3D Spot Segmentation

The plugin works with two images, one containing the seeds of the objects, that can be obtained from local maxima (see 3D Filters or 3D Maxima Finder), the other image containing signal data. The program computes a local threshold around each seeds and cluster voxels with values higher than the local threshold computed.

Three methods are available for computing the value of the local threshold, and 3 methods for clustering are also proposed. The option watershed can be chosen to avoid merging of close spots.A tutorial is also avalaible : 3D Spot Segmentation Manual.

Original image with Fire LUT, seeds are computed as local maxima

Watershed zones segmentation of the seeds

Final segmentation of the spots