The Viewer notebook

The Viewer Notebook

The Viewer Notebook is designed to provide an easy way to visualize and share tracking data formatted into the CellTracksColab format. This notebook is particularly useful for sharing data with colleagues and for publications.

Requirements

To use the Viewer Notebook, your data must be formatted in the CellTracksColab format. This involves compiling your tracking data into two main DataFrames: merged_tracks_df and merged_spots_df.

✨ Sections available in the notebook

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

Compiling Your Data

To format your tracking data into the CellTracksColab format, you can use the following notebooks:

• TrackMate Notebook: Use this notebook to compile data from TrackMate into the required format. For detailed instructions, visit the TrackMate notebook wiki.
• Custom Notebook: Use this notebook to compile data generated from other tracking software into the required format. For detailed instructions, visit the Custom notebook wiki.

Usage

Once your data is in the correct format, you can load it into the Viewer Notebook to create visualizations and plots. This is ideal for:

• Sharing data with colleagues
• Sharing data in publications
• Re-open already analysed datasets

Getting Started

To get started, simply open the Viewer Notebook using the link below: