Single-Cell Bacterial Swimming Analysis
This repository contains all code used for automated tracking and quantification of bacterial swimming behaviour, as described in our manuscript:
„Structure of the complete extracellular bacterial flagellum reveals mechanism for flagellin incorporation“
For questions, please contact the corresponding authors of the manuscript.
Overview
This pipeline processes microscopy videos of swimming bacteria into single-cell trajectory data, computes swimming speed metrics, and prepares the data for downstream analysis. It includes:
- Conversion of raw microscopy files (.nd2 / .czi) to TIFF with Jupyter notebook
- Pixel classification using Ilastik (headless mode) with Jupyter notebook
- Segmentation post-processing via Fiji macro
- Automated tracking in Fiji using TrackMate (Jython script)
- CSV merging and cleanup with Jupyter notebook
Repository Contents
File - Description
h5_to_tiff_macro.ijm - Fiji macro to convert Ilastik segmentations into TIFFs
TrackMate_Tracking.py - Jython script to batch-process TIFFs (Ilastik masks) using TrackMate
single_cell_tracking.ipynb - Jupyter Notebook for file conversion (.nd2 / .czi to .tiff) and merging and cleaning exported .csv files from TrackMate
Dependencies
- Fiji (with TrackMate plugin)
- Ilastik v1.4.0+ (for cell segmentation)
- Python 3.9 (for running the Jupyter notebook and PyImageJ if used for format conversion)