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.
| Date | Day | Sessions | Speakers | Time |
|---|---|---|---|---|
| 8 May | Day 1 | Welcome. Overview and logistics Student introductions Introduction: What is bioimage analysis? Jupyter for interactive cloud computing Cloud-hosted image data storage, visualisation and sharing Work on your own data OMERO |
Paula Sampaio & Rocco D'Antuono Kota Miura Guillaume Witz Bugra Oezdemir Rocco D'Antuono & other Trainers Petr Walczysko |
09:00 09:30 11:30 14:00 15:30 16:00 |
| 9 May | Day 2 | Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing Zero code Deep Learning tools for Bioimage Analysis Analysis of Microtubule Orientation CellProfiler for HCS data on the cloud Work on your own data |
Marcelo Zoccoler Daniel Sage and Estibaliz Gomez de Mariscal Thomas Pengo Nodar Gogoberidze & Anna Klemm Rocco D'Antuono & other Trainers |
09:00 11:30 14:00 15:00 17:00 |
| 10 May | Day 3 | Metrics and Benchmarking BIAFLOWS: A BioImage Analysis workflows benchmarking platform Machine and Deep Learning on the Cloud: Classification Machine and Deep Learning on the Cloud: Segmentation Work on your own data |
Martin Maška Sébastien Tosi, Volker Baecker, and Benjamin Pavie Felix Mercier Ignacio Arganda Carreras Rocco D'Antuono & other Trainers |
09:00 10:00 12:00 12:30 16:30 |
| 11 May | Day 4 | Symposium | ||
| 12 May | Day 5 | Symposium |
Defragmentation TS2 is part of the NEUBIAS 5th Conference: https://eubias.org/NEUBIAS/neubias2020-conference/portugal-2023/
Scientific Organizers: Paula Sampaio, Rocco D'Antuono, Aastha Mathur, Beatriz Serrano Solano, Ana Stojiljkovic, Maria Azevedo, Kota Miura, Julien Colombelli.
Event Timing:
8-12 May 2023, Porto, PT
Defragmentation TS2 Contacts:
Please use the following subject: Defragmentation TS2
Trainees are kindly asked to get ready for the TS2 by doing the following homework in advance.
Get the following accounts for :
-
Galaxy account: https://live.usegalaxy.eu/login/start?redirect=None
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Google account for Colab : Google Sign up (a working Google account, not a linked account that you manage with Google). Make sure the account has enough free space (~ several GB) on it.
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A Github account for Binder: Sign up
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follow the instructions from Dr. Bugra Oezdemir to access BAND (sent via email) and run the script that installs the needed software on the remote desktop.
React
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