-->
{
"@context": "https://schema.org/",
"@type": "LearningResource",
"@id": "https://github.com/vib-bic-training/2024_Bioimaging_data_analysis_on_HPC/",
"http://purl.org/dc/terms/conformsTo": {
"@type": "CreativeWork",
"@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE"
},
"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",
"learningResourceType": [
"tutorial"
],
"author": [
{
"@type": "Person",
"name": "Tatiana Woller"
},
{
"@type": "Person",
"name": "Benjamin Pavie"
}
],
"contributor": [
{
"@type": "Person",
"name": "Sebastian Munck"
}
]
}
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 presentation which goes alongside this material can be found here.
Schedule:
-Day 1:
-
09:30 - Introduction
-
10:00 - HPC infrastucture
-
10:30 - Coffee Break
-
10:45 - Data Transfer
-
11:15 /11:00 - Napari
-
12:15/12:00 - Lunch
-
13:15 - Napari plugins
-
14:30 - Coffee break
-
14:45 - Other software + intro notebooks
-
17:00 - End of the day
-
Day 2
-
09:30 - Notebooks
-
10:45 - Coffee Break
-
11:00 - SLURM, Containers and Worflows
-
11:45 wrap up
-
12:00 End of the day
License: Creative Commons Attribution share alike 4.0 International License
Target Audience: Researchers, biologists
Level: Beginner
Prerequisites
To be able to follow this course, learners should have knowledge in:
- Basic knowlegde of Microscopy
- Basic knowledge of BioImage Analysis
Description This course consist of .....
Learning Outcomes:
By the end of the course, learners will be able to:
Connect to the Vlaam Super Ccomputer (VSC) infrasctructure
Upload/download dataset to the HPC using Globus
Using BANDs platform to access to several bioimage analysis tools such as Napari, QuPath etc...
Use the easybuild module to run Jupyter notebook
Use venv and module to run Jupyter notebook
Have an overview with SLURM on how to submit jobs
Understand the benefit of containarization and workflows
Check more about
Time estimation: 520 minutes
Requirements: You need a VSC account and a latop .
Supporting Materials:
Acknowledgement:
Funding: : This project has received funding from VIB (nope, ask to Seb). This course is supported by a collaborative grant awarded by VSC to the Flanders Bioimaging consortium
Authors
- [Benjamin Pavie](@orcid
- Tatiana Woller
Contributors
- Bruna Pierek
- Janick Mathijs
- Alex Botzki
- Sebastian Munck
Please cite as:
- ...
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)
- 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 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.
The resources and services used in this training were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation - Flanders (FWO) and the Flemish Government thanks to a collaborative grant obtained by the Flanders Bioimaging consortium.
Editorial team for this course Authors: @orcid(Benjamin Pavie), @orcid(Tatiana Woller)
License: 