Cellpose GPU installation for QuPath and Fiji

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

[@alrooo442]

Thank you so much for your super helpful videos, Thierry! Never would've been able to do this on my own, since I never even used Anaconda before!

[@thierrypecot8747]

Glad to see it's helpful!

[@AlessioTorcinaro]

Thank you so much, Thierry! I was struggling with running cellpose on Qupath. I have also tried to uninstall and reinstall CellPose (by using Anaconda). I will take a look to your tutorial! FIngers crossed

[@thierrypecot8747]

0:31 Anaconda installation 2:24 Cuda toolkit installation 5:05 Cudnn installation 9:11 Virtual environment creation and activation 12:30 PyTorch installation 14:10 Cellpose installation 15:03 Cellpose extension for QuPath 18:53 Cellpose path definition in QuPath 20:02 Cellpose processing from QuPath 25:46 BIOP plugin installation in Fiji 26:30 Cellpose path definition in Fiji 27:21 Cellpose processing from Fiji

[@KeesieOilcorner]

Thanks!

[@thierrypecot8747]

You're very welcome!

[@scds7]

Thanks...this is extremely helpful. Will you be able to show how to get the Cellpose plugin into CellProfiler?

[@thierrypecot8747]

Hi! Glad to see it's helpful. I actually don't use CellProfiler so I don't plan to do it in a near future. You might have seen it, there's a tutorial available here: forum.image.sc/t/new-cellprofiler-4-plugin-runcellpose/56858 I hope this will be helpful!

[@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

[@AlessioTorcinaro]

Hello! How do you "re-call" your CellPoseGPUenvironment/folder the second time or the N-time you want to use it? I mean which are the command lines for that purpose, or you can just run QuPath and the CellPoseGPUenvirnonment is ready for use forever? Thank you for your tutorials!

[@thierrypecot8747]

Hi! Once the environment is well installed, you can run QuPath forever. However, whenever you change QuPath version, you'll have to install again the Cellpose extension and define again the environment path in QuPath. The last version changed and the env installation is not available any more, I'm gonna have a look at it to see if it's still possible to use the same virtual environment.

[@AlessioTorcinaro]

@@thierrypecot8747 Thank you for your reply! Yes, I have noticed that last version of CellPose extension has something different in QuPath Preferences.

[@AlessioTorcinaro]

@@thierrypecot8747 Hi, Thierry! Are you going to make an updated tutorial with the last versions of Qupath and CellPose extension?

[@thierrypecot8747]

Hi @@AlessioTorcinaro! I won't make a new one in a near future, but I think it's the change is pretty straight forward. If you're stuck, don't hesitate to send me a message, I'll help you then.

[@koungngeun8055]

Does it work in HE stain. I follow your tutorial to use in imageJ Fiji, but there was no result photo come out.

[@thierrypecot8747]

Hi! There is no pre-trained cellpose model for H&E staining. You could use the nuclei pre-trained model but you'll have to select one channel. The best way to do it with QuPath is to use the "Estimate stain vectors" functionality to separate hematoxylin from eosin and then apply the cellpose model on the estimated hematoxylin channel. Hope this will help!

[@pawesuliga8815]

Hi - very interesting video, thank you. I tried to build a model on HE stained slides but it wasn't perfect. Although it was good enough for my analysis. Estimate stain vector sounds like a good option - I will give it a try @@thierrypecot8747

[@Mainline100]

Does this workflow work for other extensions like stardist?

[@thierrypecot8747]

Hi! This workflow is designed to use cellpose. If you want to use Stardist, it's totally doable, you can check this video that shows how to use Stardist to segment cells with QuPath: kzbin.info/www/bejne/fXOpc4mKZ9ing7M

[@magdalesinski3840]

Thank you so muuch for this tutorial! I am new to coding overall and my lab has been manually measuring fiber size so I'm trying to optimize this. However this tutorial doesn't exactly match the updated scripts or updates so I'm getting errors that I'm not sure how to address. This is the error message referring to line 6 in this tutorial and 8 in the updated script from your github - ERROR: Cannot invoke "qupath.lib.projects.Project.getPath()" because the return value of "qupath.lib.scripting.QP.getProject()" is null in QuPathScript at line number 8 qupath.ext.biop.cellpose.CellposeBuilder.build(CellposeBuilder.java:801) Any help would be appreicated

[@thierrypecot8747]

Hi @magdalesinski3840! It's a bit hard to answer remotely but according to the error message, it seems that you did not create a project to start with. QuPath is designed to be used with projects, you can see how to create one here: kzbin.info/www/bejne/rKOcqJKCjtmGqdE. Hopefully this will resolve your problem!