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Pre-Cancer Atlas data analysis toolkit

Project description

PCA analysis toolkit

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.


  • 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.

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