ELIXIR Bioinformatics Industry Forum: Using open software tools and AI to improve bioimaging

Wed 23 Jun 2021 - 17:30 to Wed 23 Jun 2021 - 19:00

CEST

This event will comprise a live run-through of a radiology AI model being developed and trained within a container on a SLURM cluster. It will introduce users to the open-source imaging toolkit MONAI, cover the basic workflow of developing within containers and show users how containerised applications can be used with common schedulers.

Programme

Welcome to the event

Katharina Lauer (ELIXIR)

Panel Discussion (30-45mins)

Luciano Guerreiro Lucas (EuroBioimaging Industry board & Leica Microsystems)

Rob Holt (Mathworks)

Rob Brisk/Nadim Daher (NVIDIA)

Bjoern Gruening (ELIXIR)

Workshop

Introduction to Project MONAI (open source medical imaging AI framework)
Live Demo
- Introduction to the start environment (Ubuntu with Docker, Nvidia drivers, etc. installed)
- Pulling a GPU-enabled PyTorch container from NGC (Nvidia’s container repository)
- Installing additional dependencies inside container (MONAI)
- Scheduling / running job on a SLURM cluster
- Writing / running a short application using a Jupyter notebook
- Q&A