NVwulf Open OnDemand training

Fri, 04 Dec 2026 13:00:00 -0500

Hands-on, hybrid training (in person or on Zoom) on Friday, December 4, 2026, 1:00 to 2:30 PM in BST 6-150, presented by Alejandro Gil Gómez and Arshad Mehmood for DoIT Research Computing, Informatics & Innovation and the Institute for Advanced Computational Science (IACS).

What you’ll learn

View, analyze and check tissue images with NVwulf’s OnDemand apps (Napari, QuPath, CellProfiler, CyLinter, Minerva Author and more).
Run MCMICRO on NVwulf, from raw images to a table of cells and their features.
Pick the right GPUs, memory and session length for imaging work.

Open to everyone doing research, with no Linux or HPC experience needed. NVwulf is not approved for PHI, so use de-identified images.

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:

HPC | Alejandro Gil Gomez

NVwulf Open OnDemand training

What you’ll learn

MCMICRO for MACSima on HPC

What it does