Spatial transcriptomics

Big-FISH is a python package for the analysis of smFISH images (2D/3D). It includes various methods to analyze microscopy images, such spot detection and segmentation of cells and nuclei.

TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.