Object feature extraction

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.

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

• Introduction to Mathematical Morphology
• Morphological filtering of greyscale images
• Segmentation, e.g. focused on Watershed
• Image quantification (analysis of regions, texture analysis)

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.