NAMIC Wiki - User contributions [en]

Microscopy Image Analysis

2010-06-24T16:09:27Z

Megason: /* Participants */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Machiraju Lab- Ohio State Univ
**** Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment
**** Liya Ding - Image Analysis of Large Histology Datasets using ITK
*** 1:40pm: Palaniappan Lab- Univ of Missouri
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software
*** 2:40pm: Carolina Wahlby - Broad Institute
** 2:45pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Andinet Enquobahrie, Kitware
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Curtis Lisle, KnowledgeVis
# Tammy Riklin Raviv, CSAIL, MIT
# Marc Niethammer, UNC Chapel Hill
# Carolina Wahlby, Broad Institute

StandardsInterfaces

2010-06-24T15:59:59Z

Megason:

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==

===Image Formats===
We discussed standards for '''image formats''' at the Microscopy Breakout session. We broke this issue down into 3 components:
* '''File Types''': e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* '''Metadata''': metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* '''Meta image formats''': For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

===Microscopy Filter IO Types===
I met with Luis Ibanez and Jim Miller to discuss how the best representation for filter I/O issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

===Greatest Common Denominator===
We also discussed what the "greatest common denominator" of interchange between microscopy image analysis groups is.
* '''ITK filters''': A preferred method for sharing microscopy processing filters is by submitting a paper to the Insight Journal and a class or classes to ITK. This mechanism provides for peer reviewed publication, automatic testing, and easy access to the code.
* '''Plugins for different apps''': Another approach for collaboration amongst different groups is through the creation of plugins for existing microscopy image analysis applications. Plugins allow for extending the capabilities of an application to meet the needs of the user without having to recode all the common needs of an application such as visualization and manual editing of segmentation results. Such an approach can aid in the development cycle by providing a means for visualizing and verifying the results of a new filter and makes it easier to tune the parameters to a filter.
* '''Creation of a "microscopy data interchange format"''': Another approach is to have a standard interchange format for microscopy data that would encapsulate images, metadata, segmented cells/tracks/lineages, and object annotations. Such an approach would allow for any application in any language to work together as long as it reads and writes this format. The trick of course is defining the format and providing readers/writers. This issue is related to the meta format and filter IO format issues above.

StandardsInterfaces

2010-06-24T15:58:08Z

Megason: /* Greatest Common Denominator */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==

===Image Formats===
We discussed standards for '''image formats''' at the Microscopy Breakout session. We broke this issue down into 3 components:
* '''File Types''': e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* '''Metadata''': metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* '''Meta image formats''': For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

===Microscopy Filter IO Types===
I met with Luis Ibanez and Jim Miller to discuss how the best representation for filter I/O issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

===Greatest Common Denominator===
We also discussed what the "greatest common denominator" of interchange between microscopy image analysis groups is.
* '''ITK filters''': A preferred method for sharing microscopy processing filters is by submitting a paper to the Insight Journal and a class or classes to ITK. This mechanism provides for peer reviewed publication, automatic testing, and easy access to the code.
* '''Plugins for different apps''': Another approach for collaboration amongst different groups is through the creation of plugins for existing microscopy image analysis applications. Plugins allow for extending the capabilities of an application to meet the needs of the user without having to recode all the common needs of an application such as visualization and manual editing of segmentation results. Such an approach can aid in the development cycle by providing a means for visualizing and verifying the results of a new filter and makes it easier to tune the parameters to a filter.
* '''Creation of a "microscopy data interchange format"''': Another approach is to have a standard interchange format for microscopy data that would encapsulate images, metadata, segmented cells/tracks/lineages, and object annotations. Such an approach would allow for any application in any language to work together as long as it reads and writes this format. The trick of course is defining the format and providing readers/writers. This issue is related to the meta format and filter IO format issues above.

