Slicer3:Fluorescence and Electron Microscopy Support

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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: File:NCMIR example dataset.zip

Screenshot: