IMC Segmentation Pipeline results of example IMC data

This repository hosts the results of processing example imaging mass cytometry (IMC) data hosted at 10.5281/zenodo.5949116 using the IMC Segmentation Pipeline available at https://github.com/BodenmillerGroup/ImcSegmentationPipeline (DOI: 10.5281/zenodo.6402666). Please refer to https://github.com/BodenmillerGroup/steinbock as alternative processing framework and 10.5281/zenodo.6043600 for the data generated by <em>steinbock</em>. The following files are part of the <strong>analysis.zip</strong> folder when running the IMC Segmentation Pipeline: <strong>cpinp</strong>: contains input files for the segmentation pipeline <strong>cpout</strong>: contains all final output files of the pipeline: <em>cell.csv</em> containing the single-cell features; <em>Experiment.csv</em> containing CellProfiler metadata; <em>Image.csv</em> containing acquisition metadata; <em>Object relationships.csv</em> containing an edge list indicating interacting cells; <em>panel.csv</em> containing channel information; <em>var_cell.csv</em> containing cell feature information; <em>var_Image.csv</em> containing acquisition feature information; <em>images </em>containing the hot pixel filtered multi-channel images and the channel order; <em>masks</em> containing the segmentation masks; <em>probabilities </em>containing the pixel probabilities. <strong>histocat</strong>: contains single channel .tiff files per acquisition for upload to histoCAT (https://bodenmillergroup.github.io/histoCAT/) <strong>crops</strong>: contains upscaled image crops in .h5 format for ilastik (https://www.ilastik.org/) training <strong>ometiff</strong>: contains .ome.tiff files per acquisition, .png files per panorama and additional metadata files per slide <strong>ilastik</strong>: multi channel images for ilastik pixel classification (<em>_ilastik.full</em>) and their channel order (<em>_ilastik.csv</em>); upscaled multi channel images for ilastik pixel prediction (<em>_ilastik_s2.h5</em>); upscaled 3 channel images containing ilastik pixel probabilities (<em>_ilastik_s2_Probabilities.tiff</em>). The remaining files are part of the root directory: <strong>docs.zip: </strong>Documentation of the pipeline in markdown format I<strong>MCWorkflow.ilp: </strong>Ilastik pixel classifier pre-trained on the example data <strong>resources.zip: </strong>The CellProfiler pipelines and CellProfiler plugins used for the analysis <strong>sample_metadata.xlsx: </strong>Metadata per sample including the cancer type <strong>scripts.zip: </strong>Python notebooks used for pre-processing and downloading the example data <strong>src.zip: </strong>Scripts for the imcsegpipe python package