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NeuronStudio specifications


Unique identifier OMICS_10500
Name NeuronStudio
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Output data The output of the program is compatible with standard compartment modeling and morphometric software applications.
Operating system Windows
Computer skills Medium
Version 0.9.92
Stability Beta
Maintained Yes


No version available


  • person_outline Alfredo Rodriguez

Publications for NeuronStudio

NeuronStudio citations


Automated sorting of neuronal trees in fluorescent images of neuronal networks using NeuroTreeTracer

Sci Rep
PMCID: 5915526
PMID: 29691458
DOI: 10.1038/s41598-018-24753-w

[…] attempting to provide a complete list of relevant publications, we recall that existing automated or semi-automated methods include several academic routines– and other freeware (e.g., neuromantic, neuronstudio,) or commercial software packages (e.g., imaris, neurolucida, perkinelmer cellular imaging) offering multiple capabilities. many current methods still require significant manual […]


Soluble Tau has devastating effects on the structural plasticity of hippocampal granule neurons

PMCID: 5802513
PMID: 29217824
DOI: 10.1038/s41398-017-0013-6

[…] immersion objective; xy dimensions: 67.4 μm; z-axis interval: 0.2 µm). the dendritic length of each segment was measured on z-projections, and the number of dendritic spines was counted using the neuronstudio software (cnic, mount sinai school of medicine, 2007–2009). prior to spine analysis, images were deconvoluted using the huygens professional software (scientific volume imaging). […]


Differential impact of Met receptor gene interaction with early life stress on neuronal morphology and behavior in mice

PMCID: 5723381
PMID: 29255778
DOI: 10.1016/j.ynstr.2017.11.003

[…] of spines were obtained with a zeiss confocal microscope (lsm 710) with 63 × 1.40 na oil-immersion objective. images were processed with attenuation correction and 3d deconvolution and analyzed with neuronstudio software (, ). spines, and their length, volume and type (mushroom, stubby or thin) were automatically detected and analyzed using neuronstudio, and subsequently adjusted manually […]


Automated spatio temporal analysis of dendritic spines and related protein dynamics

PLoS One
PMCID: 5565271
PMID: 28827828
DOI: 10.1371/journal.pone.0182958

[…] classification-based [] and centerline extraction based [–]. the classification-based methods classify individual pixels into various groups such as spine, dendrite, or background []. the software neuronstudio by rodriguez et al. [] utilizes the pixel distance to the nearest surface point as a feature in classification, however, this can generate spurious spine detection and it is sensitive […]


Morphology of Dbx1 respiratory neurons in the preBötzinger complex and reticular formation of neonatal mice

Sci Data
PMCID: 5538238
PMID: 28763053
DOI: 10.1038/sdata.2017.97

[…] of dendritic trees and axons. sholl analysis, which provides branching and dendritic density information in regular distance intervals from the soma,, can be performed with software such as neuronstudio. digital morphologies can also be readily ported to simulation packages such as neuron and genesis to form compartmental mathematical models that are high-fidelity representations […]


The BDNF val 66 met Polymorphism Affects Neuronal Morphology and Synaptic Transmission in Cultured Hippocampal Neurons from Rett Syndrome Mice

PMCID: 5508027
PMID: 28751857
DOI: 10.3389/fncel.2017.00203

[…] and spine density was calculated by quantifying the number of spines per dendritic segment, and normalized to 10 μm of dendrite length. sholl analysis and branch order analyses were performed using neuronstudio software (wearne et al., ). the density of excitatory synapses was determined by the number of vglut1/glua1 co-localized puncta per length of gfp-positive dendrite, and normalized to 10 […]

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NeuronStudio institution(s)
Department of Neuroscience, Mount Sinai School of Medicine, New York, NY, USA; Laboratory of Biomathematics, Mount Sinai School of Medicine, New York, NY, USA; Computational Neurobiology and Imaging Center, Mount Sinai School of Medicine, New York, NY, USA

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