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. 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 "analysis" folder when running the IMC Segmentation Pipeline: <strong>cpinp.zip</strong>: contains input files for the segmentation pipeline <strong>cpout.zip</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 <strong>histocat.zip</strong>: contains single channel .tiff files per acquisition for upload to histoCAT (https://bodenmillergroup.github.io/histoCAT/) <strong>ilastik.zip</strong>: contains upscaled image crops in .h5 format for ilastik (https://www.ilastik.org/) training <strong>ometiff.zip</strong>: contains .ome.tiff files per acquisition, .png files per panorama and additional metadata files per slide <strong>tiffs.zip</strong>: contains multi channel .tiff files of all channels for analysis (<em>_full.tiff</em>) and their channel order (<em>_full.csv</em>); 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>); 3 channel images containing ilastik pixel probabilities (<em>_ilastik_s2_Probabilities.tiff</em>) and segmentation masks (<em>_ilastik_s2_Probabilities_mask.tiff</em>). The remaining files are part of the root directory: <strong>config.zip</strong>: containing the antibody panel used for the experiment. <strong>cp4_pipelines.zip</strong>: containing the CellProfiler pipelines for analysis. <strong>documentation.zip</strong>: containing a description of the IMC Segmentation Pipeline <strong>scripts.zip</strong>: containing a jupyter notebook to perform image pre-processing <strong>setup.zip</strong>: containing a .yml describing the dependencies to be installed via conda