Defragmentation Training School – NEUBIAS Academy & EOSC-Life 2022
A training school for the new generation of bioimage analysts.
Topics: workflow-based image analysis and new integrated methods for cloud computing applied to life sciences.
“Defragmentation: bringing BioImage Analysts to the cloud!”
Registration form:
https://docs.google.com/forms/d/e/1FAIpQLSeyiFfdfRYAcQQB73dGy7WuclvkB_RiKxHncAd_HGwN_geFgA/viewform
Registration deadline extended to 28 August 2022
Programme:
| Date | Day | Topics | Sessions |
|---|---|---|---|
| 23 September | Day 1 | Introduction to bioimage analysis, tools, and workflows | “BioImage: correlated multimodal imaging in life sciences and the problem of big data management for core facilities” Julia Fernandez-Rodriguez “Introduction to what is bioimage analysis” “Image Data Services at Euro-BioImaging: Community efforts towards FAIR Image Data and Analysis Services” “Jupyter for interactive cloud computing” “Jupyter exercises” |
| 30 September | Day 2 | FAIR principles
Cloud hosted image data and cloud infrastructures Machine and Deep Learning on the cloud I Machine and Deep Learning on the cloud II |
“Introduction to FAIR principles for computational workflows” Carole Goble “Cloud hosted image data storage, visualisation and sharing” “Machine and Deep Learning on the cloud: Classification” “Machine and Deep Learning on the cloud: Segmentation” |
| 7 October | Day 3 | Examples of bioimage analysis workflows | “Zero code tools for bioimage analysis” Daniel Sage “CellProfiler for HCS data on the cloud” “Analysis of Microtubule Orientation” |
| 14 October | Day 4 | Parallelization: from CPU to GPU – how to speed up workflows
Work on your own data |
“Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing” Robert Haase “Introduction to Galaxy workflow environment” Trainees will be split into groups and they will start working on the selected workflows to convert them into a cloud solution |
| 21 October | Day 5 | Benchmarking theory
Benchmarking tools Work on your own data |
“Metrics and Benchmarking” Michal Kozubek “BIAFLOWS: A BioImage Analysis workflows benchmarking platform” Trainees will present their cloud workflows |
Scientific Organizers: Rocco D’Antuono, Paula Sampaio, Mafalda Sousa, Clara Prats, Marion Loveaux.
Scientific Advisory Board: Julien Colombelli, Paula Sampaio, Julia Fernandez-Rodriguez, Gaby Martins.
Event Timing: Training school distributed over 5 CEST Friday afternoon classes on September 23rd and 30th – October 7th, 14th, and 21st.
Event type: Online.
Capacity: max 25 participants.
Participation fee: Euro 100 (to be paid after admission).
Registration form: https://docs.google.com/forms/d/e/1FAIpQLSeyiFfdfRYAcQQB73dGy7WuclvkB_RiKxHncAd_HGwN_geFgA/viewform
Registration deadline: 28 August 2022
Contacts: rocco.dantuono@crick.ac.uk
Please use the following subject: Defragmentation TS