MCMICRO for MACSima on HPC

Thu, 01 Jan 2026 00:00:00 +0000

Scripts and configuration files to process MACSima spatial proteomics data with the pipeline on the NVwulf high-performance computing cluster at Stony Brook University.

The workflow was optimized for tissue microarray (TMA) analysis of Pancreatic Ductal Adenocarcinoma (PDAC), using samples from the Stony Brook University Department of Pathology, to quantify the spatial dynamics of the Epithelial-Mesenchymal Transition (EMT).

What it does

Converts raw cyclic imaging data (the RawData folder from the MACSima instrument, using the high-exposure images) into OME-TIFF files with macsima2mc, with optional illumination correction.
Runs MCMICRO for image registration, Cellpose-based nuclei and cell segmentation, and single-cell quantification.
Runs ROIs in parallel with Slurm, with GPU and Singularity settings for NVwulf.
Can merge several experimental runs of the same sample into a single RawData directory.

Code and documentation:

Spatial Proteomics | Alejandro Gil Gomez

MCMICRO for MACSima on HPC

What it does