Pre-Cancer Atlas data analysis toolkit
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.
Unpack and repack ome.tif files to TIFF images.
Sample, render, and assemble single cell images.
Pixel binarization as feature generation.
Mini-tile and region-wise Pearson correlation coefficient.
Useful external code.
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