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ZEISS Microscopy Knowledge Base

Classical segmentation methods

Semantic segmentation methods are most suitable if individual objects are either well separated or can easily be separated by post-processing or the area covered by objects is relevant rather than the precise counting and measuring of individual objects.

The methods are as follows:

Global Thresholding

Applies a fixed threshold across the entire image.

Use Case: Segmenting objects with consistent intensity, such as fluorescence images.

Blue fluorescent cell nuclei with green puncta, red outlines on a black background

Background Subtraction

Employs a rolling ball algorithm to subtract uneven background before applying a global threshold.

Use Case: Segmenting images with varying background intensity.

Cluster of irregular orange blobs outlined in green on a dark background

Variance-based Thresholding

Segments objects based on intensity changes rather than consistent intensity.

Use Case: Segementing objects in brightfield images where the objects are distinguished by intensity variance.

Gray background with multiple round dark blobs each outlined in red

Dynamic Thresholding

Applies local thresholds to handle inhomogeneous backgrounds.

Use case: Segmenting images with uneven illumination.

Dark image with scattered bright red blobs outlined in green on a diffuse red background

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