Intro to BioImage Analysis with Python for Life Scientists -A distributed in-person training course


Training AI4Life eRImote

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 CESTMonday, Oct 7thTuesday, Oct 8thWednesday, Oct 9th
9:30-10:00Welcome/ArrivalOptional Q&A for CEST timezone locationsOptional Q&A for CEST timezone locations
10:00-11:30Introduction to Jupyter and Python in the context of bioimage analysisBasics: Handling images in PythonIntroduction to Artificial Intelligence and classical Machine Learning segmentation
11:30-11:45Coffee breakCoffee breakCoffee break
11:45-13:00How to create our own kernelDenoising and segmentationMachine Learning classification tasks
13:00-14:00Lunch Lunch Lunch
14:00-15:30Introduction to microscopy images – images as scientific dataFeature ExtractionIntroduction to Neural Networks and Deep Learning
15:30-15:45Coffee breakCoffee breakCoffee break
15:45-17:00Bioimage analysis workflow – example as an introduction to the rest of the courseBuilding a workflow/pipelineAccessible tools to use DL for image analysis
17:00-17:30Optional Q&A for BST timezone locationOptional Q&A for BST timezone locationsOptional Q&A for BST timezone locations