Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.

CommandSingleCellExtraction.py:

• --masks Paths to where masks are stored (Ex: ./segmentation/cellMask.tif) -> If multiple masks are selected the first mask will be used for spatial feature extraction but all will be quantified

• --image Path to image(s) for quantification. (Ex: ./registration/*.h5) -> works with .h(df)5 or .tif(f)

• --output Path to output directory. (Ex: ./feature_extraction)

• --channel_names csv file containing the channel names for the z-stack (Ex: ./my_channels.csv)

python CommandSingleCellExtraction.py --masks ./segmentation/cellMask.tif ./segmentation/membraneMask.tif --image ./registration/Exemplar_001.h5 --output ./feature_extraction --channel_names ./my_channels.csv

Denis Schapiro (https://github.com/DenisSch)

Joshua Hess (https://github.com/JoshuaHess12)

Jeremy Muhlich (https://github.com/jmuhlich)