Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing
A lecture about challenges and solutions for GPU-accelerating bio-image analysis workflows and running them in the cloud.
Collection
A collection is a software that encapsulate a set of bioimage components and/or workflows.
Fractal: A framework for processing OME-Zarr high content imaging data
Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization. Fractal provides distributed workflows that convert TBs of image data into OME-Zarr files. The platform then processes the 3D image data by applying tasks like illumination correction, maximum intensity projection, 3D segmentation using cellpose and measurements using napari workflows. The pyramidal OME-Zarr files enable interactive visualization in the napari viewer.
These slides are from an early demo of Fractal in November 2022
Napari: n-dimensional Python image viewer
Recent years have shown a diversification of commonly used platforms for specific sub-domains of image analysis. Among the currently actively developed projects, napari has taken the stage as a versatile and powerful platform for the analysis of high-dimensional (3D, time-lapse) image data.