Add ultrack wiki page

_pages/plugins/ultrack.md

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+---
+mediawiki: Ultrack FIJI's plugin
+title: Large-scale cell tracking under segmentation uncertainty
+dev-status: Beta
+support-status: Active
+description: Cell tracking and segmentation software
+Creator: 
+  - Jordão Bragantini
+  - Ilan Theodoro
+Developer: 
+  - "@ilan-theodoro"
+  - "@JoOkuma"
+doi: 10.48550/arXiv.2308.04526
+categories: [Tracking]
+---
+
+{% capture source%}
+{% include github org='royerlab' repo='ultrack' %}
+{% endcapture %}
+
+# Overview
+
+[Ultrack](https://github.com/royerlab/ultrack) is a method for large-scale 3D cell-tracking through a segmentation selection approach.
+It is effective at tracking cells across large microscopy datasets on two fronts: (i) It can solve
+problems containing millions of segmentation instances in terabyte-scale 3D+t datasets; (ii) It achieves competitive 
+results with or without deep learning, which requires 3D annotated data, that is scarce in the fluorescence microscopy 
+field. The proposed method computes cell tracks and segments using a hierarchy of segmentation hypotheses and selects 
+disjoint segments by maximizing the overlap between adjacent frames. We show that this method achieves state-of-the-art 
+results in 3D images from the cell tracking challenge and has a faster integer linear programming formulation. Moreover, 
+our framework is flexible and supports segmentations from off-the-shelf cell segmentation models and can combine them 
+into an ensemble that improves tracking.
+
+# Description
+
+## Installation 
+
+The Ultrack plugin is a Java client for Python's Ultrack tracking software. The user needs to have
+Python installed in the system, preferably managed by [conda](https://conda.io/projects/conda/en/latest/index.html).
+The FIJI plugin depends on Ultrack's optional functionalities.
+Therefore, installation must include `ultrack[api]`.
+For example:
+```bash
+pip install 'ultrack[api]'
+```
+
+For additional installation instructions, please refer to the [Ultrack documentation](https://github.com/royerlab/ultrack).
+
+This plugin will call the Ultrack routines under the hood, enabling cell tracking in 2D+t and 3D+t datasets.
+
+### FIJI integration
+
+The ultrack plugin is available after selecting the update site for ultrack in FIJI by clicking **HELP** → **Update** 
+→ **Manage Update Sites** and then searching for **Ultrack**. To activate the update site, click the checkbox in the
+**Activate** column, the leftmost one. Right after that, click **Apply and Close** and then **Apply Changes** in the now-enabled
+button at the bottom of the previous **ImageJ Update** window. That will trigger the download of the Ultrack
+plugin.
+
+After that, FIJI restart is required, and then the Ultrack plugin will be available in the **Plugins**→**Tracking**→
+**Ultrack** menu.
+
+## How to Use
+
+The steps below describe how to use the Ultrack plugin:
+
+1. Open the image sequence to be tracked.
+
+2. Click on the **Plugins** → **Tracking** → **Ultrack** menu. The Ultrack GUI will open.
+
+![Ultrack GUI](media/plugins/ultrack/00_init.png)
+
+3. (Optional but required in the first run) If Ultrack is correctly installed and accessible through the system path, 
+   the user can proceed to the next step. Otherwise, the user needs to set the path to the Ultrack executable in the 
+   **Environment**→**Select Conda Path** menu. It will open a dialog to select the `conda` executable, and 
+   then the user needs to select the preferred environment, which should be one indicated with the `[Ultrack found]` flag.
+
+4. Now you should be able to start the connection with the Ultrack software by clicking the **Start Ultrack Server** 
+   button. The plugin will update its GUI to show the available tracking options, as shown in the figure below.
+
+![Ultrack GUI with server started](media/plugins/ultrack/01_gui.png)
+
+4. The user should now select the desired tracking workflow in this section:
+
+![Ultrack GUI with tracking workflows](media/plugins/ultrack/03_workflows.png)
+
+in which the user can select the desired tracking workflow. The options are:
+ - **Auto Detection From Image**: which provides a way to track cells using solely the image as input;
+ - **Foreground & edges from user**: which is suitable for tracking cells using **edge** detection and **foreground** 
+   segmentation provided by the user;
+ - and **Segmentation from user**: which is suitable for tracking cells using segmentation labels from your favorite 
+   segmentation software, such as [Stardist](https://github.com/stardist/stardist), 
+   [Cellpose](https://github.com/MouseLand/cellpose), 
+   [MicroSAM](https://github.com/computational-cell-analytics/micro-sam) or any other.
+
+5. (Optional) After selecting your desired workflow, you can tune the tracking parameters in the **Settings** section. 
+   The parameters are workflow-dependent, and the user can 
+   [check here](https://github.com/royerlab/ultrack-dev/blob/main/ultrack/config/README.md) for more information about
+   the parameters. Not all of them are available in the FIJI interface, Python is required for full customization.
+
+![Ultrack GUI with tracking options](media/plugins/ultrack/02_options.png)
+
+6. After setting the parameters, the user can click the **Select Images** button to select the image to be tracked. 
+   It is worth mentioning that some workflows, such as **Manual Detection**, require more than one image to be selected.
+
+![Ultrack GUI with image opening](media/plugins/ultrack/04_image_opening.png)
+![Ultrack GUI with image selector](media/plugins/ultrack/05_image_selection.png)
+
+7. Finally, the user can click the **Run** button to start the tracking process. The user can follow the tracking 
+   process in the **Ultrack Log** section. 
+
+![Ultrack GUI with tracking progress](media/plugins/ultrack/06_run.png)
+
+8. To visualize the tracking results, the user can click the **View Tracks** button. Then, it will request a 
+   particular image to bind the tracks. In the end, The tracking results will be shown using the 
+   [TrackMate](https://imagej.net/plugins/trackmate/) plugin. 
+
+![Ultrack GUI with track image selection](media/plugins/ultrack/07_open_tracks.png)
+![Tracks Viewer it Trackmate](media/plugins/ultrack/08_trackmate.png)
+
+# Acknowledgments
+
+We thank the ImageJ community for providing the necessary tools to develop this plugin, such as 
+the FIJI platform and integrations. We also acknowledge the developers from [Trackmate](https://imagej.net/plugins/trackmate/) plugin for their work 
+in the tool, which we rely on to visualize the tracking results.
+
+# Citation
+If you find ultrack useful, please cite Ultrack as follows:
+
+{% include citation %}