[Insight-users] Fwd: ITKv4 & Microscopy

[Luis Ibanez]

 http://www.kitware.com/blog/home/post/50

*ITKv4 & Microscopy* by *Luis Ibanez* (Open Source, Medical Imaging)

*Small objects in Large Images*

As we mentioned briefly in our recent
post<http://www.kitware.com/blog/home/post/49>,
the upcoming version of ITKv4 <http://www.itk.org/Wiki/ITK_Release_4.0> will
provide better support for Microscopy
Applications<http://www.itk.org/Wiki/ITK_Release_4/Microscopy>
.

Here are some of the critical topics for which we will be improving ITKv4 in
order to better serve application developers in the domain of Microscopy
imaging.

   - Very Large datasets (GigaBytes / TeraBytes)
   - Temporal data (2D+t, 3D+t)
   - Multiple Components per pixel
   - Very large number of objects of interest per image
   - High throughput (thousands of datasets to analyze in batch/parallel)


Since all of these topics are far from trivial, we need the joint effort of
a larger community to address them properly. No single institution has the
"know how", access to domain experts, and technology for effectively
tackling these problems on their own.

A collaboration effort is the best approach for jointly addressing these
challenges. To that end we are coordinating with different groups that
currently work in microscopy and related biomedical fields to:

   - Gather common resources
   - Identify specific needs and challenges
   - Share effort on addressing problems


We anticipate that each one of the participants, and the community at large,
will benefit from distributing the burden of working on each one of those
individual problems.

We have already identified several critical technologies that must be added
to ITK to support microscopy, such as:

   - More explicit representation of time and channels
   - Management of multi-resolution datasets
   - Management of multi-gigabyte datasets (TeraBytes being the standard to
   look for in 5 years)


Additional needs and efforts of ITK regarding microscopy are listed here:
http://www.itk.org/Wiki/ITK_Release_4/Microscopy

This page is open to comments and contributions from the public. Please join
the conversation!


An initial list of interested groups is available here:
http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Collaborating_Groups

and of course, you all are welcome to join and participate. Let us know of
your interest, or simply edit the Wiki page and add your group to the list.

We have also collected an initial list of applications (domains of
application and specific software applications) in the following Wiki page:
http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Reference_Applications

A number of Events related to ITK and Microscopy have been listed here:
http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Related_Events

In particular:

   - A Microscopy Workshop took place at the recent NAMIC meeting in June:
   http://www.na-mic.org/Wiki/index.php/Microscopy_Image_Analysis
   - A Hackathon is ongoing at the Janelia Farm HHMI campus, to develop ITK
   plugins for the V3D application

   http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Related_Events#Hackathon_at_HHMI:_V3D-ITK_Plugins
   http://openwiki.janelia.org/wiki/display/v3dhackathon
   - A Tutorial on Microscopy Image Analysis is scheduled for the upcoming
   MICCAI 2010 conference:
   http://penglab.janelia.org/proj/miccai2010


We are also looking at Microscopy as a testbed for the ITK Simplified Layer
that is one of the initiatives of ITKv4:
http://www.itk.org/Wiki/ITK_Release_4/SimpleITK

We will be happy to hear your feedback and suggestions on these exciting
activities.


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