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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


Mental Illnesses Associated Fxr1 and Its Negative Regulator Gsk3β Are Modulators of Anxiety and Glutamatergic Neurotransmission

PMCID: 5906571
PMID: 29706865
DOI: 10.3389/fnmol.2018.00119
call_split See protocol

[…] a, ON, Canada). Pictures were taken using a confocal microscope (Zeiss LSM 700) with a voxel size of 0.1 × 0.1 × 0.55 μm. Spines counting and dendrite length measurements were performed blindly using NeuronStudio (Icahn School of Medicine at Mount Sinai (ISMMS, New York, NY, United States).Following primary antibodies were used: mouse anti-Gsk3β (1:500, Abcam 93926, Cambridge, United Kingdom, for […]


Cryopreservation of Primary Mouse Neurons: The Benefit of Neurostore Cryoprotective Medium

PMCID: 5874515
PMID: 29623032
DOI: 10.3389/fncel.2018.00081
call_split See protocol

[…] ed in blind using a LSM Zeiss 510 confocal microscope with Zeiss 20×, 40× or 63× objective (Karl Zeiss, Jena, Germany) at a resolution of 2048 × 2048 pixels. All the measurements were performed using NeuronStudio. Neurites were automatically traced and quantified by the software in terms of length, number and morphology (Wearne et al., ; Rodriguez et al., ). Data were then logged and analyzed in M […]


Chronic Stress Reduces Nectin 1 mRNA Levels and Disrupts Dendritic Spine Plasticity in the Adult Mouse Perirhinal Cortex

PMCID: 5859075
PMID: 29593501
DOI: 10.3389/fncel.2018.00067
call_split See protocol

[…] o-noise ratio was set to 12.5. After deconvolution, image brightness and contrast were adjusted using ImageJ. The density, volume, head diameter, and length of dendritic spines were analyzed with the NeuronStudio software (Dumitriu et al., ; Heck et al., ) by an investigator blind to the experimental conditions. For spine density analysis, data were processed by first averaging all dendritic segme […]


Cortactin regulates endo lysosomal sorting of AMPARs via direct interaction with GluA2 subunit

Sci Rep
PMCID: 5841360
PMID: 29515177
DOI: 10.1038/s41598-018-22542-z

[…] times and analyzed using FiJi software. For spine density analysis, each image consisted of a 2–2.5 μm z-stack at 0.2 μm intervals and maximum projections were taken for each series and analyzed with NeuronStudio. […]


Sumoylation regulates FMRP mediated dendritic spine elimination and maturation

Nat Commun
PMCID: 5823917
PMID: 29472612
DOI: 10.1038/s41467-018-03222-y
call_split See protocol

[…] d for two of them). At the time of acquisition, laser power was adjusted so that all spines were below the saturation threshold. To analyze dendritic protrusions, projection images were imported into NeuronStudio software, which allows for the automated detection of immature and mature dendritic spines. The length of individual spines was automatically measured and data were imported in GraphPad P […]


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

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

[…] oil 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). A minimu […]


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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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