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🧬 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.