In this example we'll segment nuclei in 3D from a confocal image stack and measure some basic shape properties.
Animation showing detection and measurement of nuclei in 3D. (Left) Image stack with background subtraction applied. Animation cycles through slices of the z-stack. (Right) Detected nuclei visualised with white outlines and semi-transparent overlays, colour-coded by their diameter (longest chord) measurement. Unique ID for each nucleus shown as white text.
This example introduces the following concepts:
- Loading images into the MIA
- Performing basic image processing steps
- Segmentation of objects from binarised images
- Measuring detected objects and filtering based on these measurements
- Visualising detected objects with overlays
- Exporting object measurements to spreadsheet