DOI: 10.5281/zenodo.6043600
title: steinbock results of IMC example data

description: This repository hosts the results of processing example imaging mass cytometry (IMC) data hosted at zenodo.org/record/5949116 using the <em>steinbock </em>framework available at github.com/BodenmillerGroup/steinbock. Please refer to <strong>steinbock.sh </strong>for how these data were generated from the raw data. The following files are part of this repository: <strong>panel.csv</strong>: contains channel information regarding the used antibodies in <em>steinbock</em> format <strong>img.zip</strong>: contains hot pixel filtered multi-channel images derived from the IMC raw data. One file per acquisition is generated <strong>images.csv</strong>: contains metadata per acquisition <strong>pixel_classifier.ilp</strong>: ilastik pixel classifier (same as the one in zenodo.org/record/6043544) <strong>ilastik_crops.zip</strong>: image crops on which the ilastik classifier was trained (same as the ones in zenodo.org/record/6043544) <strong>ilastik_img.zip</strong>: contains multi-channel images (one per acquisition) in .h5 format for ilastik pixel classification <strong>ilastik_probabilities.zip</strong>: 3 channel images containing the pixel probabilities after pixel classification <strong>masks_ilastik.zip</strong>: segmentation masks derived from the ilastik pixel probabilities using the <strong>cell_segmentation.cppipe</strong> pipeline <strong>masks_deepcell.zip</strong>: segmentation masks derived by <em>deepcell</em> segmentation <strong>intensities.zip</strong>: Contains one .csv file per acquisition. Each file contains single-cell measures of the mean pixel intensity per cell and channel based on the files in <strong>img.zip </strong>and <strong>masks_deepcell.zip</strong>. <strong>regionprops.zip</strong>: Contains one .csv file per acquisition. Each file contains single-cell measures of the morphological features and location of cells based on <strong>masks_deepcell.zip</strong>. <strong>neighbors.zip</strong>: Contains one .csv file per acquisition. Each file contains an edge list of cell IDs indicating cells in close proximity based on <strong>masks_deepcell.zip</strong>. <strong>ome.zip</strong>: contains .ome.tiff files derived from img.zip; one file per acquisition <strong>histocat.zip</strong>: contains single-channel .tiff files with segmentation masks derived from <strong>masks_deepcell.zip</strong> for upload to histoCAT (bodenmillergroup.github.io/histoCAT) <strong>cells.csv</strong>: contains intensity and regionprop measurements of all cells <strong>cells_csv.zip</strong>: contains intensity and regionprop measurements of all cells per acquisition <strong>cells.fcs</strong>: contains intensity and regionprop measurements of all cells in fcs format <strong>cells_fcs.zip</strong>: contains intensity and regionprop measurements of all cells per acquisition in fcs format <strong>cells.h5ad</strong>: contains intensity, regionprop and neighbor measurements of all cells in <em>anndata </em>format <strong>cells_h5ad</strong>: contains intensity regionprop and neighbor measurements of all cells per acquisition in <em>anndata </em>format <strong>graphs.zip</strong>: contains spatial object graphs in .graphml format; one file per acquisition