Why attend

NVwulf's Open OnDemand portal gives you GPU-ready imaging apps in your web browser, with no command line needed to get started. This session shows how to use them for tissue experiments, and how to run MCMICRO, a Nextflow pipeline that turns multiplexed whole-slide tissue images into single-cell data.

What you'll learn

• Use NVwulf's OnDemand imaging apps to view, analyze and quality-check tissue images
• Run the MCMICRO Nextflow pipeline on NVwulf, from raw image cycles to a cell-by-feature table
• Choose the right GPUs, memory and session length for imaging work

About MCMICRO

MCMICRO is an end-to-end pipeline for highly multiplexed tissue imaging (such as CyCIF, CODEX and MIBI), developed at Harvard Medical School's Laboratory of Systems Pharmacology. It stitches and registers the image tiles (ASHLAR), segments the cells, and quantifies each marker per cell (MCQuant), producing a table ready for downstream analysis. Learn more at nf-co.re/mcmicro.

NVwulf apps for tissue imaging

• Napari
• QuPath
• CellProfiler
• CyLinter
• Minerva Author
• Jupyter Notebook
• NVwulf Desktop
• ParaView

See all 19 NVwulf OnDemand apps.

Open to everyone doing research: undergraduates, graduate students, postdocs, faculty and staff in any field. No experience with Linux, HPC or Open OnDemand needed. Bring a laptop if you'd like to follow along.

A note on data: NVwulf is not approved for protected health information (PHI). Use de-identified images. For projects that use PHI, see ClinWulf.