SNT: A Unifying Toolbox for Quantification of Neuronal Anatomy

Abstract

Quantification of neuronal morphology is essential for understanding neuronal connectivity and many software tools have been developed for neuronal reconstruction and morphometry. However, such tools remain domain-specific, tethered to specific imaging modalities, and were not designed to accommodate the rich metadata generated by recent whole-brain cellular connectomics. To address these limitations, we created SNT: a unifying framework for neuronal morphometry and analysis of single-cell connectomics for the widely used Fiji and ImageJ platforms. We demonstrate that SNT -that replaces the popular Simple Neurite Tracer software- can be used to tackle important problems in contemporary neuroscience, validate its utility, and illustrate how it establishes an end-to-end platform for tracing, proof-editing, visualization, quantification, and modeling of neuroanatomy. With an open and scriptable architecture, a large user base, and thorough community-based documentation, SNT is an accessible and scalable resource for the broad neuroscience community that synergizes well with existing software.

Subtle Roles of Down Syndrome Cell Adhesion Molecules in Embryonic Forebrain Development and Neuronal Migration

“…MGE explant migration was quantified by measuring linear distances from explant edge of TdTomato+ neurons on mixed brightfield-fluorescence confocal images (2 μm step maximum Z-stacks projections) ( Figures 7B–E ) with the ImageJ Measure function. Morphological analysis of MGE explant-derived neurons was performed using the SNT ImageJ plugin (Longair et al, 2011 ; Arshadi et al, 2020 ). A minimum of 9 explants obtained from at least two experimental replicates were analyzed per treatment group.…”

Excitable axonal domains adapt to sensory deprivation in the olfactory system

“…The AnkG+ AIS of MCs extended directly off of the MC soma, often immediately into the first myelinated internode (Figure 1B', white arrowheads mark AIS start, yellow mark the end). AISs were measured in 3D volumes using the ImageJ/Fiji plugin Simple Neurite Tracer (SNT) (Arshadi et al, 2020), starting at the AnkG label originating at the base of the Nissl+ cell body and terminating at the distal end of the AnkG label. The mean length of MC AISs in the OB was 25.7 ± 3.81µm (lengths are given as mean ± standard deviation [SD], n = 687 AISs from 4 animals [Figure 1C]).…”

“…We traced from the origin of the AnkG signal at the base of the Nissl+ soma to the termination of the AnkG signal (typically ending abruptly in a Plp+ myelin sheath, see Figure 1). We then used the Fit Paths option in SNT to automatically optimize path fits using 3D intensity around each traced node (Arshadi et al, 2020) before exporting length measurements as comma separated value (CSV) spreadsheets for analysis using R. AIS length analysis was performed for treatment group (Control vs. Naris Occlusion), within group (Left vs. Right for Control, Open vs. Occluded for Naris Occlusion), and between group (Control vs. Open vs. Occluded).…”

Brainrender: a python-based software for visualizing anatomically registered data

“…More advanced software such as natverse (Bates et al 2020) offers extensive data visualization and analysis functionality but currently it is mostly restricted to data obtained from the drosophila brain. Simple Neurite Tracer (Arshadi et al 2020), an ImageJ-based software, can render neuronal morphological data from public and user-generated datasets and is compatible with several reference atlases. However, this software does not support visualization of data other than neuronal morphological reconstructions nor can it be easily adapted to work with different or new atlases beyond the ones already supported.…”