MATRIX by Gonzalo, Liu, Dufour and Shade 2026

This repository contains the raw image data and processed .csv files containing the single-cell observations from the images. With the associated analysis scripts (GitHub: process_quantom and MATRIX), users should be able to reproduce all Figures and analyses found within this work:
Gonzalo M, X Liu, YS Dufour and A Shade. 2026. MATRIX: Rapid Quantification of Total and Active Microbial Cells with Single‑Cell Phenotypes for Environmental Microbiomes.
There are two types of the data, each organized by Figure.
1) microscope images analyzed in support of Gonzalo, Liu, Dufour and Shade 2026
These images were generated on the QUANTOM Tx TM microbial cell counter (Logos Biosystems Inc., South Korea). The QUANTOM captures cells visible with an excitation of 470/30 nm and an emission of 530/50 nm. An LED level of 5 was used for all images.
2) output CSV files from the process_quantom script for automated image analysis by Figure and including experimental metadata.