Bacterial_image_analysis

Macros and methods to analyse bacterial bioimages

This repository describes the macros used in the manuscript Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth found here.

Python code to analyse the distance between the bacterial membrane and DNA

1. 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

2. Open the file dna-membrane-dist.py inside 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/'

Python code to randomize intensity time traces for circular cross-correlation

1. 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

2. Open the file MreB_randomization_GMM_circular_xCORR.py inside the Python folder and change the path and parameters:

sigma=0.15 
number_random_sample=1
all_plots=False 
folder=r'D:\dSTORM_DATA\GMM\Data'

Fiji macros

Overview

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