFilter and OtsuThresholdSegmentation:<br /> <br /> &lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;<br /> &lt;modules xmlns=&quot;http://www.na-mic.org/clm&quot; xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot; xsi:schemaLocation=&quot;http://www.na-mic.org/schemas/chainCLM.xsd&quot;&gt;<br /> &lt;module id=&quot;GaussianBlurImageFilter&quot;/&gt;<br /> &lt;module id=&quot;OtsuThresholdSegmentation&quot;&gt;<br /> &lt;argument name=&quot;inputVolume&quot; value-ref=&quot;GaussianBlurImageFilter.outputVolume&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;/modules&gt;<br /> <br /> [[Image:Chain1GeneratedUI.png]]<br /> <br /> * Chaining modules dwiNoiseFilter, CurvatureAnisotropicDiffusion and GradientAnisotropicDiffusion:<br /> <br /> &lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;<br /> &lt;modules xmlns=&quot;http://www.na-mic.org/clm&quot; xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot; xsi:schemaLocation=&quot;http://www.na-mic.org/schemas/chainCLM.xsd&quot;&gt;<br /> &lt;module id=&quot;dwiNoiseFilter&quot;/&gt;<br /> &lt;module id=&quot;CurvatureAnisotropicDiffusion&quot;&gt;<br /> &lt;argument name=&quot;inputVolume&quot; value-ref=&quot;dwiNoiseFilter.outputVolume&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;module id=&quot;GradientAnisotropicDiffusion&quot;&gt;<br /> &lt;argument name=&quot;inputVolume&quot; value-ref=&quot;CurvatureAnisotropicDiffusion.outputVolume&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;/modules&gt;<br /> <br /> [[Image:Chain2GeneratedUI.png]]<br /> <br /> * Chaining modules brainsegCLP, AffineRegistration, BSplineDeformableRegistration, ResampleVolume2, CortThickCLP<br /> <br /> &lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;<br /> &lt;modules xmlns=&quot;http://www.na-mic.org/clm&quot; xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot; xsi:schemaLocation=&quot;http://www.na-mic.org/schemas/chainCLM.xsd&quot;&gt;<br /> &lt;module id=&quot;brainsegCLP&quot;/&gt;<br /> &lt;module id=&quot;AffineRegistration&quot;/&gt;<br /> &lt;module id=&quot;BSplineDeformableRegistration&quot;&gt;<br /> &lt;argument name=&quot;inputVolume&quot; value-ref=&quot;AffineRegistration.ResampledImageFileName&quot; /&gt;<br /> &lt;argument name=&quot;InitialTransform&quot; value-ref=&quot;AffineRegistration.OutputTransform&quot; /&gt;<br /> &lt;argument name=&quot;FixedImageFileName&quot; value-ref=&quot;AffineRegistration.FixedImageFileName&quot; /&gt;<br /> &lt;argument name=&quot;MovingImageFileName&quot; value-ref=&quot;AffineRegistration.MovingImageFileName&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;module id=&quot;ResampleVolume2&quot;&gt;<br /> &lt;argument name=&quot;InitialTransform&quot; value-ref=&quot;BSplineRegistration.OutputTransform&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;module id=&quot;CortThickCLP&quot;&gt;<br /> &lt;argument name=&quot;SegmentationInput&quot; value-ref=&quot;brainseg.SegmentationFile&quot; /&gt;<br /> &lt;argument name=&quot;ParcellationOption&quot; value-ref=&quot;ResampleVolume2.outputVolume&quot; /&gt;<br /> &lt;/module&gt;<br /> &lt;/modules&gt;<br /> <br /> [[Image:RegionalCorticalThicknessChain.jpg]]<br /> <br /> = Key Investigators =<br /> <br /> * UCSD: Marco Ruiz<br /> * Isomics: Steve Pieper<br /> * GE: Jim Miller</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Engineering:UCSD&diff=34195 2009-01-05T15:01:39Z

<p>Jgrethe: </p> <hr /> <div>= UCSD Progress (in preparation for SLC AHM) =<br /> <br /> <br /> <br /> = Monthly Progress (since July 2007) =<br /> <br /> ''July - September 2007''<br /> * Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE).<br /> <br /> ''October 2007''<br /> * Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])<br /> <br /> ''December 2007''<br /> * Launch of GWE's: <br /> ** [http://www.gridwizardenterprise.org/ project site]<br /> ** [http://issues.nbirn.net/browse/GWE issue tracking system] <br /> ** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]. <br /> <br /> ''January 2008''<br /> * Unit tests of GWE's first release candidate components.<br /> * Internal pre-release of first version of GWE.<br /> * Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].<br /> <br /> ''February 2008''<br /> * First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.<br /> <br /> ''March 2008''<br /> * GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).<br /> * Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].<br /> <br /> ''April 2008''<br /> * GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * Wrote paper &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot; to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].<br /> <br /> ''May 2008''<br /> * Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):<br /> ** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].<br /> ** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].<br /> <br /> ''June 2008''<br /> * GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> * NAMIC summer week presentations and projects:<br /> ** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]<br /> ** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]<br /> <br /> ''July 2008''<br /> * Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.<br /> <br /> ''August 2008''<br /> * GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> <br /> ''September 2008''<br /> * Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf &quot;Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise&quot;] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.<br /> <br /> ''October 2008''<br /> * Collected user requests at the BIRN AHM.<br /> <br /> ''November 2008''<br /> * GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** Major re-architecture to allow running GWE without clusters and with daemons per user.<br /> ** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database]. <br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]<br /> ** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]<br /> <br /> ''December 2008''<br /> * GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.<br /> ** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).<br /> ** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] (NAMIC Winter Project Week 2009)<br /> ** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.<br /> * Step by step tutorials:<br /> ** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]<br /> <br /> ''January 2009''<br /> * NAMIC Winter Project Week and AHM 2009.<br /> * [[2009_Winter_Project_Week_GWE_Catalogs|&quot;GWE integration with catalog files&quot; project]] at the NAMIC Winter Project Week 2009.<br /> <br /> <br /> = Miscellaneous =<br /> <br /> * Weekly NAMIC engineering teleconferences.<br /> * GWE testbed and user's support.<br /> <br /> == Dissemination Activities Prior to Monthly Progress Outlined Above==<br /> * Introductory meeting and demonstration with Tina Kapur &amp; Birn-CC.<br /> * Hosted NAMIC dissemination event (February 17-18).<br /> * Taught Data Grid course at UCSD dissemination event.<br /> * Attended NAMIC dissemination event.<br /> * Attended SLC AHM.<br /> * Instructions available for deploying a &quot;tunneled&quot; SRB server.<br /> <br /> == Infrastructure Prior to Monthly Progress Outlined Above==<br /> * Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.<br /> * A server co-located at BWH will be discussed at the AHM.<br /> * Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.<br /> * Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms<br /> * Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool<br /> <br /> == Data Sharing Prior to Monthly Progress Outlined Above==<br /> * Hosting NAMIC data on data grid accessible to all NAMIC participants.<br /> * Providing data grid and Portal support to all NAMIC participants.<br /> * Provided custom project space for NAMIC in BIRN Portal.<br /> * Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.<br /> * Working with Isomics to assist core 3 sites in their data uploads.<br /> * Provided template data hierarchy constructs and integration of hierarchy in data grid.<br /> * Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=29475 2008-08-15T17:02:58Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> This page is under construction<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]&lt;br&gt;Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3- WARNING UNDER CONSTRUCTION NOT READY FOR USE ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]&lt;br&gt;<br /> This tutorial takes the trainee through the slicer3 diffusion display and processing options.<br /> See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]]&lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.xcat|ChageTracker-Tutorial-Data.xcat ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]<br /> This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for more information.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 '''here'''] for more information.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Sample Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=29474 2008-08-15T17:02:39Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> This page is under construction<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]&lt;br&gt;Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3- WARNING UNDER CONSTRUCTION NOT READY FOR USE ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]&lt;br&gt;<br /> This tutorial takes the trainee through the slicer3 diffusion display and processing options.<br /> See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]]&lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.xcat|ChageTracker-Tutorial-Data.xcat ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]<br /> This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for more information.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 '''here'''] for more information.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip| Microscopy Samle Data (90 MB) ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe https://www.na-mic.org/w/index.php?title=Slicer3.2:Training&diff=29473 2008-08-15T17:01:25Z

<p>Jgrethe: /* Training Compendium */</p> <hr /> <div>__NOTOC__<br /> = Welcome to the 3D Slicer3.2 User Training 101=<br /> This page is under construction<br /> The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * Slicer 3 has been designed as<br /> ** an easy-to-use application for 3D image analysis and visualization,<br /> ** an open-source environment for software development,<br /> ** a technology delivery platform for community breakthroughs.<br /> *Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.<br /> *This page contains training materials and data sets for self-guided training in the use of Slicer3<br /> <br /> *For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).<br /> | style=&quot;background: #ebeced&quot; colspan=&quot;2&quot; align=&quot;center&quot;| &lt;b&gt;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]&lt;/b&gt;<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]] <br /> |}<br /> <br /> = Software Installation =<br /> The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.<br /> <br /> =Training Compendium=<br /> {| border=&quot;1&quot; cellpadding=&quot;5&quot;<br /> |- style=&quot;background:#BBE9E2; color:black&quot; align=&quot;left&quot; <br /> | style=&quot;width:5%&quot; | '''Category/#'''<br /> | style=&quot;width:35%&quot; | '''Tutorial'''<br /> | style=&quot;width:30%&quot; | '''Sample Data''' <br /> | style=&quot;width:10%&quot; | '''Image''' <br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:SceneRestore.png|200px|LoadingandVisualization]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]&lt;br&gt;Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]&lt;br&gt;Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3- WARNING UNDER CONSTRUCTION NOT READY FOR USE ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]&lt;br&gt;<br /> This tutorial takes the trainee through the slicer3 diffusion display and processing options.<br /> See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]<br /> |-<br /> | style=&quot;background:#9BF2C5; color:black&quot; align=&quot;Center&quot;| '''1.5'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]]&lt;br&gt;<br /> This tutorial consists of two MR scans of a patient with meningioma.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:ChangeTracker-Tutorial-Data.xcat|ChageTracker-Tutorial-Data.xcat ]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]<br /> This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:HelloWorld.zip|HelloWorld.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:HelloWorld.png|200px|Plug-In]]<br /> |-<br /> | style=&quot;background:#8EDEB5; color:black&quot; align=&quot;Center&quot;| '''2.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]&lt;br&gt;<br /> See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.<br /> This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.1'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]<br /> This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.<br /> | style=&quot;background:#D1FFF9; color:black&quot;| <br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.2'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for more information.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Atlas.png|200px|Brain Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.3'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 '''here'''] for more information.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]<br /> |-<br /> | style=&quot;background:#72b291; color:black&quot; align=&quot;Center&quot;| '''3.4'''<br /> | style=&quot;background:#D1FFF9; color:black&quot;| Slicer 3 as a Research Tool for Microscopy Data<br /> This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit [http://ccdb.ucsd.edu '''the Cell Centered Database'''] for freely available data sets.<br /> | style=&quot;background:#D1FFF9; color:black&quot;|[[Media:astrocyte_sampleData.zip Microscopy Samle Data (90 MB)]]<br /> | style=&quot;background:#C3D1C3; color:black&quot; align=&quot;Center&quot;| [[Image:Slicer_Astrocyte.jpg|200px|Astrocyte Visualized in Slicer]]<br /> |}<br /> <br /> * Category 1 = Basic functionality<br /> * Category 2 = Advanced functionality<br /> * Category 3 = Specialized application packages<br /> <br /> =Additional Materials=<br /> For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].<br /> &lt;br /&gt; Back to [[Training:Main|Training:Main]]</div>

Jgrethe