A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
This is the first release of
In this version, provided nuclear image data can be preprocessed, with second image inputs supported. Three image-based segmentation tools are available as segmentation options and masks can be filtered. Previously called spots (provided as input) are filtered and assigned to cells based on the segmentation masks and quantified, with appropriate QC metrics returned. Additionally, crop creation for training segmentation models (after preprocessing) is supported. Final output is an AnnData object in SquidPy format.