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.