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Fix the TrackMate Cellpose-SAM doc page.
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_pages/plugins/trackmate/detectors/trackmate-cellpose-sam.md

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title: TrackMate-Cellpose-SAM
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categories: [Segmentation,Tracking,Deep Learning]
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icon: /media/icons/cellpose.png
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description: cellpose-SAM integration in TrackMate.
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description: Cellpose-SAM integration in TrackMate.
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categories: [Segmentation,Tracking,Machine Learning]
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artifact: sc.fiji:TrackMate-Cellpose
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---
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{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-R2_multiC.gif" width='400' %} {% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-01.png" width='200' %}
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{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-R2_multiC.gif" width='400' %} {% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-01.png" width='200' %}
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This page describes a detector module for [TrackMate](/plugins/trackmate/index) that relies on the latest version of [cellpose](https://cellpose.readthedocs.io/en/latest/) to segment cells in 2D. It is not included in the core of TrackMate and must be installed via its own [update site](/update-sites/following). It also requires cellpose to be installed on your system and working independently. This tutorial page gives installation details and advices at how to use the cellpose integration in TrackMate.
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### Cellpose parameters in the TrackMate UI
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{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-01.png" align='center' width='400' %}
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{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-01.png" align='center' width='400' %}
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We document these parameters from top to bottom in the GUI.
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##### `Conda environment`
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Specify in what conda environment you installed Cellpose-SAM.
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If you get an error at this stage, it is likely because the conda path for TrackMate was not configured properly. Check [this page]((/plugins/trackmate/trackmate-conda-path).
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If you get an error at this stage, it is likely because the conda path for TrackMate was not configured properly. Check [this page](/plugins/trackmate/trackmate-conda-path).
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##### `Pretrained model`
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With all channels:
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{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-allchannels.png" align='center' %}
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{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-allchannels.png" align='center' %}
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Channel 1 only, in which nuclei are painted in red:
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{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-channel-1.png" align='center' %}
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{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-channel-1.png" align='center' %}
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Channel 2 only, in which the cell cytoplasm appears in green:
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{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-channel-2.png" align='center' %}
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{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-channel-2.png" align='center' %}
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Channel 3 only, which is empty:
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{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-channel-3.png" align='center' %}
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{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-channel-3.png" align='center' %}
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