Difference between revisions of "Slicer3:Fluorescence and Electron Microscopy Support"

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<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Fluorescence_and_Electron_Microscopy_Support  here]</font></big>a
 
 
'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.
 
 
 
'''Progress:'''
 
Reading 3-D TIFF images and generating surface models has been easily accomplished.
 
 
 
* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
 
** Works in Linux, not OS X.
 
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
 
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
 
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
 
** Can ParaView be used as visualization tool for surface rendering?  Is it faster?
 
 
 
'''Key Investigators:'''
 
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
 
* Isomics: Steve Pieper
 
 
 
'''Links:'''
 
 
 
* Some sample data are available here: [[Image:NCMIR example dataset.zip|NCMIR dataset]]
 
 
 
'''Screenshot:'''
 
 
 
[[Image:SlicerAstrocyte.jpg]]
 

Latest revision as of 17:48, 10 July 2017

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Note: We are migrating this content to the slicer.org domain - The newer page is herea