|
2 | 2 | title: TrackMate-Cellpose-SAM |
3 | 3 | categories: [Segmentation,Tracking,Deep Learning] |
4 | 4 | icon: /media/icons/cellpose.png |
5 | | -description: cellpose-SAM integration in TrackMate. |
| 5 | +description: Cellpose-SAM integration in TrackMate. |
6 | 6 | categories: [Segmentation,Tracking,Machine Learning] |
7 | 7 | artifact: sc.fiji:TrackMate-Cellpose |
8 | 8 | --- |
9 | 9 |
|
10 | | -{% 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' %} |
| 10 | +{% 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' %} |
11 | 11 |
|
12 | 12 | 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. |
13 | 13 |
|
@@ -76,13 +76,13 @@ If you have not done it yet, you need to [configure the TrackMate conda path in |
76 | 76 |
|
77 | 77 | ### Cellpose parameters in the TrackMate UI |
78 | 78 |
|
79 | | -{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-01.png" align='center' width='400' %} |
| 79 | +{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-01.png" align='center' width='400' %} |
80 | 80 | We document these parameters from top to bottom in the GUI. |
81 | 81 |
|
82 | 82 | ##### `Conda environment` |
83 | 83 |
|
84 | 84 | Specify in what conda environment you installed Cellpose-SAM. |
85 | | -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). |
| 85 | +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). |
86 | 86 |
|
87 | 87 | ##### `Pretrained model` |
88 | 88 |
|
@@ -121,14 +121,14 @@ This image comes from the lab of Guillaume Jacquemet and was used in {% include |
121 | 121 |
|
122 | 122 |
|
123 | 123 | With all channels: |
124 | | -{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-allchannels.png" align='center' %} |
| 124 | +{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-allchannels.png" align='center' %} |
125 | 125 |
|
126 | 126 | Channel 1 only, in which nuclei are painted in red: |
127 | | -{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-channel-1.png" align='center' %} |
| 127 | +{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-channel-1.png" align='center' %} |
128 | 128 |
|
129 | 129 | Channel 2 only, in which the cell cytoplasm appears in green: |
130 | | -{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-channel-2.png" align='center' %} |
| 130 | +{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-channel-2.png" align='center' %} |
131 | 131 |
|
132 | 132 | Channel 3 only, which is empty: |
133 | | -{% include img src="/media/plugins/trackmate/detectors/trackmate-cellpose-sam-channel-3.png" align='center' %} |
| 133 | +{% include img src="/media/plugins/trackmate/detectors/cellpose/trackmate-cellpose-sam-channel-3.png" align='center' %} |
134 | 134 |
|
0 commit comments