Skip to content

← All apps

CellTracksColab

Compile, visualise and analyse cell tracking data across fields of view, biological repeats and conditions.

Analysis

CellTracksColabDocumentation

About

Import and compile cell tracking data from TrackMate (CSV or XML), multiwell plate exports, or other compatible CSV files. Explore trajectories and track metrics, filter tracks, and inspect variability across fields of view, biological repeats and conditions.

Separate notebooks visualise compiled data, explore movement phenotypes with UMAP, t-SNE and HDBSCAN, analyse spatial clustering with Ripley's L, and measure distances to regions of interest. Use the notebooks in Google Colab or through the desktop app.

Works with

The authors say it works with:

  • TrackMate CSV (spots and tracks) or XML exports, organised by condition and biological repeat (TrackMate)
  • TrackMate CSV exports from multiwell or plate-based experiments (TrackMate Plate)
  • Compatible tracking CSV files from CellProfiler, Icy, ilastik or Fiji Manual Tracker; column mapping may be required (Custom)
  • Compiled CellTracksColab spots and tracks tables (CSV or CSV.gz) for Viewer and advanced notebooks
  • TIFF ROI masks matched to tracked fields of view for Distance to ROI

Produces

The authors say it produces:

  • Compiled spot and track tables (CSV/CSV.gz), identified by field of view, biological repeat and condition
  • Trajectory plots, track metrics (speed, directionality and more), quality-control plots and condition comparisons
  • UMAP and t-SNE embeddings, HDBSCAN clusters and representative trajectories (Dimensionality Reduction)
  • Ripley's L spatial clustering curves and Monte Carlo comparisons (Track Clustering)
  • Distances from tracks to ROI masks, derived metrics and visual checks (Distance to ROI)

Get it on your computer

Install the app on your own computer: download the installer for your system, and the steps for that system open below the buttons. You do this once; installing needs an internet connection, because the installer downloads the app's Python packages.

v1.1.5 · 22 October 2026 · files come from github.com/CellMigrationLab/CellTracksColab/releases

Windows

Windows installer310.1 MB · .exe

Installers built with LabConstrictor are not code-signed yet, so Windows may warn you. Run files only from this app's GitHub release. See the Windows steps.

macOS

Apple Silicon (M1 or later)170.4 MB · .pkgIntel176.6 MB · .pkg

Not sure which? Open the Apple menu, then About This Mac: Intel means Intel, M1 or later means Apple Silicon. If macOS refuses to open it, see the macOS steps.

Linux

Linux installer205.6 MB · .sh

Needs a terminal. Run it with: bash <file name>. See the Linux steps.

How to install on Windows
  1. Download the .exe file and double-click it.

  2. If Windows shows "Windows protected your PC", click "More info" and then "Run anyway". The installers are not code-signed yet.

    Windows protected your PC: click More info, then Run anyway

  3. Follow the on-screen prompts. Launch the app from the Start Menu or your desktop.

How to install on macOS
  1. Choose your file: open the Apple menu, then About This Mac. If the Chip or Processor says Intel, download the Intel installer; if it says M1, M2 or similar, download the Apple Silicon one.
  2. Double-click the .pkg file. If macOS refuses to open it, go to System Settings, Privacy & Security, scroll down to the message about the package and click "Open Anyway" (it appears only after you tried to open the file once). If you do not see it, try opening the file again, then check this page again.
  3. Follow the prompts (we recommend "Install only for me"). Launch the app from your Applications folder.
How to install on Linux
  1. Download the .sh file.
  2. Open a terminal in the download folder and run bash followed by the name of the file you downloaded, for example: bash MyApp-0.1.0-Linux-x86_64.sh
  3. Follow the prompts, then launch the app from your applications menu.

All systems, with pictures: Install an app.

Notebooks to open in your browser

These run on Google's servers in Google Colab: you need an internet connection and a Google account, and any data you load into the notebook is handled by Google. The desktop app runs on your computer.

Using it

  1. Choose TrackMate, TrackMate Plate or Custom to import data; Viewer and advanced analyses need compiled CellTracksColab tables
  2. Desktop: install CellTracksColab, launch it and choose your notebook from the Welcome dashboard
  3. Google Colab: open a notebook below, run Load key dependencies and connect Google Drive when prompted
  4. Select the input folder or compiled spot/track files and choose a results folder
  5. For Distance to ROI, check the matching TIFF masks and the track-to-image calibration
  6. Inspect plots and field-of-view/repeat quality control before comparing conditions

For any LabConstrictor desktop app: after installing, open the app from the Start menu (Windows), the Applications folder (macOS) or your applications menu (Linux). A terminal window opens with it: keep it open while you work. Its Welcome notebook lists the app's notebooks; the notebook usage guide shows how to work with it.

Read more: Documentation.

Limitations

The authors say:

  • Does not yet support track merging or splitting
  • Viewer, Dimensionality Reduction, Track Clustering and Distance to ROI require compiled CellTracksColab tables
  • Custom imports need correct column mapping and spatial/time calibration
  • ROI analysis needs masks matched to each field of view and consistent coordinate calibration
  • Dimensionality reduction and clustering are exploratory; results depend on the selected features and parameters

How to cite

The authors give this publication to cite: doi:10.1371/journal.pbio.3002740

Read the paper

Name the version you used (latest release: v1.1.5 · 22 October 2026).

All downloads

Every installer of version 1.1.5 (7 files, with checksums)

Released 22 October 2026. Files come straight from the app's GitHub release.

Installers of the latest release
SystemFormatSizeFileSHA-256 (from GitHub)
Linux 64-bit (x86_64).sh205.6 MBCellTracksColab-1.1.5-Linux-x86_64.sh3baa235045304de82a6dd22eceeb03a4d93b2658bc5a0493b4e8c02ebaa27d8d
macOS (Apple Silicon).pkg170.4 MBCellTracksColab-1.1.5-MacOSX-arm64.pkgf115a2e50b31e6e162f83f66510e42517308a3129624a1903a86bca04cc6c3b3
macOS (Apple Silicon).sh171.1 MBCellTracksColab-1.1.5-MacOSX-arm64.sh519d2e1d9866f72f291673eb547a41d703fdc8f845026b349ad3a1c24bdb6fc3
macOS (Intel).pkg176.6 MBCellTracksColab-1.1.5-MacOSX-x86_64.pkga499db0a73cc03caf7683c58e3b53ce556c4b6169d8e16552819c2f77d1b606d
macOS (Intel).sh177.2 MBCellTracksColab-1.1.5-MacOSX-x86_64.shedd6637aaaf746d63e480e74946d02a255bf22af7f33003348cad4e81a571e24
Windows 64-bit (Intel/AMD, x86_64).exe310.1 MBCellTracksColab-1.1.5-Windows-x86_64.exeb15874874df431bb08ab013bdf5768cbba0ff2bbeccb31cb90b99f11545bc72c
Windows 64-bit (Intel/AMD, x86_64).msi307.9 MBCellTracksColab-1.1.5-Windows-x86_64.msi80c965104b50c39770ca4fed7883aa9d50fcb05dd0220f4cd29f97de2d4f180e

Details

Kind
Analysis
Development status
Not stated by the authors
Latest release
v1.1.5 · 22 October 2026
License
MIT
Repository owner
CellMigrationLab
Topics
cell tracking, cell migration, trajectory analysis, TrackMate
Links
Report a problem · Documentation

Edit this page on GitHub