End-to-end pipeline for bacterial single-cell lineage, growth, and morphology analysis from TrackMate exports with publication-ready plots (Colab-friendly).
Automated analysis pipeline for bacterial cell lineage tracking, morphology quantification, and multi-condition population comparisons. Analyzes shape mutants, growth rates, division timing, and cell geometry across generations.
- Lineage Memory Analysis: Mother-daughter growth correlations
- Sister Cell Symmetry: Division timing asymmetry quantification
- Size Control Models: Adder/Timer/Sizer classification
- Geometric Profiling: Length, width, aspect ratio, circularity across 12 metrics
- Statistical Rigor: Mann-Whitney U tests + Cliff's Delta effect sizes with FDR correction
- Upload your files to Google Drive
- Click the "Open in Colab" badge above
- Mount Google Drive
- Set Parameters to your liking
- Click Runtime → Run All
- Select folder containing your paired spots.csv and edges.csv using interactive folder selector
- Wait for files to process
- Visualize by selecting an output folder using the interactive folder selector at the end of the code
- Download results from the output folder
CSV files from TrackMate required: _spots.csv and _edges.csv Files should be saved in Date_Mutatation_Gene_Location format (example: 20260101_L206K_mreB_s1_spots.csv / 20260101_L206K_mreB_s1_edges.csv
- Plots: 15+ publication-ready figures (PNG, 150 DPI)
- Stats Table:
Boss_Summary_Table.csvwith medians & sample sizes - Raw Data:
Total_Population_Dataset.csvfor custom analysis
If you use this pipeline, please credit me: Joseph A. Villanueva, PhD Orchid ID: 0000-0003-3131-7150
MIT License - See LICENSE file
Questions? JoeVPhD@gmail.com