NAMIC Wiki - User contributions [en]

File:ScreenshotImportMITK.PNG

2017-06-30T12:33:05Z

JasminMetzger: JasminMetzger uploaded a new version of File:ScreenshotImportMITK.PNG

Project Week 25/DICOM Segmentation Support for Cornerstone and OHIF Viewer

2017-06-30T12:29:44Z

JasminMetzger:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Erik Ziegler (Open Health Imaging Foundation, USA)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics, Inc., USA)
*[https://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
*[http://www.spl.harvard.edu/pages/People/tkapur Tina Kapur] (Brigham and Women's Hospital, Harvard Medical School, USA)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Overall goal is to facilitate zero-footprint image annotation
** Runs in browser
** Fast and usable by clinicians
** Interoperable (DICOM-based)
* Cornerstone has great platform
** Needs segmentation display
** Needs suite of editing tools (plugin architecture)
** Needs DICOM Segmentation object support
** Needs DICOM Structured Report container for image measurements (lines, points, ROIs)
|
* Review architectures and experiments so far
** SAKE viewer tool (http://sakeviewer.com/)
** Experiments with Segmentation read/write in javascript
** Discussions and prototypes with Dana-Farber Cancer Institute
* Try building an end-to-end proof of concept
** Read grayscale and segmentation
** Edit segmentation
** Write out segmentation (store to server)
* Discuss how to harden and integrate with production systems
* What other work is needed
|
*Progress
** Added layered image support to Cornerstone master (version 0.12.1)
*** User-controls colormap, opacity, and visibility
** Added layered image stack support to Cornerstone Tools (version 0.9.0)
** Created '''dcmjs''' repository (https://github.com/pieper/dcmjs) to release Steve's client-side DICOM I/O support
** Created examples for DICOM Segmentation (binary only) display and creation from the browser
** Discussed plans for client-side Structured Report export
* Next Steps
* Bug fixing for layer support in Cornerstone and Cornerstone Tools
* Fix brush tool to store drawings on multiple images
* Cleanup dcmjs examples to allow user-uploaded data
* Cleanup dcmjs repository to release as a usable library
* Use dcmjs for client-side sorting of uploaded files, link this to OHIF Standalone Viewer
|}

==Illustrations==
[[image:OHIF Study List.png|800px]]

[[image:OHIF Viewer Screenshot.png|800px]]

==Background and References==

SIIM2017 Learning Lab introduction to Cornerstone / OHIF
* Slides: https://www.dropbox.com/s/bg4mm7s9kek0708/SIIM2017%20-%20Build%20your%20own%20zero%20footprint%20web%20viewer.pptx?dl=1
* Repository: https://github.com/chafey/byozfwv

OHIF Community Forum Slides
* https://docs.google.com/presentation/d/1iYZoU7v7KHSLHiKwH1_9_wweAkG7RGnyxrWeeHva4zQ/edit#slide=id.g17e0507313_1_46
* https://docs.google.com/presentation/d/1K9Y6eP5DYTXoDlfwCZE6GkCUp83AK4_40YQS0dlzVBo/edit#slide=id.g17df770847_0_0

Repositories
* https://github.com/chafey/cornerstone
* https://github.com/chafey/cornerstoneTools
* https://github.com/chafey/cornerstoneWADOImageLoader
* https://github.com/OHIF/Viewers

Work thus far on segmentations / overlays in Cornerstone
* https://github.com/chafey/cornerstone/pull/68
* https://github.com/chafey/cornerstone/pull/109
* https://rawgit.com/swederik/cornerstone/composition/example/testSeg/index.html
* http://sakeviewer.com/

Progress
[[File:Screen Shot 2017-06-30 at 12.55.25.png|thumb|Exporting from Cornerstone and importing into Slicer]]
[[File:ScreenshotImportMITK.PNG|thumb|Importing into MITK]]

File:ScreenshotImportMITK.PNG

2017-06-30T12:28:27Z

JasminMetzger:

Project Week 25/DICOM for Quantitative Imaging and Integration with Processing Applications

2017-06-26T08:24:25Z

JasminMetzger:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* [https://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
* [https://www.dkfz.de/en/mic/team/people/Jasmin_Metzger.html Jasmin Metzger] (German Cancer Research Center (DKFZ), Germany)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
* [http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov](remote) (Brigham and Women's Hospital, Harvard Medical School, USA)
* Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Discuss topics related to using the DICOM standard for storing results of quantitative image analysis
** DICOM Structured Reports (SR)
** DICOM Segmentation (SEG) objects
** DICOM Parametric map (PM) objects

|
* Fix packaging issues of dcmqi (see [https://github.com/QIICR/dcmqi/issues/260 dcmqi issue #260])
* Preparing the satellite event at MICCAI 2017

|

|}

==Illustrations==
<gallery heights=400px mode="packed">
Image:DICOM_QI_Slicer-read-td4.png|Slicer
Image:DICOM_QI_MITK_td4-read-prostate.png|MITK
</gallery>



