Helix/bwVisu/QuPath

From bwHPC Wiki
< Helix‎ | bwVisu
Revision as of 16:26, 2 September 2025 by H Schumacher (talk | contribs) (Instructions for adding the Cellpose extension)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search
Attention.svg

GPU support and CellPose are work in progress.

QuPath offers a powerful set of tools for a wide range of image formats, including many whole slide formats.


Add Extensions

CellPose

The official installation and usage instructions for the extension can be found at https://github.com/BIOP/qupath-extension-cellpose.

To summarize:

  1. Install Cellpose
    • Cellpose and the extra dependency scikit-image are already installed. This step can be skipped.
  2. Add the extension
    1. Install and setup the qupath-biop-catalog
    2. Add the Cellpose extension (Extensions -> Manage Extensions)
    3. Restart QuPath / the bwVisu Job
  3. First time setup
    • Go to Edit > Preferences > Cellpose/Omnipose
    • Add the path to the Python executable: "/opt/cellpose/bin/python3.9"
Retrieved from "https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/QuPath&oldid=15266"