MEGA-FISH documentation
MEGA-FISH (Multi-omics Extensible GPU-Accelerated FISH analysis framework) is a Python package designed to process large-scale fluorescence images for spatial omics applications, including SeqFISH, SeqIS, and decoding-based FISH methods.
MEGA-FISH stitches sequentially captured tile images into a large, chunked single image and utilizes efficient computational resources (GPU or multi-threaded/multi-process CPU) for each processing step.
Users can generate a cell-by-gene expression matrix by combining simple functions such as image registration, segmentation, and spot detection.