StandardsInterfaces

2010-06-24T15:47:43Z

Megason: /* Microscopy Filter IO Types */

StandardsInterfaces

2010-06-24T15:45:32Z

Megason: /* Progress */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==

===Image Formats===
We discussed standards for '''image formats''' at the Microscopy Breakout session. We broke this issue down into 3 components:
* '''File Types''': e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* '''Metadata''': metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* '''Meta image formats''': For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

===Microscopy Filter IO Types===
I met with Luis Ibanez and Jim Miller to discuss how related issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

===Greatest Common Denominator===
We also discussed what the "greatest common denominator" of interchange between microscopy image analysis groups is.
* '''ITK filters''': A preferred method for sharing microscopy processing filters is by submitting a paper to the Insight Journal and a class or classes to ITK

StandardsInterfaces

2010-06-24T15:37:28Z

Megason: /* Progress */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==
I met with Luis Ibanez and Jim Miller to discuss how related issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

We also discussed standards for '''image formats''' at the Microscopy Breakout session. We broke this issue down into 3 components:
* '''File Types''': e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* '''Metadata''': metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* '''Meta image formats''': For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

StandardsInterfaces

2010-06-24T15:36:48Z

Megason: /* Progress */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==
I met with Luis Ibanez and Jim Miller to discuss how related issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

We also discussed standards for ''image formats'' at the Microscopy Breakout session. We broke this issue down into 3 components:
* ''File Types'': e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* ''Metadata'': metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* ''Meta image formats'': For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

StandardsInterfaces

2010-06-24T15:35:11Z

Megason: /* Progress */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==
I met with Luis Ibanez and Jim Miller to discuss how related issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

We also discussed standards for **image formats** at the Microscopy Breakout session. We broke this issue down into 3 components:
* *File Types*: e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* *Metadata*: metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* *Meta image formats*: For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

StandardsInterfaces

2010-06-24T15:34:43Z

Megason: /* Progress */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==
I met with Luis Ibanez and Jim Miller to discuss how related issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

We also discussed standards for *image formats* at the Microscopy Breakout session. We broke this issue down into 3 components:
* *File Types*: e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* *Metadata*: metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* *Meta image formats*: For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

StandardsInterfaces

2010-06-24T15:33:50Z

Megason: /* Progress */

__NOTOC__

We are intreated in getting feedback on creating standards and interfaces for microscopy image analysis in ITK

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
There are now several groups using ITK to develop filters for microscopy image analysis. However there are a number of possibilities for the input and output formats for these filters. For filters from different groups to be interchangeable, it is important that these filters use a defined interface. The goal of this project is to solicit opinions from both groups working on microscopy image analysis as well as those with experience designing interfaces for image processing in other domains.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
If you have opinions, suggestions, or interfaces you are already using please talk to Sean and come to the Microscopy Image Analysis breakout session on Wed afternoon.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Issues</h3>
Specifically we would like to define functional groups of filters (e.g. denoising, seeding, segmentation, tracking, lineaging, post-processing, quantitation, classification) to allow for filter swapping within a group and then to define input/output types between these groups. ImageToImage filters are a sufficient interface for some filter groups but are problematic for others due to changes in dimension (tracking, lineaging), excess size (seeding), and differences with the "natural" output of an algorithm (e.g. a segmentation algorithm may output a mesh rather than image).
</div>

==Progress==
I met with Luis Ibanez and Jim Miller to discuss how related issues have been handled in ITK previously. They suggested itk::SpatialObject and itk::LabelObject. LabelObject seems like a good intermediate between an image based representation and an object(cell) based representation, and allows for either perspective depending on which is more convenient. LabelObject uses run-length enconding of objects in an image which results in a lot of compression. LabelObject also allows for objects to be attributed with values (e.g. cell size, intensity, velocity). One downside is that there are not currently many filters in ITK that use LabelObjects. In our research, we (Kishore) have already been working with LabelObjects as the output to segmentation filters. This seems like a promising approach. We need to standardize the representation of cells in xy, xyt, xyz, xyzt, xyzt+division using LabelObjects and the associated cellular attributes. We are also working on a filter for converting LabelObjects into a GoFigure IO file format.

