The NEUBIAS Academy at home about CLIJ2 gives an introduction to accelerated image processing using Graphics Processing Units (GPUs) in ImageJ/Fiji. Core concepts are explained as well as usage of the tools with the ImageJ Macro recorder and auto-completion in Fijis script editor. Furthermore, an outlook is provided of how the CLIJ project will develop in the coming years to provide long-term maintained access to GPU-acceleration in the Bio-Image Analysis context.
A workflow is a set of components assembled in some specific order to
- Measure and estimate some numerical parameters of the biological system or
for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.
The one-day course is focused on processing microscopy images showing cells and nuclei. We will dive through segmenting objects, measuring their properties, managing measurements in tables and plotting results.
A lecture about challenges and solutions for GPU-accelerating bio-image analysis workflows and running them in the cloud.
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