BioImage.IO Meeting Minutes

May 14th 2025

Time: 4:00PM CET (your timezone)
Where: Zoom Channel
Meeting Minutes: GitHub Issue

Please, make sure to add your names on the attendees list!!!
Information for the Helsinki event demos and presentations:
- AI4Life agenda in the webpage
Workshops:
- Workshop 1: AI4Life for scientists
  - Session 1: Introduction to the BioImage Model Zoo: AI tools for image analysis in the life sciences (Anna, 1h)
    - BMZ
    - BioImage.IO Chatbot
  - Session 2: AI4Life community spotlight: Connecting users with community partners (Arrate chairing, 1h)
    - BiaPy
    - SpotMAX
    - QuPath
    - deepIcy
  - Session 3: Getting your data AI-ready at the BioImage Archive (Teresa, 45min)
    - BioImage Archive
- Workshop 2: AI4Life for AI scientists, software developers and image analysts
  - Session 1: Creating, Uploading, Deploying and Containerising BioImage Model Zoo Models (Esti & Fynn, 1h)
    - BMZ and Python
    - DL4MicEverywhere
  - Session 2: Bring BioEngine In-House: Self-Hosted AI Models for Bioimage Analysis (Wei, 1h)
    - BioEngine
  - Session 3: Present and future of data and AI model standards (Matthew, Anna & Florian 45min)
    - BioImage Archive
    - RDA Interest Group FAIR4ML
  - Session 4: So what’s this all good for? A story about the potential of shared and FAIR resources (Florian, 30min)
Anna and Florian cannot join on Wednesday. An alternative meeting will be hold also on Friday at 13:00h at least on Anna's side. People's invited to join on zoom.

WP2-Session 1: Creating, Uploading, Deploying and Containerising BioImage Model Zoo Models (Esti & Fynn, 1h)
- Have the notebooks prepared and everything.
- Plan:
  - Loading and using a BMZ-model (merge the following notebooks and write instructions in a github repository in the bioimageio community) (Esti)
    - https://github.com/bioimage-io/spec-bioimage-io/blob/main/example/load_model_and_create_your_own.ipynb
    - https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_usage.ipynb
  - Creating a BMZ-model from the GUI (e.g., fill the missing text with the row affable shark model + test numpy images as an example) (Thomas & Fynn)
  - Contianerise Affable-shark with a loading&use notebook (live demo Esti)
WP2-Session 2: Session 2: Bring BioEngine In-House: Self-Hosted AI Models for Bioimage Analysis (Wei, 1h)
AI4Life success story talks, tentative slides