==Background and References==

* [http://qiicr.org/dicom4miccai/ Tutorial satellite event at MICCAI 2017 DICOM4MICCAI]
* [https://github.com/QIICR/dcmqi dcmqi] - tools to convert image analysis results into DICOM objects

File:DICOM QI MITK td4-read-prostate.png

2017-06-26T08:14:10Z

JasminMetzger:

File:DICOM QI Slicer-read-td4.png

2017-06-26T08:08:16Z

JasminMetzger:

Project Week 25/DICOM for Quantitative Imaging and Integration with Processing Applications

2017-06-14T12:13:53Z

JasminMetzger: /* Project Description */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* [https://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (DKFZ, Germany)
* [https://www.dkfz.de/en/mic/team/people/Jasmin_Metzger.html Jasmin Metzger] (DKFZ, Germany)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)
* [http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov](remote) (Brigham and Women's Hospital, Harvard Medical School, USA)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Discuss topics related to using the DICOM standard for storing results of quantitative image analysis
** DICOM Structured Reports (SR)
** DICOM Segmentation (SEG) objects
** DICOM Parametric map (PM) objects

|
* Preparing the satellite event at MICCAI 2017

|

|}

==Illustrations==





==Background and References==

* [http://qiicr.org/dicom4miccai/ Tutorial satellite event at MICCAI 2017 DICOM4MICCAI]
* [https://github.com/QIICR/dcmqi dcmqi] - tools to convert image analysis results into DICOM objects

Project Week 25/DICOM for Quantitative Imaging and Integration with Processing Applications

2017-06-14T12:10:31Z

JasminMetzger: /* Key Investigators */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* [https://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (DKFZ, Germany)
* [https://www.dkfz.de/en/mic/team/people/Jasmin_Metzger.html Jasmin Metzger] (DKFZ, Germany)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)
* [http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov](remote) (Brigham and Women's Hospital, Harvard Medical School, USA)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

|

|

|}

==Illustrations==





==Background and References==

* [http://qiicr.org/dicom4miccai/ Tutorial satellite event at MICCAI 2017 DICOM4MICCAI]
* [https://github.com/QIICR/dcmqi dcmqi] - tools to convert image analysis results into DICOM objects

Project Week 25/DICOM for Quantitative Imaging and Integration with Processing Applications

2017-06-14T12:08:55Z

JasminMetzger: /* Background and References */

Project Week 25/DICOM for Quantitative Imaging and Integration with Processing Applications

2017-06-12T11:38:06Z

JasminMetzger: Create project page DICOM QI

Project Week 25

2017-06-12T11:23:02Z

JasminMetzger: /* Projects */ Add project link for DICOM QI

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 click here] to join the videoconference (zoom is the tool as of May 31)

#(Tina Kapur) Hangout #1: April 5 ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: April 12: Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine;
#(Andras Lasso) Hangout #3: April 19: Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality;
#(Tina Kapur) Hangout #4: April 26: Deep Learning for Detection of Cancer and Instruments;
#(Simon Drouin) Hangout #5: May 3: Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];
#(Tina Kapur) Hangout #6: May 10: For new participants: What is project week and how to get the most out of participating in it?
#(Andrey Fedorov) Hangout #7: May 17:DICOM for Quantitative Imaging and integration with processing applications. ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: May 24:Discussion of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer.
#(Francesca Spadea) Hangout #9: May 31: Review of local logistics -- all registered attendees should join
#(Tina Kapur) Hangout #10: June 7: Discussion of Projects, Project Pages
#(TBD) Hangout #11: June 14: Review of Project Pages
#(Francesca Spadea) Hangout #12: June 21: Review of local logistics -- all registered attendees with questions should join

==Logistics==
*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#[[Project_Week_25/NeedleSegmentation | Needle Segmentation]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
#[[Project_Week_25/Deep_Learning_Data_augmentation_for_prostate_segmentation | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]] (Simon Drouin, Christian Hansen, David Black)
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#CNN for PseudoCT Generation from T1/T2 MRI (Giampaolo Pileggi, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Gino Gulamhussene, Anneke Meyer)
#Internationalizing Slicer Modules (Juan Ruiz Alzola)
#Interfacing Slicer to Mobile Phone-controlled Sensors (Juan Ruiz Alzola)
#Slicer and 3D Printing (Juan Ruiz Alzola, Mike Halle, Christian Hansen)
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]]
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]]
#SlicerCIP: Interactive Bronchiectasis Definition (Pietro Nardelli, Raúl San José Estépar)

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, University of Groningen, The Nederlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University Of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: Universität Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: Universität Magdeburg, Germany
# Mewes, André :: Universität Magdeburg, Germany
# Hatscher, Benjamin :: Universität Magdeburg, Germany
# Hettig, Julian :: Universität Magdeburg, Germany
# Meyer, Anneke :: Universität Magdeburg, Germany
# Gulamhussene, Gino :: Universität Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, USA
# Metzger, Jasmin :: DKFZ, Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: DKFZ, Germany
# Jorge Quintero Nehrkorn :: Canary Islands, Spain