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Bioimaging data analysis on the HPC

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  "@id": "https://github.com/vib-bic-training/2024_Bioimaging_data_analysis_on_HPC/",

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  "description": "Bioimaging data analysis on the HPC.",
  "keywords": "BioImage, Microscopy, Analysis, HPC, Napari, Globus, Jupyter, Python",
  "name": "Bioimaging data analysis on the HPC",
  "license": "https://creativecommons.org/licenses/by/4.0/",
  "educationalLevel": "beginner",
  "competencyRequired": "none",
  "teaches": [
    "Understand the scientific high-performance computing(HPC) infrastructure",
    "Learn to access to the supercomputer infrastructures in Flanders (VSC)",
    "Transfert, store bioimage/microscopy dataset on the VSC",
    "Find and load modules available on the VSC to analyze the bioimage/microscopy dataset",
    "Understand the benefit of using the HPC/VSC infrastructure to analyze bioimage/microscopy dataset",
    "Run pre-installed solution on the HPC/VSC (Ilastik/Fiji/Napar...) for bioimage analysis tasks (segmentation, denoising etc...)",
    "Run image analysis pipeline using a jupyter notebook",
    "Adapting existing solution (zerocost, bioimage zoo) on the VSC",
    "Discuss how to improve reproducibility in image analysis"
  ],
  "audience": "biologist, bio-image-analyst",
  "inLanguage": "en-US",
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  "author": [
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      "name": "Tatiana Woller" 
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    {
      "@type": "Person",
      "name": "Benjamin Pavie"
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  "contributor": [
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      "@type": "Person",
      "name": "Sebastian Munck"
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General context

Welcome to our @workshop_name workshop! We are very happy to have you here.

This is the @workshop_edition edition of this workshop, jointly organised by the VIB Bioimaging Core, Leuven, BE with the help of the VSC

• The session (10 October 2024) is dedicated to .

The presentation which goes alongside this material can be found here.

Schedule

Schedule:

• 09:30 - Introduction
• 10:00 - HPC infrastucture
• 10:30 - Coffee Break
• 10:45 - Data Transfer
• 11:15 - Napari
• 12:15 - Lunch
• 13:15 - Napari plugins
• 14:30 - Coffee break
• 14:45 - Jupyter notebooks
• 17:00 - End of the day

Lesson overview

License: Creative Commons Attribution share alike 4.0 International License

Target Audience: Researchers, biologis

Level: Beginner

Prerequisites
To be able to follow this course, learners should have knowledge in:

1. Basic knowlegde of Microscopy
2. Basic knowledge of BioImage Analysis

Description This course consist of .....

Learning Outcomes:
By the end of the course, learners will be able to:

1. Connect to the Vlaam Super Ccomputer (VSC) infrasctructure

2. Upload/download dataset to the HPC using Globus

3. Using BANDs platform to access to several bioimage analysis tools such as Napari, QuPath etc...

4. Run some pipeline

5. Use the easybuild module to run Jupyter notebook

Check more about

Time estimation: 360 minutes

Requirements: You need a VSC account and a latop .

Supporting Materials:

1. Exercises and solutions
2. Slides

Acknowledgement:

• VIB Technologies
• Vlaams Supercomputer Centrum - VSC

Funding: : This project has received funding from VIB.

Authors and Contributors

Authors

• [Benjamin Pavie](@orcid

Contributors

• Tatiana Woller
• Sebastian Munck

Citing this lesson

Please cite as:

1. ...

Chapters List

Chapter	Title
1	Chapter 1 : Infrasctructure
2	Chapter 2 : Data Trasnfer and Management
3	Chapter 3 : BAND

References

Here are some great tips for learning and to get inspired for writing your own pipelines:

• VSC Tier 1 documentation (link)
• Globus (link)
• EasyBuild(link)
• QuPath (link)
• QuPath (link)
• Napari (link)
• DevBio (link)
• BioImage Analysis Notebooks from Robert Haase(link)

We are using the interactive Open Educational Resource online/offline course infrastructure called LiaScript. It is a distributed way of creating and sharing educational content hosted on github. To see this document as an interactive LiaScript rendered version, click on the following link/badge: LiaScript

About us

About VSC

The Flemish Supercomputer Center (Vlaams Supercomputer Centrum - VSC) is a partnership between the five Flemish universities and their university associations: Associatie Universiteit & Hogescholen Antwerpen, Universitaire Associatie Brussel, Associatie Universiteit Gent, Associatie KU Leuven and Associatie Universiteit-Hogescholen Limburg. This consortium brings together knowhow in scientific and technical computing (including high performance computing, high throughput computing, cloud computing and data processing) in Flanders, and houses infrastructure in four hubs: the datacenters of the universities of Antwerp, Brussels, Ghent and Leuven. The VSC is managed by the Research Fund – Flanders (FWO).

About VIB and VIB Technologies

VIB is an entrepreneurial non-profit research institute, with a clear focus on groundbreaking strategic basic research in life sciences and operates in close partnership with the five universities in Flanders – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University.

As part of the VIB Technologies, the 12 VIB Core Facilities, provide support in a wide array of research fields and housing specialized scientific equipment for each discipline. Science and technology go hand in hand. New technologies advance science and often accelerate breakthroughs in scientific research. VIB has a visionary approach to science and technology, founded on its ability to identify and foster new innovations in life sciences.

The goal of VIB Technology Training is to up-skill life scientists to excel in the domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management.

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Editorial team for this course Authors: @orcid(Benjamin Pavie), @orcid(Tatian Woller)

License: