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.
Workflow
A workflow is a set of components assembled in some specific order to
- Measure and estimate some numerical parameters of the biological system or
- Visualization
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.
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
Tracking cells in microscopy image data
Cell tracking is a common bio-image analysis task. In this session we will learn about the basic principles behind cell tracking. We will go through cell segmentation, spot detection techniques such as Difference of Gaussian, linking, matching and will see how to do cell tracking in practice using TrackMate in Fiji.
