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qupath-extensions-0.6.0v2

This container provides access to QuPath 0.6.0 with pre-installed extensions for segmentation using GPU acceleration. Those include: - qupath-extension-cellpose v0.11.1 with support for cellpose v3 models as well as cpsam_v2 - qupath-extension-spotiflow v0.3.1 with support for spotiflow - Instanseg v0.1.5 - qupath-extension-stardist for nuclei segmentation with stardist v0.6.0 - qupath-extension-warpy v0.4.2 for image registration - qupath-extension-abba v0.4.0 for image registration using brain atlases

Requirements

  • Apptainer

Build Instructions

To build the container, run the following command in the terminal:

apptainer build qupath-extensions-0.6.0v2.sif build.def

Run Instructions

This container runs by default qupath with:

apptainer run --nv qupath-extensions-0.6.0v2.sif

Notes

This container is adapted from the BIOP-desktop QuPath container covered by an Apache 2.0 license. Extensions and models are downloaded from BIOP’s zenodo covered by a CC BY 4.0 license.