<a href="http://www.kitware.com/blog/home/post/50" target="_blank">http://www.kitware.com/blog/home/post/50</a><br><div class="gmail_quote"><div><br>
<i>ITKv4 & Microscopy</i> by <b>Luis Ibanez</b> (Open Source, Medical Imaging)
<br><br><b>Small objects in Large Images</b><br><br>
As we mentioned briefly in <a href="http://www.kitware.com/blog/home/post/49" target="_blank">our recent post</a>, the upcoming version of <a href="http://www.itk.org/Wiki/ITK_Release_4.0" target="_blank">ITKv4</a> will provide better support for <a href="http://www.itk.org/Wiki/ITK_Release_4/Microscopy" target="_blank">Microscopy Applications</a>.<br>
<br>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.<br><ul><li> Very Large datasets (GigaBytes / TeraBytes) </li>
<li> Temporal data (2D+t, 3D+t) </li><li> Multiple Components per pixel</li><li> Very large number of objects of interest per image</li><li>High throughput (thousands of datasets to analyze in batch/parallel)</li></ul><br>
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.<br>
<br>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: <br><ul><li>
Gather common resources</li><li>Identify specific needs and challenges</li><li>Share effort on addressing problems</li></ul><br>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.<br>
<br>We have already identified several critical technologies that must be added to ITK to support microscopy, such as:<br><ul><li>More explicit representation of time and channels</li><li> Management of multi-resolution datasets</li>
<li> Management of multi-gigabyte datasets (TeraBytes being the standard to look for in 5 years)</li></ul> <br>Additional needs and efforts of ITK regarding microscopy are listed here:<br> <a href="http://www.itk.org/Wiki/ITK_Release_4/Microscopy" target="_blank">http://www.itk.org/Wiki/ITK_Release_4/Microscopy</a><br>
<br> This page is open to comments and contributions from the public. Please join the conversation!<br><br><br>An initial list of interested groups is available here:<br><a href="http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Collaborating_Groups" target="_blank">http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Collaborating_Groups</a><br>
<br>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.<br><br> We have also collected an initial list of applications (domains of application and specific software applications) in the following Wiki page:<br>
<a href="http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Reference_Applications" target="_blank">http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Reference_Applications</a><br><br>A number of Events related to ITK and Microscopy have been listed here:<br>
<a href="http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Related_Events" target="_blank">http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Related_Events</a><br><br>In particular:<br><ul><li>A Microscopy Workshop took place at the recent NAMIC meeting in June: <br>
<a href="http://www.na-mic.org/Wiki/index.php/Microscopy_Image_Analysis" target="_blank">http://www.na-mic.org/Wiki/index.php/Microscopy_Image_Analysis</a></li><li>A Hackathon is ongoing at the Janelia Farm HHMI campus, to develop ITK plugins for the V3D application<br>
<a href="http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Related_Events#Hackathon_at_HHMI:_V3D-ITK_Plugins" target="_blank">http://www.itk.org/Wiki/ITK_Release_4/Microscopy/Related_Events#Hackathon_at_HHMI:_V3D-ITK_Plugins</a><br>
<a href="http://openwiki.janelia.org/wiki/display/v3dhackathon" target="_blank">http://openwiki.janelia.org/wiki/display/v3dhackathon</a></li><li>A Tutorial on Microscopy Image Analysis is scheduled for the upcoming MICCAI 2010 conference:<br>
<a href="http://penglab.janelia.org/proj/miccai2010" target="_blank">http://penglab.janelia.org/proj/miccai2010</a></li></ul><br>We are also looking at Microscopy as a testbed for the ITK Simplified Layer that is one of the initiatives of ITKv4: <br>
<a href="http://www.itk.org/Wiki/ITK_Release_4/SimpleITK" target="_blank">http://www.itk.org/Wiki/ITK_Release_4/SimpleITK</a><br><br>We will be happy to hear your feedback and suggestions on these exciting activities.<br>
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