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NA-MIC Project Weeks

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Confocal Microscopy in Slicer

Key Investigators



See how Slicer can be used for microscopy images.

Approach and Plan

  1. Compare with other tool (ImageJ / FIJI)
  2. Identify key operations
  3. Identify sample data

Progress and Next Steps

  1. Experimented with 7Gig 15 slice 7 channel images in nrrd format
  2. Looked at data in FIJI (often crashed, java exceptions…)
  3. Loaded in Slicer
    • confirmed that we can view and interact
    • ran SimpleITK filters
    • volume rendered


Click image to see movie:

Confocal images in Slicer

Background and References