github.com/iwc-workflows/tissue-microarray-analysis/main

Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and interactive image viewers including: Pyramidal OME-TIFF images, nuclear segmentation masks (TIFF), quantified feature tables (CSV, h5ad) with cell type annotations, and an interactive Vitessce dashboard that combines image viewing with linked single-cell data visualizations.