Updates the example pipeline outline to CP4 and imctools v2 - Githubissues

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

https://bodenmillergroup.github.io/ImcSegmentationPipeline/

MIT License

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Updates the example pipeline outline to CP4 and imctools v2 #53

Closed votti closed 3 years ago

votti commented 3 years ago

Updates the example pipeline outline to CP4 and imctools v2

This is the step-by-step descriptive workflow.

This is an adaptation of the previous workflow that uses imctools v2 and the latest CellProfiler.

Notable changes to the last version:

imctools v2: changed naming of .ome.tiff files and content of ome folders
Adds to output:
- Metadata annotation files for the measurement columns (var_*.csv)
- A copy of the panel.csv used

Apart from this everything should work and perform as in the old version.