Workshops and courses

ELIXIR node event Bioimaging data analysis using High Performance Computing (HPC)

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Date: 18 - 19 September 2025

Language of instruction: English

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Asa datasets grow in size and complexity, traditional desktop tools often fall short. This introductory training shows you how to leverage the Flemish Supercomputer Center (VSC) infrastructure for efficient and reproducible image analysis. It is intended for scientists who work with microscopy or bioimage data and want to scale up their analysis using high-performance computing (HPC)You will learn to access HPC resources via the Open OnDemand portal, run GUI-based tools (like napari or Fiji), and adapt existing pipelines (e.g., from ZeroCostDL4Mic or the BioImage Model Zoo) in a Jupyter notebook environment.  

Keywords: Artificial Inteligence, HPC, imaging

Venue: Leuven - Campus Gasthuisberg, Herestraat 49

City: Leuven

Country: Belgium

Postcode: 3000

Learning objectives:

  • “Adapt existing image analysis pipelines (from ZeroCostDL4Mic or BioImage Model Zoo) to run efficiently on the HPC infrastructure”
  • “Evaluate the reproducibility of bioimage analysis workflows and propose improvements using HPC-based solutions”
  • “Execute pre-installed bioimage analysis tools (Ilastik Fiji Napari) on the VSC for tasks such as segmentation and denoising”
  • “Run image analysis pipelines using a Jupyter notebook”
  • “Transfer and organize microscopy data on the HPC system to prepare scalable analysis workflows”

Organizer: VIB

Event types:

  • Workshops and courses

Sponsors: Flanders BioImaging, Vlaams Supercomputer Centrum

Instructors: Sebastian Munck, Tatiana Woller, Benjamin Pavie

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