3D

pyimagej provides a set of wrapper functions for integration between ImageJ and Python.

It also provides a high-level entry point for invoking ImageJ server APIs.

Execute Nuclei Segmentation in 3D images using pixel classification with ilastik.

The macro will segment nuclei and separate clustered nuclei in a 3D image using a 2D Gaussian blur, followed by Thresholding, 2D hole filling and a 2D watershed. As a result an index-mask image is written for each input image.

This plugin computes for each image element (pixel/voxel) the eigenvalues of the Hessian, which can be used for example to discriminate locally between plate-like, line-like, and blob-like image structures

3D spot detection using the Determinant of Hessian (DoH) and the detection of 3D minima.