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 deadline extended to 28 August 2022
|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”
“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”
|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”
“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”
“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”
“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
Work on your own data
|“Metrics and Benchmarking”
“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 deadline: 28 August 2022
Please use the following subject: Defragmentation TS