Trace, quantify, and model multi-signal neuron morphology

Published: 30 April 2021| Version 1 | DOI: 10.17632/wpzd2wxtgn.1
Contributors:
Sumit Nanda,
Shatabdi Bhattacharjee,
Daniel Cox,
Giorgio Ascoli

Description

The zipped folder contains eight separate folders: i) Finalized Imagestacks, ii) Repair, iii) Scaling, iv) Quantify, v) Simulate, vi) TREES1.15, and vii) Vaa3D_MultiChannel_Compiled_Library, viii) StepByStepFiles Details:   i) Finalized_Imagestacks: Finalized imagestacks for three neuron types that are used to trace the neurons and produce the multi-signal swc files.    ii) Repair: Topological repair folder. Copy the initially traced files here and then repair them. iii) Scaling: Scaling folder. Copy the outputs from the Multi-channel plugin folder, scale the multisignal files (from voxel to physical dimension) to finalize them. iv) Quantify: Quantification of Cytoskeletal morphometrics folder. Several subfolders contain different parts of the Quantification process. v) Simulate: Simulation of virtual neuron arbor: subfolders for each three neurontype simulation and analysis. vi) TREES1.15: TREES Toolbox package with a few custom updates. vii) Vaa3D_MultiChannel_Compiled_Library: Compiled Multi-channel swc libraries for Vaa3d 3.1 (for both windows and mac) vii) StepByStepFiles: Intermediate and finalized image stack and Reconstruction of an example Class IV Wild Type neuron.

Files

Steps to reproduce

Follow the steps described in the paper to reproduce the analysis and simulation.