adyprat/quantification

Quantification module for mcmicro

This fork contains modificaitons for passing a qptiff file as input

python CommandSingleCellExtraction.py --masks ../../Mask.tif --channel_names ../../Markers.csv --image ../../xyz.qptiff --output ../../Documents/xyz

Single cell quantification

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)

• --mask_props Space separated list of additional metrics to be calculated for every mask. This is intended for metrics that depend only on the cell mask. If the metric depends on signal intensity, use --intensity-props instead. See list at https://scikit-image.org/docs/dev/api/skimage.measure.html#regionprops

• --intensity_props Space separated list of additional metrics to be calculated for every marker separately. By default only mean intensity is calculated. If the metric doesn't depend on signal intensity, use --mask-props instead. See list at https://scikit-image.org/docs/dev/api/skimage.measure.html#regionprops Additionally available is gini_index, which calculates a single number between 0 and 1, representing how unequal the signal is distributed in each region. See https://en.wikipedia.org/wiki/Gini_coefficient. For example, to calculate the median intensity, specify --intensity_props median_intensity.

Run script

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

Main developer

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

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

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