coppafish is a data analysis pipeline for decoding coppaFISH (combinatorial padlock-probe-amplified fluorescence in situ hybridization) datasets. coppaFISH is a method for in situ transcriptomics which produces a series of images arranged in terms of tiles, rounds and channels. coppafish then determines the distribution of genes via image processing, spot detection, registration and gene calling.
Python >= 3.8
For more information on installation and usage, please see the documentation.