Skeletons - lucadellasantina/ObjectFinder GitHub Wiki

ObjectFinder makes use of digital skeletons to computer linear density of objects along the skeleton path and Sholl analysis. Support for digital skeletons of these formats is available:

Skeletons created with ImageJ/Fiji's Simple Neurite Tracer Plugin

To use a skeleton of this kind, copy the skeleton (.traces file) into your Experiment/I/ folder When pressing "Load Images" the skeleton will be automatically converted and used by ObjectFinder

Skeletons created with Imaris's Filament function

To sure a skeleton of this kind:

• first install the custom Imaris XTensions that come with ObjectFinder
• Start Imaris, select the Filament to export, then select Process -> Filament Functions -> ObjectFinder export Filament to MATLAB
• Select as destination your Experiment/ folder, a file Skel.mat will be created in the destination
• Select again Experiment/ folder in ObjectFinder to make use of the skeleton