Python package used to extract all radial intensity profiles from segmented objects.
This package was used to quantify chromatin reorganisation in C. elegans upon starvation. See paper on Nature Cell Biology
Please, follow our Installation guide
To use this tool you will first need to segment the nuclei of the cells of interest (e.g., intestine cells) using our other software called Cell-ACDC. You can find the source code with links to extensive documentation here.
Note that the data to be analysed must reside in the folder ChromRings/data.
Once you have the segmentation of the nuclei with the correct data structure (as requested by Cell-ACDC) the chromatin distribution analysis is fully automatic.
To run the analysis, you need to create a JSON file in the following location:
ChromRings/chromrings/data_info.json
This file contais information about the location of the data and the pairs of conditions you want to compare. You can find example JSON files in this folder ChromRings/examples_data_info_jsons.
Example:
{
"1_test_3D_vs_2D": {
"folder_path": "data/1_test_3D_vs_2D",
"experiments": ["2D_seg/str", "3D_seg/str", "2D_seg/fed", "3D_seg/fed"],
"channel": "SDC488",
"plots": [
"2D_seg/str;;3D_seg/str",
"2D_seg/fed;;3D_seg/fed"
],
"figs": [""],
"colors": {
"2D_seg/str": "firebrick",
"3D_seg/str": "orangered",
"2D_seg/fed": "darkturquoise",
"3D_seg/fed": "royalblue"
}
}
}In the example above the folder data/1_test_3D_vs_2D_01-02-2023 contains the subfolders listed at the "experiments" entry (e.g., ChromRings/data/1_test_3D_vs_2D/2D_seg/fed). These are the experiment folders containing the individual Position folders generated with Cell-ACDC.
At the entry "plots" you can define the pairs of conditions you want to compare. In any case, you will get one heatmap for each condition (one condition, one experiment folder).
The JSON file will contain information about all the experiments you want or you will analyse.
Next, rename the file ChromRings/chromrings/_example_current_analysis.py to current_analysis.py. Finally, you need to tell the software which experiment you want to analyse. To do so you need to modify the following variable in the ChromRings/chromrings/current_analysis.py:
batch_name = '1_test_3D_vs_2D'
where the batch_name is the experiment you want to analyse, in this example the 1_test_3D_vs_2D experiment.
Next, you can run the analysis by running the ChromRings/chromrings/main.py file (we recommend using VS code to run Python scripts, alternatively you can run them in the terminal with the command python "path to python file". To plot the results run the ChromRings/chromrings/plot/0_plot_dataset.py file.
If you use this tool in your publication, please cite our publication here as follows:
Al-Refaie, N., Padovani, F., Hornung, J., Pudelko, L., Binando, F., Fabregat d.C., Zhao, Q., Towbin, B. D., Cenik, E. S., Stroustrup, N., Padeken, J., Schmoller, K. M., Cabianca, D. S., Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis. Nat Cell Biol 26, 1903–1917 (2024).