The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Initial release of nf-core/imcyto, created with the nf-core template.
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Split image acquisition output files (
mcd,ome.tiffortxt) by ROI and convert to individualtifffiles for channels with names matching those defined in user-providedmetadata.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 (CellProfiler). -
Use selected
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 compositetiffgenerated in step 3 will be used in subsequent steps instead. -
Use probability/composite
tiffand pre-processed full stacktifffor segmentation to generate a single cell mask astiff, and subsequently overlay cell mask onto full stacktiffto generate single cell expression data incsvfile (CellProfiler).