Analysis toolkit for the Pre-Cancer Atlas project. This toolkit is meant for exploratory analyses that changes rapidly.
Images, mostly acquired through the CyCIF technology, are assumed to be processed first by mcmicro-nf, where most of the heavy computation for illumination correction, stitching, registration, nuclei & cell segmentation, and feature quantification are done. The images are then passed to this toolkit for rapid iterations of exploratory analyses.
Currently only support pip
:
pip install pcatk
convert
Unpack and repack ome.tif files to TIFF images.exemplar
Sample, render, and assemble single cell images.feature
Pixel binarization as feature generation.measure
Mini-tile and region-wise Pearson correlation coefficient.util
Utility functions.external
Useful external code.