Simple Neurite Tracer
From Fiji
| Simple Neurite Tracer (ImageJ) | |
|---|---|
| Author | Mark Longair and others |
| Maintainer | Mark Longair |
| File | Simple_Neurite_Tracer.jar |
| Source | on gitweb |
| Development status | stable |
The main documentation for this plugin can be found at: http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/
To help you to get started with using this plugin, there is an explanatory screencast here: http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/new-instructions.html
Simple Neurite Tracer from Mark Longair, showing a traced neurons in an adult Drosophila brain.
The plugin GUI (left) guides the user into creating paths semi-automatically, by clicking starting and ending points throughout the stack. Any ending point serves as starting point for a new segment of the same trace, unless the trace is declared complete. Paths can start and / or end on any other path in order to create a branching structure.
The "Pick Sigma and Maximum" window can be brought up by clicking on the "Pick Sigma Visually" button. This provides an easy way to choose parameters that affect the diameter of tube-like structures that "Hessian based analysis" option picks out.
In the center, the image stack is shown in the XY plane with all traces in the volume projected onto that slice.
On the right, the ongoing tracing is shown in the context of the 3D volume view of the stack (via 3D Viewer plugin). From the 3D Viewer, traces can be exported as meshes in wavefront or DXF formats for further processing in 3D applications like Blender.
