Merge pull request #396 from imagej/trackmate-yolo

Doc for TrackMate YOLO

Author: tinevez

_pages/plugins/trackmate/detectors/trackmate-yolo.md

@@ -0,0 +1,54 @@
+---
+title: TrackMate-YOLO
+categories: [Detection,icTracking,Deep Learning]
+icon: /media/icons/YOLO-logo.png
+description: Cellpose-SAM integration in TrackMate.
+categories: [Segmentation,Tracking,Machine Learning]
+artifact: sc.fiji:TrackMate-YOLO
+---
+
+{% include img src="/media/plugins/trackmate/detectors/YOLO/trackmate-yolo-detector-03.png" width='400'  %}{% include img src="/media/plugins/trackmate/detectors/YOLO/trackmate-yolo-detector-02.png" width='300'  %}
+
+{% include img src="/media/plugins/trackmate/detectors/YOLO/trackmate-yolo-detector-01.gif" width='600'  align='center' %}
+
+This page describes a detector module for [TrackMate](/plugins/trackmate/index) that relies on [YOLO](https://github.com/ultralytics/ultralytics), an AI-based detection algorithm, popular for natural images. 
+It is not included in the core of TrackMate and must be installed via its own [update site](/update-sites/following). 
+It also requires YOLO to be installed on your system and working independently. 
+
+If you use this detector for your research, please cite the YOLO webiste
+
+_Jocher, G., Qiu, J., & Chaurasia, A. (2023). Ultralytics YOLO (Version 8.0.0) [Computer software]. https://github.com/ultralytics/ultralytics_
+
+
+## Installation
+
+We need to subscribe to an extra update site in Fiji, and have a working installation of cellpose on your system.
+
+### TrackMate-YOLO update site
+
+In Fiji, go to {% include bc path='Help|Update...' %}. Update and restart Fiji until it is up-to-date. Then go to the update menu once more, and click on the `Manage update sites` button, at the bottom-left of the updater window. A new window containing all the known update sites will appear. Click on the  **TrackMate-YOLO** check box and restart Fiji one more time. 
+
+
+### YOLO
+
+This step requires you to have a working conda installation, like for any of the Python tools integrated in TrackMate. 
+We recommend [miniforge](https://github.com/conda-forge/miniforge).
+
+For YOLO specifically, we copy below the installation instruction from the [YOLO GitHub repo](https://github.com/ultralytics/ultralytics#-documentation)
+
+```zsh
+conda create --name yolo python=3.10
+conda activate yolo
+pip install ultralytics
+```
+
+Once this is done, still in the same terminal, test that YOLO was properly installed with e.g.:
+
+```zsh
+❯ yolo version
+8.3.168
+```
+
+### TrackMate conda configuration
+
+If you have not done it yet, you need to [configure the TrackMate conda path in Fiji](/plugins/trackmate/trackmate-conda-path). 

_pages/plugins/trackmate/index.md

@@ -140,6 +140,10 @@ TrackMate has a modular design and ships several algorithms of several types: de
 Many of these extra modules connect with an external tool, typically in Python, that needs to be installed via Conda or Mamba. 
 TrackMate needs to know where your conda environments are installed, and this is explained here: [trackmate-conda-path](trackmate-conda-path)
 
+Since v8, TrackMate ships better track and segmentation editing. 
+Track editing (correcting missing or spurious links over time) is mainly done in the main view and [TrackScheme](views/trackscheme).
+The shape of objects can be edited in the new [segmentation editor](tutorials/trackmate-segmentation-editor).
+
 
 ### Downloadable documents and tutorials