This workflow describes a semi-automatic image segmentation procedure for 3D reconstructions of the coronary arterial tree, after which how different morphometric features are automatically extracted, including vessel lumen diameter of the three main coronaries.

video tutorial on 3D vessel segmentation of synchrotron phase contrast tomography

Submitted by czhang on Tue, 01/29/2019 - 20:32

In this tutorial video, a coronary arterial tree is used as the demo example to show in detail how the semi-automatic segmentation workflow, Carving from the open-source image analysis software ilastik, can be used. Tips on how and why a preprocessing is done, as well as parameter settings are provided.


IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

Included are two programs with graphical interface: 3dmod, for displaying and segmenting 2D images and 3D volumes; etomo, for reconstructing tomographic volumes from tilt series of images.

Processing can be distributed on multiple cores and executed in batch mode.