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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.
CellTracksColab is inspired by several key projects in cell tracking and analysis. We acknowledge the influential contributions of Traject3d, CellPhe, CelltrackR, the MotilityLab website, and Cellplato on Zenodo. The innovative use of UMAP and HDBSCAN for analyzing tracking data, as featured in CellTracksColab, was first introduced in CellPlato.
To begin your analysis journey, click the "Open In Colab" button below, corresponding to your data type. For a seamless experience, right-click the button and select "Open in a new tab."
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For TrackMate Data:
- Delve into your TrackMate data with our specialized notebook.
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Analysis for Other Data Types:
- Explore our general-purpose notebook for analyzing diverse tracking datasets.
Maximize your analysis with our supplementary tools and modules.
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CellTracksColab - Viewer:
- Ideal for loading datasets in CellTracksColab format or sharing data with colleagues.
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CellTracksColab - TrackMate - Plate:
- This notebook can handle TrackMate data structured in a plate format, such as file names commonly produced by incubator microscopes like Incucytes.
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CellTracksColab - Track Clustering Analysis:
- Dive deeper into your dataset with our track spatial clustering analysis module.
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CellTracksColab - Distance to ROI:
- This notebook is specifically designed to analyze movement tracks in relation to designated Regions of Interest (ROIs). Its primary aim is to compute and analyze the distances between moving objects (tracks) and ROIs, which may also be dynamic.
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More to come soon
Prepare for your analysis journey. Understand the data requirements, familiarize yourself with the recommended folder hierarchy, and get hands-on with our test dataset.
- 🛠 Prepare the Session and Load Your Data
- 📈 Compute Additional Metrics
- 🎨 Plot Track Parameters
- 🔎 Quality Control
- 🌌 Explore Your High-dimensional Data
Each section breaks down complex analysis into digestible steps, ensuring a smooth and comprehensive understanding.
Make CellTracksColab truly yours. Add custom analyses, expand its capabilities, and contribute to the community. Learn the best practices and get creative!
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
