Why attend

NVwulf's Open OnDemand portal runs imaging apps on GPUs, right in your web browser. You don't need the command line to start. This session shows how to use them for tissue experiments, and how to run MCMICRO, a Nextflow pipeline that turns tissue images with many markers into data for each cell.

What you'll learn

• View, analyze and check tissue images with NVwulf's OnDemand apps.
• 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.

About MCMICRO

MCMICRO is a pipeline for tissue images that show many markers at once, such as CyCIF, CODEX and MIBI. It was built at Harvard Medical School's Laboratory of Systems Pharmacology. It joins the image tiles (ASHLAR), finds the cells, and measures each marker in each cell (MCQuant). The result is a table ready for 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.