Cellpose installation for QuPath and Fiji

This video shows how to install Cellpose to be processed with the CPU within QuPath and Fiji. The fluorescence image used in this video showing muscle fibers was acquired at APEX (www6.inrae.fr/....

[@thierrypecot8747]

0:31 Anaconda installation 2:13 Virtual environment creation and activation 8:15 Cellpose installation 9:46 Cellpose extension for QuPath 12:17 Cellpose path definition in QuPath 14:38 Cellpose processing from QuPath 21:25 BIOP plugin installation in Fiji 24:12 Cellpose path definition in Fiji 25:07 Cellpose processing from Fiji

[@thierrypecot8747]

!!!!QuPath update!!!! QuPath extension >= 0.7.0 have a different preferences window than shown in the video. Now, when you open the Edit -> Preferences... window, in the Cellpose/Omnipose section, you need to define the Cellpose 'python.exe' location. If you installed the virtual environment at location , you need to define in "Cellpose 'python.exe' location" within the Edit -> Preferences... window the following path: \Scripts\python.exe

[@katiehanna8528]

Hi @thierrypecot8747 thank you so much for your very helpful videos. I would not have been able to get to the point that I have without your help. I think my problem is downloading the pretrained models. I am unsure what path I need to input into the anaconda prompt. Thank you

[@thierrypecot8747]

Hi! Normally, when you run Cellpose the first time, it's gonna download automatically the pre-trained model you want to use. If it does not work, you need to open an anaconda prompt, activate the virtual environment and then copy the command line (from the script editor inQuPath under the script or from the console in Fiji) just above "This command should run directly if copy-pasted into your shell" in the anaconda prompt, that should run fine and download the pretrained models if downloading failed previously. I hope this will help!