The TrackMate notebook

🛠 Working with TrackMate Files

TrackMate is a Fiji plugin fully equipped with a GUI, multiple segmentation strategies, and trackers. It also has a very easy-to-use batcher for processing large datasets. The TrackMate notebook supports both TrackMate XML files and CSV files: XML Files: Convenient for directly reading the tracked information, but they are large and may be cumbersome to upload in Google Colab. CSV Files: Smaller and easier to upload.

✨ Sections available in the notebook

• 🎇 Track Visualization
• 🔍Track Filtering
• 📈 Track Metrics
• ✅ Quality Control
• 📉 Plotting Track Metrics

📄 Data Requirements

TrackMate XML Files

• XML files generated by TrackMate (either the GUI or the batcher).
• Make sure your data are calibrated during tracking.
• Track splitting is not supported by CellTracksColab and should be disabled during tracking.

TrackMate CSV Files

• The CellTracksColab - TrackMate notebook is optimized to work with TrackMate batcher output. Files generated by the TrackMate GUI are also compatible but ensure that your files are named with the suffixes -spots.csv and -tracks.csv.
• Make sure your data are calibrated during tracking.
• Track splitting is not supported by CellTracksColab and should be disabled during tracking.

📂 Data Organization

To load your TrackMate outputs, your dataset should be meticulously organized into a two-tiered folder hierarchy as depicted below:

TrackMate XML Files

• 📁 Experiments
  • 🌿 Condition_1 (The term ‘condition’ is derived from this folder name)
    • 🔄 R1 (The term ‘repeat’ is derived from this folder name)
      • 📄 FOV1.xml
      • 📄 FOV2.xml
    • 🔄 R2
      • 📄 FOV1.xml
      • 📄 FOV2.xml
  • 🌿 Condition_2
    • 🔄 R1
    • 🔄 R2

TrackMate CSV Files

Required files for each field of view:

1. Tracks files: These files contain information about track metrics (e.g., FOV1-tracks.csv).
2. Spots files: These files contain information about each tracked spot, including their coordinates (e.g., FOV1-spots.csv).

• 📁 Experiments
  • 🌿 Condition_1 (The term ‘condition’ is derived from this folder name)
    • 🔄 R1 (The term ‘repeat’ is derived from this folder name)
      • 📄 FOV1-spots.csv
      • 📄 FOV1-tracks.csv
      • 📄 FOV2-spots.csv
      • 📄 FOV2-tracks.csv
    • 🔄 R2
      • 📄 FOV1-spots.csv
      • 📄 FOV1-tracks.csv
      • 📄 FOV2-spots.csv
      • 📄 FOV2-tracks.csv
  • 🌿 Condition_2
    • 🔄 R1
    • 🔄 R2

Organizing your data this way will ensure that your conditions and repeats are correctly loaded in the notebook.

Data Samples

Spots Data Sample

ID	POSITION_X	POSITION_Y	POSITION_Z	POSITION_T	QUALITY	TRACK_ID
0	687.991	150.047	0.0	0.0	43.165	0.0
1	1255.994	467.008	0.0	0.0	26.326	1.0
2	171.994	853.024	0.0	0.0	48.963	2.0
... (and so on)

Tracks Data Sample

TRACK_ID	TRACK_START	TRACK_STOP	TRACK_DURATION	TRACK_DISPLACEMENT
0	0.0	29.0	30.0	209.8
1	0.0	29.0	30.0	67.6
2	0.0	29.0	30.0	196.9
... (and so on)

You can also check our test dataset here.