Napari-Bigfish is a plugin for the multi-dimensional image viewer napari. It provides an alternative graphical user interface to parts of the Big-FISH python package. Big-FISH is a python package for the analysis of smFISH images.

The parts currently available via the plugin are

• Gaussian Background Removal

• Automated Spot Detection

  • minimum spot distance

  • removal of duplicates

  • auto-threshold detection

• Dense Region Decomposition

• Counting of spots per cell and category cytoplasm/nucleus (not from bigfish)

• Batch-Processing

MRI users can find napari with napari-bigfish installed on the analysis pcs of the core imaging facility.