We also discussed standards for image formats at the Microscopy Breakout session. We broke this issue down into 3 components:
* File Types: e.g. jpg, png, tif, lsm. The problem of needing to read a bunch of different file types has been around a long time. This problem is still not ideally solved (there is no BSD licensed library that will read all microscopy formats), but there are enough workarounds that this issue is now more of an inconvenience than a road block. In practice most groups only use 1 maybe 2 types of microscopes and have solved their problem locally. A global solution would make it easier for groups to work together and would thus be preferable. However, current file types do not meet the needs of advanced imaging applications anyway (see "meta" file types below) so efforts should be aimed at both creating BSD readers for existing file types as well as meta file types.
* Metadata: metadata refers to all the nonimage data that is part of an imaging experiment. Metadata include image acquisition parameters (objective, laser power, PMT gain, filters, pixel dwell time) much of which is microscope specific. It can also include information about how the specimen was labeled and and its stage and orientation for imaging. It can even include a full description of the experiment (genotype, drugs...). Current solutions are to store the data in XML files, databases, and image headers. Metadata is very heterogeneous and user-specific and thus needs a flexible format.
* Meta image formats: For advanced microscopy applications, an experimental unit almost never corresponds to a single image file. Many microscopy file formats (e.g. Zeiss LSM) are designed for the one experiment one file paradigm with encapsulated metadata, but these scale very poorly. For advanced microscopy applications, it is more common to use a "meta" format consisting of many image files of some standard file type along with an XML or database schema that organizes the data across experimental dimensions and stores experimental metadata. This meta format approach has been widely and independently adopted because of its flexibility and scalability. In our own work we use something called the MegaCapture format which consists of an XML file for metadata along with a set of image files. These image files are stored as 2d, single channel images in any common format (TIF, JPG, PNG), and their file names reflect their coordinates in the dimensions of z, time, x-tile, y-tile, row, column, and plate. This schema is reflected in the database used by GoFigure. Several other groups have developed similar meta approaches. To the extent possible it would be nice for these formats to be compatible to allow for interchange between groups and perhaps more importantly to allow for the creation of ITK filters where the input is a meta image rather than a single image. ITK filters with meta image input are important for streamlined, HPC based processing for advanced microscopy applications.

StandardsInterfaces

2010-06-24T15:16:19Z

Megason: /* Progress */

StandardsInterfaces

2010-06-24T14:50:27Z

Megason:

Microscopy Image Analysis

2010-06-23T17:35:44Z

Megason: /* Schedule */

Microscopy Image Analysis

2010-06-22T16:22:18Z

Megason: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Ohio State Univ
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Andinet Enquobahrie, Kitware
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Curtis Lisle, KnowledgeVis
# Tammy Riklin Raviv, CSAIL, MIT

StandardsInterfaces

2010-06-19T15:51:48Z

Megason: /* Key Investigators */

StandardsInterfaces

2010-06-19T15:50:53Z

Megason: /* Key Investigators */

StandardsInterfaces

2010-06-19T15:48:45Z

Megason: /* Key Investigators */

StandardsInterfaces

2010-06-18T19:45:23Z

Megason: /* Key Investigators */

StandardsInterfaces

2010-06-18T19:43:47Z

Megason:

StandardsInterfaces

2010-06-18T19:21:43Z

Megason: Created page with '__NOTOC__ ==Key Investigators== * Harvard - Sean Megason <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3> We are develo…'

__NOTOC__

==Key Investigators==
* Harvard - Sean Megason

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>

2010 Summer Project Week

2010-06-16T13:59:48Z

Megason: /* Microscopy Image Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#Intraoperative Brain Shift Monitoring Using Shear Model Transcranial Ultrasound (Jason White, Steve Pieper?, Pratik Patel?)
#Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
# Liver Ablation (Haiying Liu)
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#Module Inventory (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]]Superbuild (David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

Microscopy Image Analysis

2010-06-10T16:16:05Z

Megason: /* Participants */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Univ of Ohio
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard - CoSMo
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.

Microscopy Image Analysis

2010-06-10T15:54:35Z

Megason: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Univ of Ohio
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard - CoSMo
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.

