The AI4Life May Hackathon held in Milan ended with successful contributions and progress made across several key areas. Here’s a summary of the event’s highlights:

Consultation Phase of the Second Open Call 

The consultation phase of the second Open Call started during the week of the hackathon. In-person participants engaged in calls with the Open Call applicants to advise them on their projects and better assess the complexity of possible solutions. These consultations addressed a variety of bioimage analysis and deep learning challenges, providing valuable insights and advice to projects from all over Europe. 

Public Challenges

Participants provided critical feedback on the AI4Life-MDC24 challenge pages hosted on the Grand Challenge platform. This included testing data downloads and attempting to train their own denoising models.

Infrastructure Improvement for Better Scalability

A significant milestone was achieved in upgrading Hypha and the BioEngine. This involved:

• Transitioning the deployment base image from Hypha to the BioEngine.
• Building a separate Hypha image with necessary plugins to better support the BioEngine.
• Setting up environment requirements to facilitate this transition, ensuring the new BioEngine image can include additional apps like Cellpose and ImageJ.

Enhancements also included integrating a Ray cluster to manage compute tasks, providing a scalable and efficient alternative to the Kubernetes API. This upgrade is essential for the fine-tuning of models, ensuring better performance and resource management.

Model Uploader

Efforts were concentrated on developing the new model uploader and the model review feature. Detailed coordination plans were discussed for migrating the old collection to the new system, ensuring a smooth transition and improved functionality.

Crowdsourcing Interactive Annotations

Participants worked on the creation of a crowdsourcing annotation tool, enabling collaborative image annotations by multiple users. This tool is accessible here.

Interactive Annotation Tool

Another project focused on an interactive annotation tool based on Kaibu and micro-SAM, resulting in a browser-compatible prototype.

BioImage.IO-Google Colab Project

A project was prototyped to connect the BioEngine with Kaibu for collaborative annotations. This included documenting the bioimageio_core and bioimageio_spec and updating an example notebook for local or Google Colab use, showcasing annotation with BioImageIO-Colab and fine-tuning a Cellpose model.

Thank you to all the participants for making the best out of this event and providing the scientific community with new improvements and achievements.