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Welcome to CellTracksColab, your comprehensive platform for analyzing cell migration tracks. Whether you're a beginner or an experienced researcher, our platform offers intuitive guidance every step of the way. You'll find detailed explanations in the notebooks to help you navigate the analysis process. Plus, a test dataset is provided to get you started immediately.
Tutorial 1: Getting Started with CellTracksColab using Google Colab |
Tutorial 2: Using CellTracksColab locally using Jupyter |
Tutorial 3: Using CellTracksColab locally using Google Colab |
ℹ️ Tutorials 2 and 3 were recorded before the desktop app existed. The overall workflow is the same, but follow the Running CellTracksColab locally page for the current installation commands.
CellTracksColab has been tested with tracking outputs from:
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|---|---|---|---|---|
| TrackMate | CellProfiler | Icy | ilastik | Fiji Manual Tracker |
But may also be compatible with other tracking software exporting tracking results that meet our minimal requirements. Ensure your data is well-organized according to the recommended folder hierarchy. This structure helps in managing and analyzing the data efficiently.
The same notebooks run either in the cloud with Google Colaboratory or on your own computer.
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Google Colaboratory: Nothing to install and free computational resources. Your data is read from Google Drive. Click the Open in Colab badges below.
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On your computer: Run on your own hardware for more control and privacy. Your data stays on your computer.
- Desktop app (recommended): a one-click installer for Windows, macOS and Linux that bundles Python, JupyterLab and all dependencies. Install the desktop app
- Your own conda environment: for users who prefer to manage Python themselves.
- Learn more about running CellTracksColab locally
We provide three notebooks for loading and analyzing your data depending on its format. The Link column opens each notebook in Google Colab. In the desktop app, all notebooks are listed in the Welcome dashboard.
| Notebook | Purpose | Required File Format | Link |
|---|---|---|---|
| CellTracksColab - TrackMate | Load and analyze TrackMate data. More info on how to prepare the data here. | CSV or XML files |
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| CellTracksColab - Custom | Analyze data from CellProfiler, ICY, ilastik, or Fiji Manual Tracker. More info on how to prepare the data here. | CSV files |
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| CellTracksColab - Viewer | Load and share data in the CellTracksColab format. | CellTracksColab format |
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These notebooks require your dataset to be in the CellTracksColab format.
| Notebook | Purpose | Required File Format | Link |
|---|---|---|---|
| CellTracksColab - Dimensionality Reduction | Utilize advanced dimensionality reduction techniques. | CellTracksColab format |
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| CellTracksColab - Track Spatial Clustering Analysis | Dive deeper into your dataset with track clustering analysis. | CellTracksColab format |
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| CellTracksColab - Distance to ROI | Analyze movement tracks in relation to designated ROIs. | CellTracksColab format |
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More to come
- Handle TrackMate CSV files structured in a plate format, such as file names commonly produced by incubator microscopes like Incucytes.
- Test Dataset: Start exploring with our test datasets in CellTracksColab CSV format, or TrackMate CSV format.
- Data Structure: Organize with our two-tiered folder hierarchy. Details here.
- Data Requirements: Note that CellTracksColab does not yet support track merging or splitting.
- Estibaliz Gómez-de-Mariscal
- Hanna Grobe
- Joanna W. Pylvänäinen
- Laura Xénard
- Ricardo Henriques
- Jean-Yves Tinevez
- Guillaume Jacquemet
We welcome your insights and improvements! There are several ways you can contribute to the CellTracksColab project:
If you encounter any bugs, have suggestions for improvements, or want to discuss new features, please raise an issue on our GitHub Issues page.
We are excited to see new analysis notebooks built on the CellTracksColab platform. If you have developed a new notebook, please submit it via a pull request. All submitted notebooks should include a test dataset to showcase their functionality. Each notebook will be tested by a member of the team before being released.
We expect all contributors to adhere to our simple code of conduct:
- Be respectful and considerate of others.
- Provide constructive feedback.
- Collaborate openly and honestly.
By participating in this project, you agree to abide by these guidelines.
Thank you for contributing to CellTracksColab! Your support and contributions help us improve and expand the platform for everyone in the community.
Licensed under the MIT License. Details here.
If you use CellTracksColab in your research, please cite the following paper:
Guillaume Jacquemet. (2023). CellTracksColab—A platform for compiling, analyzing, and exploring tracking data. bioRxiv. https://doi.org/10.1101/2023.10.20.563252
