Fractal: A Framework for Processing OME-Zarr High Content Imaging Data

Presentation of the Fractal framework at the PoL BIAS 2023.Fractal: An Open-Source Framework for Processing OME-Zarr High Content Imaging DataJoel Lüthi, BioVisionCenter, University of Zurich, Switzerland, Aug 31st 2023, 14:00Quantitative, image-based cell profiling requires accessible & scalable image processing workflows. A large diversity of image storage formats and processing approaches has made the exchange of workflows complicated, but the work on an OME next-generation file format offers the chance to come together and create more shareable workflows. At the BioVisionCenter at the University of Zurich, we are developing Fractal (https://fractal-analytics-platform.github.io), an open-source framework for processing high content imaging data in the OME-Zarr format. Fractal converts microscopy data into OME-Zarr and provides tools to process high content screening OME-Zarr files. Among other things, Fractal allows users to orchestrate the image analysis of TBs of high content images on high performance clusters, to perform instance segmentation and to extract high-dimensional measurements of multiplexed, 3D image data. We are providing a web front-end for users to easily interact with Fractal and submit image analysis jobs to a slurm cluster. And by relying on the napari image viewer, Fractal enables researchers to interactively visualize terabytes of remote image data and the results of their image processing workflows.Google slides with movies are available here: https://docs.google.com/presentation/d/1Y3SLWrSuSJxrtD1nIC1d5hJuUunVlqKDvv2uZlVGbXkOr click on any of the videos to access it in a web player.