TrackMate_CellPose_Bacterial_Generation_Determination

End-to-end pipeline for bacterial single-cell lineage, growth, and morphology analysis from TrackMate exports with publication-ready plots (Colab-friendly).

Bacterial Cell Growth & Shape Analysis Pipeline

Overview

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.

Key Features

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

Quick Start (No Coding Required!)

Option 1: Google Colab (Recommended)

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

Option 2: Local Installation

See Installation Guide

Input Data Format

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

Download sample dataset