Microscopy Image Analysis

2010-06-10T15:53:00Z

Megason: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Univ of Ohio
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard - CoSMo
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.

2010 Summer Project Week

2010-06-10T15:22:17Z

Megason: /* Microscopy Image Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi)
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith)
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
* [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
* [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Ross Whitaker)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Ron Kikinis)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Eckbo Ryan , BWH
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Li Rui , MGH
# Lisle Curtis , KnowledgeVis, LLC
# Liu Haiying , Brigham and Women's Hospital
# Liu Yanling , SAIC-Frederick, Inc.
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS

Microscopy Image Analysis

2010-06-10T15:17:14Z

Megason: /* Participants */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.

MedianTexture

2010-06-10T15:04:44Z

Megason:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

MedianTexture

2010-06-10T15:04:03Z

Megason: Created page with 'sdasd'

sdasd

2010 Summer Project Week

2010-06-10T15:00:31Z

Megason: /* Microscopy Image Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi)
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith)
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
* [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Ross Whitaker)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Ron Kikinis)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Eckbo Ryan , BWH
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Li Rui , MGH
# Lisle Curtis , KnowledgeVis, LLC
# Liu Haiying , Brigham and Women's Hospital
# Liu Yanling , SAIC-Frederick, Inc.
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS

2010 Summer Project Week

2010-06-10T14:59:55Z

Megason: /* Microscopy Image Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi)
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith)
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set][ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
* [[MedianTexture][Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Ross Whitaker)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Ron Kikinis)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Eckbo Ryan , BWH
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Li Rui , MGH
# Lisle Curtis , KnowledgeVis, LLC
# Liu Haiying , Brigham and Women's Hospital
# Liu Yanling , SAIC-Frederick, Inc.
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS

Microscopy Image Analysis

2010-06-03T18:58:02Z

Megason: /* Preparation */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:54:39Z

Megason: /* Preparation */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:53:55Z

Megason: /* Preparation */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:53:31Z

Megason: /* Preparation */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:53:08Z

Megason: /* Preparation */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] list on the main page
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:51:33Z

Megason: /* Projects */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:51:05Z

Megason: /* Projects */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:50:31Z

Megason: /* Projects */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[Microscopy Image Analysis Project |2010_Summer_Project_Week#Analysis]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:49:13Z

Megason: /* Projects */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[Microscopy Image Analysis Project | 2010_Summer_Project_Week#Microscopy Image Analysis]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:47:33Z

Megason: /* Projects */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[Microscopy Image Analysis Project][2010_Summer_Project_Week#Microscopy_Image_Analysis]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

2010 Summer Project Week

2010-06-03T18:45:53Z

Megason: /* Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, ?)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo)

=== IGT ===
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)

=== Python ===
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

#Aucoin, Nicole, BWH
#Audette, Michel, Kitware
#Aylward, Stephen, Kitware, Inc
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories
#Bouix, Sylvain, BWH
#Budin, Francois, UNC
#Burdette, Everette, Acoustic MedSystems, Inc.
#Chen, Min, Johns Hopkins University
#Datar, Manasi, SCI Institute
#Eckbo, Ryan, BWH
#Fedorov, Andriy, Surgical Planning Lab
#Fillion-Robin, Jean-Christophe, Kitware Inc.
#Finet, Julien, Kitware Inc
#Fishbaugh, James, SCI Institute
#Gao, Yi, Gerogia Tech
#GELAS, Arnaud, Harvard Medical School
#gouaillard, alexandre, CoSMo Software
#Gouttard, Sylvain, SCI Institute
#Haehn, Daniel, University of Pennsylvania
#Hageman, Nathan
#Hahn, Dieter, University Erlangen
#Hamel, Corentin, UNC Chapel Hill
#Hata, Nobuhiko, Brigham and Women's Hospital
#Hayes, Kathryn, Brigham and Women's Hospital
#Holton, Leslie, Medtronic Navigation
#Ibanez, Luis, KITWARE Inc.
#Johnson, Hans, University of Iowa
#Kapur, Tina, Brigham and Women's Hospital
#Kikinis, Ron, Brigham and Women's Hospital
#Kim, Minjeong, UNC-Chapel Hill
#Kolesov, Ivan, Georgia Institute of Technology
#Larson, Garrett, UNC-CH
#Li, Rui, MGH
#Lisle, Curtis, KnowledgeVis, LLC
#Liu, Haiying, Brigham and Women's Hospital
#Liu, Yanling, SAIC-Frederick, Inc.
#Magnotta, Vincent, The University of Iowa
#malaterre, mathieu, CoSMo Software
#Mastrogiacomo, Katie, Brigham and Women's Hospital
#Matsui, Joy, University
#Megason, Sean, Harvard Medical School
#Meier, Dominik, BWH, Boston MA
#menze, bjoern, CSAIL MIT
#Mosaliganti, Kishore, Harvard Medical School
#Niethammer, Marc, UNC Chapel Hill
#Norton, Isaiah, BWH Neurosurgery
#Paniagua, Beatriz, University of North Caolina at Chapel Hill
#Papademetris, Xenophon, Yale University
#Partyka, David, Kitware Inc
#Pathak, Sudhir, Univeristy Of Pittsburgh
#Peroni, Marta, Politecnico di Milano
#Perrot-Audet, Antonin, Harvard Medical School
#Pieper, Steve, Isomics, Inc.
#Plesniak, Wendy, BWH
#Pohl, Kilian, IBM
#Pujol, Sonia, Brigham and Women's Hospital
#Rannou, Nicolas, Harvard Medical School
#Riklin Raviv, Tammy, MIT, CSAIL
#Ruiz, Marco, UCSD
#Schroeder, William, Kitware
#Scully, Mark, The Mind Research Network
#Sharp, Greg, MGH
#Shi, Yundi, UNC Chapel Hill
#Shusharina, Nadya, MGH
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)
#Souhait, Lydie, Harvard Medical School
#Spinczyk, Dominik, Silesian University of Technology
#Srinivasan, Padmapriya
#Tao, Xiaodong, GE Research
#Ungi, Tamas, Queen's University
#Vachet, Clement, UNC Chapel Hill
#Veni, Gopalkrishna, SCI Institute
#Wassermann, Demian, SPL/LMI/PNL
#Wells, Sandy, BWH
#Wu, Guorong, University of North Carolina at Chapel Hill

Microscopy Image Analysis

2010-06-03T18:40:26Z

Megason: /* Open Workshop on Microscopy Image Analysis in ITK and VTK */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:36:13Z

Megason: /* Open Workshop on Microscopy Image Analysis in ITK and VTK */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your project to this page in the "Project" section below
* Add your name to the "Participants" section below
* Register for the overall conference from the [[2010_Summer_Project_Week]] home page
* Create a wiki page describing your project following the instructions on the [[2010_Summer_Project_Week]] home page

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:31:00Z

Megason: /* Open Workshop on Microscopy Image Analysis in ITK and VTK */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:28:27Z

Megason: /* Open Workshop on Microscopy Image Analysis in ITK and VTK */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [2010_Summer_Project_Week] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:28:13Z

Megason: /* Open Workshop on Microscopy Image Analysis in ITK and VTK */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the 2010_Summer_Project_Week at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-06-03T18:27:52Z

Megason: /* Open Workshop on Microscopy Image Analysis in ITK and VTK */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week][2010 Summer Project week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital

Microscopy Image Analysis

2010-05-10T16:14:18Z

Megason: /* Projects */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* , Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo

Microscopy Image Analysis

2010-04-11T16:23:46Z

Megason:

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week
* Wednesday afternoon
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below
* --
* --

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware

Microscopy Image Analysis

2010-04-10T17:49:00Z

Megason: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday- 1 slide lightning talk of project planned for the week
* Tuesday morning
** Current efforts (15 minute talks per lab)
** Roundtable discussion of standards/interfaces
*** Image file type
*** Segmentation/tracking filters input/output interface
*** Calculated data output format
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week
* The rest of the time will be spent coding on projects

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Badri Roysam, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware