ChromoLooping

Code and data in this repository comes from publication Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

You can use UCSF Chimera or any other viewer to visualize models and points in .pdb format.

Installation Guide

Requirements for Python packages can be found in requirements.txt

Requirements:

• Python 3.6 or later
• Jupyter Notebook
• UCSF Chimera or other visualization software

The installation on desktop computer shouldn't take longer than 30 minutes.

The easiest way to run the code is to open Jupyter notebooks:

$ git clone https://github.com/SFGLab/ChromoLooping.git
$ cd ChromoLooping
$ jupyter notebook

...and select one of the two available .ipnyb files:

• statistics and image data processing
• modelling pipeline

The existing examples in Jupyter notebooks can also be viewed directly on GitHub.

Jupyter Notebooks

All examples of usage of the full processing pipeline step by step can be found in Jupyter notebooks. In notebook image_statistics.ipynb you can find all the operations on ASCII files with image peaks exported from PeakSelector:

• reading and processing iPALM data from ASCII files
• statistics
• plotting histograms
• plotting convex hull

In image_driven_modeling.ipynb we put whole modeling procedure:

• exporting image peaks to .pdb format
• Traveling Salesman Problem solver
• Spline interpolation
• Calculating distance maps from 3D models
• Distance maps visualization

This tasks do not require any heavy computations and running the examples in Jupyter notebooks shouldn't exceed 5 minutes on a standard desktop computer.

Data

The results from our work can be fully reproduced using the code from this repository.

All data files used in our publications are located in data/ascii_files.

All models obtained from our iPALM imaging are in data/3d_models. The models are in .pdb format and can be opened via USCF Chimera software.

example:

$ cd data/3d_models
$ chimera image7_smooth3331.pdb

The model will look like this:

To get the presentation of the model as in our publication open the command line Favorites > Command Line and type two commands:

setattr m stickScale 8
rainbow

Then you can rotate the model to desired orientation. The final result will look like this:

The example output data of full reconstruction of the image processing and modelling pipeline is located in data/example_image_21.