This repository contains the latex files, data and Python scripts used in the article: Thédié D., Lepore A., McLaren L, El Karoui, M. (2024). (Insert title here) bioRxiv. DOI: (Insert DOI here)
The Dataset list table lists all datasets used in this study, with a unique identifier ("Name"), and other basic information (ciprofloxacin concentration, strain used, overexpressed proteins...). Dataset names can be used to find:
- Raw images on (link to be added)
- Processed BACMMAN datasets (see the BACMMAN datasets folder)
- Clone this repository to your computer
- If you do not wish to re-process the images in BACMMAN, skip to step 5.
- Download the raw images from (update when available)
- Install the BACMMAN Fiji plugin
- Open the BACMMAN plugin in Fiji
- Set the
BACMMAN_datasetsfolder of this repository as working directory - Open the dataset of interest (refer to Dataset_list for more details)
- Re-link the raw images by selecting the matching folder (in BACMMAN, select "Run" then "Import/Re-link images")
- Run Pre-processing and Processing. Note this will erase any manual curation of cells that had been done by the authors
- If required, open images in the "Data Browsing" tab and curate objects manually (e.g. remove badly segmented cells)
- Run Measurements and Extract Measurements
- Set the
- Open a Jupyter Notebook from the Notebooks folder
- If you have not already, install the PyBerries package and its dependencies
- Run the cells of the Notebook to generate Figures (the code does not need to be updated)