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:

Registration deadline extended to 28 August 2022


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”
Kota Miura

“Image Data Services at Euro-BioImaging: Community efforts towards FAIR Image Data and Analysis Services”
Aastha Mathur

“Jupyter for interactive cloud computing”
Guillaume Witz

“Jupyter exercises”
Guillaume Witz

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”
Christian Tischer

“Machine and Deep Learning on the cloud: Classification”
David Rousseau

“Machine and Deep Learning on the cloud: Segmentation”
Ignacio Arganda-Carreras

7 October Day 3 Examples of bioimage analysis workflows “Zero code tools for bioimage analysis”
Daniel Sage

“CellProfiler for HCS data on the cloud”
Beth Cimini and Anna Klemm

“Analysis of Microtubule Orientation”
Thomas Pengo

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”
Beatriz Serrano-Solano and Björn Grüning

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”
Sébastien Tosi, Volker Baecker and Benjamin Pavie

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:

Registration deadline: 28 August 2022

Please use the following subject: Defragmentation TS