NA-MIC Project Weeks

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Confocal Microscopy in Slicer

Key Investigators

• Steve Pieper ([Isomics][isomics])
• Brad Lowekamp (NIH NIAID)
• Andrey Fedorov (BWH)

Description

Objective

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

Illustrations

Click image to see movie:

Background and References