How to use Napari

Napari is a fast, interactive, multi-dimensional image viewer for Python, widely used in bioimaging to explore and visualize large microscopy datasets.

Install

Install Napari 0.4.17, then launch the application and open the IPython console (icon >_).

Install CosMx plugin

pip install napari_CosMx-0.4.17.3-py3-none-any.whl

Download the napari_cosmx_launcher folder from the provided link and drag it into the Napari window.

Run stitching

  • Select the parent folder that contains your CosMx run

  • Choose the output folder

  • Click Stitch

  • Wait until the loading completes

The output directory will now contain:

  • an images folder with all FOVs

  • a targets.hdf5 file containing transcripts

Restart Napari

Restart Napari 0.4.17 and drag the project folder into the window.

Explore

Use the Napari panels to visualize and manage data:

  • Morphology images: add fluorescent channels

  • RNA transcripts: add transcripts

  • Layer list: manage transcripts, channels, and segmentation

  • Layer controls: adjust visualization settings