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CellTracksColab Wiki

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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.

⭐️ Acknowledgments

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.

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🛠️ Quick Start

The easiest way to start using CellTracksColab is in the cloud using Google Collaboratory, but it can also be used on your own computer using Jupyter Notebooks. See our wiki for installation instructions.

1. Load and Plot Your Data

We provide three notebooks for loading and analyzing your data depending on its format:

For TrackMate Data (CSV or XML files):

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• See how to prepare the data in the TrackMate notebook wiki.

For Data Generated in CellProfiler, ICY, ilastik, or the Fiji Manual Tracker (CSV files):

• Explore our general-purpose notebook for analyzing diverse tracking datasets.
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• See how to prepare the data in the General notebook wiki.

For Data Already in the CellTracksColab Format:

• CellTracksColab - Viewer: Ideal for loading datasets in CellTracksColab format or sharing data with colleagues.
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2. Advanced Analysis Modules

These notebooks require your dataset to be in the CellTracksColab format.

CellTracksColab - Dimensionality Reduction:

• Utilize advanced dimensionality reduction techniques to facilitate the interpretation of complex, high-dimensional data.
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CellTracksColab - Track Spatial Clustering Analysis:

• Dive deeper into your dataset with our track clustering analysis module.
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CellTracksColab - Distance to ROI:

• Analyze movement tracks in relation to designated Regions of Interest (ROIs). Compute and analyze the distances between moving objects (tracks) and dynamic ROIs.
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More to come

Other Notebooks

CellTracksColab - TrackMate - Plate:

• Handle TrackMate data structured in a plate format, such as file names commonly produced by incubator microscopes like Incucytes.
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🚀 Before Getting Started

Prepare for your analysis journey. Understand the data requirements, familiarize yourself with the recommended folder hierarchy, and get hands-on with our test dataset.

• Check the data requirements and the supported software

• Check how to run CellTracksColab in GoogleColab

• Check how to run CellTracksColab locally

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📜 Citation

If you use CellTracksColab in your research, please cite the following paper:

Reference

Guillaume Jacquemet. (2023). CellTracksColab—A platform for compiling, analyzing, and exploring tracking data. bioRxiv. https://doi.org/10.1101/2023.10.20.563252

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