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 steinbock.

The following files are part of the "analysis" folder when running the IMC Segmentation Pipeline:

• cpinp.zip: contains input files for the segmentation pipeline
• cpout.zip: contains all final output files of the pipeline: cell.csv containing the single-cell features; Experiment.csv containing CellProfiler metadata; Image.csv containing acquisition metadata; Object relationships.csv containing an edge list indicating interacting cells; panel.csv containing channel information; var_cell.csv containing cell feature information; var_Image.csv containing acquisition feature information
• histocat.zip: contains single channel .tiff files per acquisition for upload to histoCAT (https://bodenmillergroup.github.io/histoCAT/)
• ilastik.zip: contains upscaled image crops in .h5 format for ilastik (https://www.ilastik.org/) training 
• ometiff.zip: contains .ome.tiff files per acquisition, .png files per panorama and additional metadata files per slide
• tiffs.zip: contains multi channel .tiff files of all channels for analysis (_full.tiff) and their channel order (_full.csv); multi channel images for ilastik pixel classification (_ilastik.full) and their channel order (_ilastik.csv); upscaled multi channel images for ilastik pixel prediction (_ilastik_s2.h5); 3 channel images containing ilastik pixel probabilities (_ilastik_s2_Probabilities.tiff) and segmentation masks (_ilastik_s2_Probabilities_mask.tiff).

The remaining files are part of the root directory:

• config.zip: containing the antibody panel used for the experiment.
• cp4_pipelines.zip: containing the CellProfiler pipelines for analysis.
• documentation.zip: containing a description of the IMC Segmentation Pipeline
• scripts.zip: containing a jupyter notebook to perform image pre-processing
• setup.zip: containing a .yml describing the dependencies to be installed via conda