This repository describes the macros used in the manuscript Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth found here.
- Clone the repository: Open up the terminal and paste the following commands
git clone https://github.com/CKSpahn/Bacterial_image_analysis.git
cd Bacterial_image_analysis
mamba env create -f environment.yml
mamba activate bacteria_ia
- Open the file
dna-membrane-dist.pyinside the Python folder and change the following paths accordingly:
root_folder = '/Users/user1/Documents/data/DNA_membrane_distance_diff_treatments_2024-08-05'
results_folder = '/Users/user1/Documents/results/'
The following table specifies the individual macros used in the manuscript
| Macro | Purpose | Input | Input format | #Channels | Output | Comments | Link |
|---|---|---|---|---|---|---|---|
| M1 | Extracting of the experimental PSF | z-stack | TIFF | 1 | Individual PSFs, Average PSF | - | Macro M1 |
| M2 | Smoothing of cell outlines for selection of individual bacteria | Single- or multi-channel SMLM images | TIFF | 1+ (in this study: 3) | Smoothed membrane image, opened in Fiji | - | Macro M2 |
| M3 | Rotation, straightening of bacterial cells | CLSM image, ROIs | TIFF | 3 | Single bacteria as individual TIFF images | ROIs need to be opened in Fiji, adjust scaling if required | Macro M3 |
| M4 | Normalization of straightened bacteria | Output of Macro M3 | TIFF | 3 | Normalized cells as individual TIFF image | Membrane: Channel 1 | Macro M4 |
| M5 | Determination of relative nucleoid expansion | Output Macro 3 | TIFF | 3 | .txt file summarizing cell and nucleoid length, as well as the relative nucleoid expansion | Membrane: Channel 1, DNA: Channel 2 | Macro M5 |
| M6 | Determination of the relative MreB distribution | Population average image | TIFF | 3 | .txt file with MreB intensities at poles and cell cylinder, ROIs | Membrane: Channel 1, DNA: Channel 2, MreB: Channel 3 | Macro M6 |
| M7 | Erosion analysis for radial intensity distribution analysis | SMLM image | TIFF | 3 | .txt files with intensity distributions for each cell, Eroded ROIs as .zip, overlay PNG | Channel order can be defined | Macro M7 |
| M8 | Plotting intensities along cell perimeter | SMLM images, ROIs | TIFF | 2+ | Intensity traces of DNA and MreB channels | Image and ROIs need to be opened in Fiji | Macro M8 |
| M9 | Simulation of 3-color images for circular x-corr | - | - | 3 | Simulated 3-color image and ROIs | Simulate points within a circular cell with varying number, shift and radial position | Macro M9 |
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