RNAFish

FishFeats: napari plugin to perform quantification of multimodal labeling at the single-cell level in 3D tissues.

FishFeats allows to perform together in the same pipeline several analysis to quantify epithelia cells in 3D tissue, analysing cell morphology, nuclei, immuno-staining or RNA expression. The plugin allows flexibility to let the user choose the relevant step for a specific biological question.

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.