🧬 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.