🧬 polymer-model-analyses-of-chromatin-mFISH-data
Multiplexed FISH Data Analysis Script
This Python script, developed by Loucif Remini and Midas Segers serves as a tool for the analysis of multiplexed FISH (Fluorescence In Situ Hybridization) data from Bintu et al (2018). The script is designed to process any data from a CSV file giving the 3D spatial coordinates of fluorescent probes and provides comprehensive insights into chromatin structure based on the methodology outlined in the publication "Chromatin structure from high-resolution microscopy: scaling laws and microphase separation" by Remini et al. (2023).
Features
Identification of Coexisting Chromatin Phases The script analyzes pairwise probability distance distributions, providing evidence of two coexisting chromatin phases. Gain insights into the dynamic organization of chromatin structures.
Scaling Behavior Analysis Explore the scaling behavior of effective chromatin and distinct phases. This feature offers valuable insights into the hierarchical organization of chromatin structures.
Phases Radii Summary Visualize phases radii for any pair of tags (i, j) through informative heatmaps. Understand the spatial relationships and structural nuances within chromatin.
Single Cell Analysis and Fit The script offers a detailed single-cell analysis, including fitting procedures. Dive into the behavior of chromatin at the individual cell level for a more nuanced understanding.
Beta Phase Position Prediction Predict the position of the beta phase in single cells, enhancing predictive capabilities. This feature contributes to a deeper understanding of chromatin dynamics.
💻 Usage
To utilize the script, input your data in CSV format and execute the provided functions. The script will generate visualizations and summaries, offering a comprehensive overview of your multiplexed FISH data. The data used can be downloaded from Bogdan Bintu's repository.
📄 Publication Reference
The script is based on the methodology outlined in the publication "Chromatin structure from high-resolution microscopy: scaling laws and microphase separation" by Remini et al. (2023). Read the publication
Date
This script was last updated on November 21, 2023.
📑 How to Cite
If you find this script helpful in your research, please consider citing the related publication.