Cell migration analysis for microfluidic ATPS channels
Project description
cytoscan
Cell migration analysis for microfluidic ATPS channels. Detects cells, channel walls, and the membrane interface from brightfield + fluorescent microscopy frames; produces per-cell distance and category data.
Install
pip install cytoscan
Usage
cytoscan init my_experiment # scaffold dir + config
# drop tifs (br/fl/mx triples) into my_experiment/
cytoscan run my_experiment # full pipeline
cytoscan validate my_experiment # detection-only, with flag table
cytoscan version
Outputs land in my_experiment/output/:
cells.csv,frames.csv,interface.csv,summary.txtoutput_frame*.png(visual overlays)
Built for the Sun Lab — https://www.sunlabutsa.org/ by Mateo McKee
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