Intro to BioImage Analysis with Python for Life Scientists -A distributed in-person training course
When
October 7–10, 2024
Where
Sweden - France - Portugal
Interested in learning python for your image analysis needs? Want to understand how Jupyter notebooks can make your analysis workflows easier?
The upcoming distributed "Image analysis with Python" beginners course is your chance. The course will take place October 7th-9th 2024 and as a distributed course will be held in-person in several locations with a joint training program and common lectures and in-person hands-on support.
The course will be held on location across different Euro-BioImaging Nodes at the following locations:
- University of Gothenburg, Sweden - NMI Sweden Node
- Institut Pasteur, Paris, France - France BioImaging Node
- Gulbenkian Institute of Molecular Medicine (GIMM), Oeiras, Portugal - PPBI Node
This course is organised by Rafael Camacho, CCI University of Gothenburg, Jean-Yves Tinevez, Institut Pasteur, and Gaby G. Martins, GIMM, with support from the Euro-BioImaging team as part of the eRImote project.
Prerequisites for participation
- Working with biological imaging techniques and having a clear image analysis question. You have to submit a 1 pdf page + 1 png image explaining your image analysis problem and what analysis you have tried already (if anything).
- Basic knowledge of ImageJ (opening datasets, basic processing techniques & particle analysis).
- Students must be able to attend the whole 3-day course.
- Please bring a laptop with minimum 8GB RAM, Wifi or Ethernet, at least 14-16” screen + mouse (not just mousepad) for the course
What’s included in the course?
The course will implement a joint virtual platform for all attendees at all sites, ensuring everyone has access to the same environment for their analysis and learning. This virtual platform is the BAND remote desktop, developed as part of the Euro-BioImaging involvement in the EOSC-Life project by Jean-Karim Heriche and Yi Sun from EMBL [link]. This training event also benefits from the EGI Training Infrastructure service supported by national resource providers in the EGI Federation. In particular, CESNET is providing the computational resources and support to host BAND for this training event
Program
| Time in CEST | Monday, Oct 7th | Tuesday, Oct 8th | Wednesday, Oct 9th |
|---|---|---|---|
| 9:30-10:00 | Welcome/Arrival | Optional Q&A for CEST timezone locations | Optional Q&A for CEST timezone locations |
| 10:00-11:30 | Introduction to Jupyter and Python in the context of bioimage analysis | Basics: Handling images in Python | Introduction to Artificial Intelligence and classical Machine Learning segmentation |
| 11:30-11:45 | Coffee break | Coffee break | Coffee break |
| 11:45-13:00 | How to create our own kernel | Denoising and segmentation | Machine Learning classification tasks |
| 13:00-14:00 | Lunch | Lunch | Lunch |
| 14:00-15:30 | Introduction to microscopy images – images as scientific data | Feature Extraction | Introduction to Neural Networks and Deep Learning |
| 15:30-15:45 | Coffee break | Coffee break | Coffee break |
| 15:45-17:00 | Bioimage analysis workflow – example as an introduction to the rest of the course | Building a workflow/pipeline | Accessible tools to use DL for image analysis |
| 17:00-17:30 | Optional Q&A for BST timezone location | Optional Q&A for BST timezone locations | Optional Q&A for BST timezone locations |