Workshop material

After the session you will be able to built your own CellProfiler pipeline, including:

• Image data import
• Object segmentation (e.g. detect nuclei in an image) using the modules "IdentifyPrimaryObjects" and "IdentifySecondaryObjects"
• Object feature measurements (e.g. measure size, shape and intensity of cells)
• Measurements export to a spreadsheet
• Creating and saving quality control images

Workshop session about sharing and licensing materials such as [raw] data, manuscripts, code, slides. The slides cover the FAIR principles, terminology such as authors, copyright holders, licensees.

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