Code for Epigenomic MERFISH

This repository contains code for image and sequence analysis for epigenomic MERFISH (https://doi.org/10.1016/j.cell.2022.09.035).

Please check github.com/ZhuangLab for the latest version of this code.

The corresponding datasets could be found by DOI: https://doi.org/10.5281/zenodo.7075964

The codes include:

1. Barcode assignment for each locus
2. Probe design with barcode assigned
3. Spot decoding in single cells with speckle quantification
4. Spot decoding in embryonic tissue (no single cell)
5. Quantification of layer specificity
6. Quantification of region specificity and loci clustering by the spatial distribution
7. Quantification of RNA MERFISH in mouse adult cortex

All the codes are written in Matlab(2021a).

Some MATLAB functions used in the code are from https://github.com/ZhuangLab/MERFISH_analysis and https://www.mathworks.com/matlabcentral/fileexchange.

Correspondence: Tian Lu ([email protected]) and Xiaowei Zhuang ([email protected])