Description:

pcatk 0.1

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.
Modules

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.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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