Quantitative Expansion Microscopy for In Situ Estimation of Endogenous Target Abundance

This repository contains the code and example datasets used to generate the figures for the manuscript:

Quantitative Expansion Microscopy for In Situ Estimation of Endogenous Target Abundance
Authors: Matthew D. Lycas, Juan C. Landoni, Benedetta Noferi, Christian E. Zimmerli, Kyle M. Douglass, Suliana Manley
DOI: https://doi.org/10.64898/2026.01.18.700178

Repository structure (figures)

• Expansion_method_SNR/ — Figure 1
• NPC/ — Figure 2
• RC/ — Figure 3
• SC/ — Figure 4

Each folder contains:

• The source code used for that figure
• A Demo/ subfolder with a small, abbreviated dataset and a run_demo.py script
• A dedicated README.md with system requirements, installation steps, demo instructions, and usage notes

Quick start (demo)

Pick a figure folder and run its demo script, for example:

python Expansion_method_SNR/Demo/run_demo.py

See each folder’s README.md for the expected outputs and runtime.

Full datasets (centers and masks)

Full versions of the centers and mask datasets are hosted on Zenodo: https://doi.org/10.5281/zenodo.18340724
Please use the Zenodo archive if you need the complete datasets beyond the demo subsets.
Source: https://doi.org/10.5281/zenodo.18340724

Experimental protocol

Detailed expansion microscopy protocol: https://github.com/LEB-EPFL/qExM_protocol/blob/main/Expansion%20Microscopy.md
Source: https://raw.githubusercontent.com/LEB-EPFL/qExM_protocol/main/Expansion%20Microscopy.md

Citation

If you use this code or dataset in your work, please cite the manuscript and the Zenodo dataset:

• Manuscript DOI: https://doi.org/10.64898/2026.01.18.700178
• Zenodo dataset DOI: https://doi.org/10.5281/zenodo.18340724