Introduction
In many studies of 3D morphology and circuits of mammalian neurons, a large tissue needs to be sectioned before imaging due to the limitation on penetration depth of microscopy. These individual sections need to be stitched together subject to the condition that there is little overlap between adjacent sections. Neuron Stitcher is a robust and efficient automated stitching tool to match and stitch neurons reconstructed in sliced 3D stacks. The framework matches separated dendritic or axonal branches on the section plane using a set of rotation invariant features that include neighborhood relationship and the orientation of separated branches. It is implemented in C/C++ as a plugin of Vaa3D which is a publicly available open source platform with user friendly interface for 3D+ image analysis and visualization.Please check demo video below for more informations.
Demo Videos
Automatically match and align neuron segments
Load images to assist visual inspection of border tips matching result
Visually inspect and interactively stitch matched border tips
Manually match border tips to stitch
Save results
Manually Alignment and Visualization Tool