Abstract
Reconstructing neurons from 3D image-stacks of serial sections of thick brain tissue is very time-consuming and often becomes a bottleneck in high-throughput brain mapping projects. We developed NeuronStitcher, a software suite for stitching non-overlapping neuron fragments reconstructed in serial 3D image sections. With its efficient algorithm and user-friendly interface, NeuronStitcher has been used successfully to reconstruct very large and complex human and mouse neurons.
Highlights
Reconstructing neurons from 3D image-stacks of serial sections of thick brain tissue is very time-consuming and often becomes a bottleneck in high-throughput brain mapping projects
This is a non-trivial task for algorithms because there could be missing tissues as well as distortions during sectioning, making stitching neuronal segments across multiple sections much more challenging in comparison with stitching overlapping tiles within single sections [6, 7] (Fig. 1c)
Several studies [8,9,10,11,12] aimed at aligning traced neuron fragments (Supplement, Section 1) because a neuron reconstruction often gives a concise and less noisy description of neuron morphology than the respective raw image
Summary
Reconstructing neurons from 3D image-stacks of serial sections of thick brain tissue is very time-consuming and often becomes a bottleneck in high-throughput brain mapping projects. Keywords Neuron Á Stitch Á Neuron stitcher Á Reconstruct morphology Á Alignment Á Vaa3D Digital reconstructions of neurons from very large threedimensional (3D) brain images are crucial for modern neuroscience [1,2,3].
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