SNT › Complementary Tools

Tool	Description	Comments
Spot Spine	Detection and count of dendritic spines, segmentation of spine heads, and quantitative morphological measurements of spines	Under active development
BigTrace	Semi-automated/automated tracing of unbranched structures using BigVolumeViewer	Under active development
NeuronJ	Semi-automated tracing in 2D only	No longer maintained. SNT reads NDF files

Tool	Description
HortaCloud	Cloud-based, open-source platform for collaborative reconstruction of long-range projection neurons from whole-brain light microscopy data. This is SNT’s development team recommended tool for tracing Terabyte-size datasets

BICCN Tools	List of tools supporting NIH’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN)
Blue Brain’s Morphology Suite	Blue brain’s collection of tools (mostly Python) to build, analyze and visualize morphologies. Currently supported by the Open Brain Institute
Cajal	A Python package for the analysis of single-cell morphological data using Gromov-Wasserstein (GW) distances
HBP Morphology Viewer	WebGL-based viewer with Allen Cell Types and Neuromorpho.org integration
L-measure	Classic toolkit for quantitative analyses of neuronal reconstructions of neurons (cf. metrics)
natverse	Complete neuroanatomical data analysis in R
TREES Toolbox	Complete neuroanatomical data analysis and modeling in MATLAB