Image Mass Cytometry analysis pipeline
[1.0.0] - 2020-05-29
Initial release of nf-core/imcyto, created with the nf-core template.
Split image acquisition output files (
txt) by ROI and convert to individual
tifffiles for channels with names matching those defined in user-provided
metadata.csvfile. Full and ilastik stacks will be generated separately for all channels being analysed in single cell expression analysis, and for channels being used to generate the cell mask, respectively (imctools).
Apply pre-processing filters to full stack
tifffiles in ilastik stack to generate a composite RGB image representative of the plasma membranes and nuclei of all cells (CellProfiler).
Use composite cell map to apply pixel classification for membranes, nuclei or background, and save probabilities map as
tiff(Ilastik). If CellProfiler modules alone are deemed sufficient to achieve a reliable segmentation mask this step can be bypassed using the
--skip_ilastikparameter in which case the composite
tiffgenerated in step 3 will be used in subsequent steps instead.
tiffand pre-processed full stack
tifffor segmentation to generate a single cell mask as
tiff, and subsequently overlay cell mask onto full stack
tiffto generate single cell expression data in