Workflow

The macro will segment nuclei and separate clustered nuclei using a binary watershed. As a result an index-mask image is written for each input image.

Multimodal image registration based on manual selection of matching pairs of landmarks. This image registration workflow is based
on MATLAB’s image processing toolbox using the identification of sites of clathrin-mediated endocytosis by correlative light electron microscopy (CLEM) as an example.

Tracking tools, such as TrackMate, produce tracks and their role stops there. However, tracks are just an intermediate data structure in the workflow. Their subsequent analysis produces the numbers upon which scientific conclusions are made. The track analysis is most often specific to the scientific question to be addressed, and therefore tracking tools remain generic and seldom include specialized analysis modules. Another toolset is required for track analysis; this workflow focuses on using MATLAB.

This workflow presents single-particle tracking in Fiji using Track-Mate, and track motility analysis in MATLAB using @msdanalyzer. 

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.