Hackaton Whole slide analysis

The Data Analysis/Data Management (DA/DM) workgroup recently organized the third hackathon, this time focussed on analysis workflows of whole slide image data. The full day event, held on 20 April 2023 at the Leiden University Medical Center (LUMC), brought together eight microscopy enthusiasts from different microscopy facilities, who worked collaboratively to explore new and innovative ways to analyze whole slide image data.

The focus of the event was on collaboration, and participants were encouraged to work together to tackle issues and share their knowledge and experience.

Participants worked on a variety of exciting projects, including using QuPath for automated image analysis, exploring deep learning-based image segmentation with Cellpose, and implementing Warpy and pixelwise H-score for quantitative image analysis. Other tools and techniques that were discussed and tested include Libvips and OMERO.

Over the course of the event, participants had the opportunity to share their work, ask for feedback and guidance, and receive input from fellow microscopy enthusiasts with different expertise and perspectives. The event ended with drinks and snacks, providing a relaxed and informal setting for participants to network and share their experiences.

The hackathon was a success, providing a valuable opportunity for microscopy enthusiasts to come together, collaborate, and learn from each other. The NVvM and the DA/DM workgroup plan to continue organizing similar events in the future to continue fostering collaboration and innovation in the microscopy community.