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Update trackmate-cellpose.md - for cellpose 3
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_pages/plugins/trackmate/detectors/trackmate-cellpose.md

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@@ -291,14 +291,41 @@ Finally, click `Open` on one last confirmation panel:
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Once you cellpose installed, run the GUI to confirm that it works and can segment images on your system. Again, in the `Path to cellpose / Python executable` text field in the TrackMate detector UI, you will just need to enter the path to this executable.
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#### With Anaconda
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#### With conda, mamba environment managers
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{% include notice icon="tech"
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content="This is the recommended way to install Python tools to be used with TrackMate." %}
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Using mamba (a better conda) is the most common way to run scientific Python tools on your computer. Recommendations keep evolving and we try to update this page.
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If you don't have mamba, follow these instructions to install it: https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html
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Go to the cellpose GitHub webpage and follow the [installation procedures](https://github.com/MouseLand/cellpose#local-installation).
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If you chose Anaconda to install cellpose, and put it in a dedicated environment, you need to enter the path to the _python executable_ of this conda environment. For instance if made a conda environment named `cellpose` for cellpose, it will be something like this:
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`C:\Users\tinevez\anaconda3\envs\cellpose\python.exe`
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##### Install cellpose 3 on a Mac
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For instance on Mac: (on the computer used in example below, conda is an alias to microsmamba)
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```zsh
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>> conda create --name cellpose-3 python=3.10
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>> conda activate cellpose-3
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>> pip install 'cellpose[gui]==3.1.1.2'
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>> cellpose --version
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cellpose version: 3.1.1.2
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platform: darwin
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python version: 3.10.18
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torch version: 2.7.1
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```
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This will install the version 3 of cellpose. As mid 2025, GPU-acceleration is used on this OS, as you can attest in the log when running cellpose:
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```
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2025-07-11 11:13:53,625 [INFO] ** TORCH MPS version installed and working. **
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2025-07-11 11:13:53,625 [INFO] >>>> using GPU (MPS)
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```
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#### BIOP Conda installation for GPU support on Windows
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The excellent people of the BIOP facility mentioned above also prepared a Conda spec list and recommendations for libraries dependencies to robustly achieve GPU support with cellpose. We give a procedure here, but all credits should go to them. It supports an older version of cellpose but works really well. Also the procedure describes one and one only way of getting GPU support with Python, that might not stand any deviation from it. Such is Python.

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