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Neuroexplorer software

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NeuroExplorer is a software package designed for the analysis of electrophysiological data, particularly neural signals. It provides advanced tools for visualizing, processing, and analyzing various types of neural data, including spike trains, local field potentials, and other electrophysiological measurements.

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Lab products found in correlation

Neurolucida software, by MBF Biosciences (5 mentions) Neurolucida morphometry software, by MBF Biosciences (4 mentions) Axiophot 2 microscope, by Zeiss (3 mentions) Axioplan 2, by Zeiss (2 mentions) Neurolucida 360, by MBF Biosciences (2 mentions) Axiovert lsm510, by Zeiss (1 mentions) Plan apochromat, by Zeiss (1 mentions) Neuroexplorer, by MBF Biosciences (1 mentions) Vt 100m, by Leica (1 mentions) Ds u3, by Nikon (1 mentions) Fd rapid golgistain kit, by FD NeuroTechnologies (1 mentions) Eclipse ci l microscope, by Nikon (1 mentions) Axio imager z1, by Zeiss (1 mentions) Eutasil, by Ceva (1 mentions)

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NeuroExplorer (22 citations)

14 protocols using neuroexplorer software

1

Microglial Morphological Analysis in Hippocampus

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Images were captured using a confocal microscope (Zeiss Axiovert LSM510, Carl Zeiss). 20X images were used to assess microglial density by counting Iba-1+ cells within the dentate gyrus (DG), CA1 and CA3 of the hippocampus. The computer-based cell tracing software Neurolucida 360 (MBF Bioscience, VT) was used for 3D reconstruction of Iba-1+ cells within the CA3 pyramidal layer of the hippocampus. NeuroExplorer software (MBF Bioscience, VT) was used to analyze microglial soma size and branch length and volume for ≥ 15 cells per animal. Sholl analysis was used to determine branch tree morphology by placing 3D concentric circles in 5 μ m increments starting at 5μ m from the soma.
Franklin T.C., Wohleb E.S., Zhang Y., Fogaça M., Hare B, & Duman R.S. (2017). Persistent increase in microglial RAGE contributes to chronic stress Induced priming of depressive-like behavior. Biological psychiatry, 83(1), 50-60.
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2

Microglial Morphology Quantification Using NeuroExplorer

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NeuroExplorer software (MBF Biosciences, VT, USA) was used to generate metric analyses of reconstructed microglia. The cell body perimeter, number of primary processes, number of nodes (branch points), total length of all processes, and total volume of all processes were measured. The area encompassed by the entire cell was measured as the convex hull area, determined from the polygon created from straight lines connecting the most distal points of the microglial processes. A box counting protocol determined the fractal dimension of each cell (k-dim) to determine how fully the cell occupied its convex hull area [28 (link)]. To account for changes in the cell’s complexity in relation to distance from the cell soma, Sholl analyses were performed for each microglial cell. Concentric circles (radii) were spaced 5 μm apart, originating from the soma [29 (link)]. The number of branch points (nodes) and processes that intersected the radii, and process length, surface area, volume and average diameter were measured as a function of the distance from the cell soma for each radius.
Kongsui R., Beynon S.B., Johnson S.J, & Walker F.R. (2014). Quantitative assessment of microglial morphology and density reveals remarkable consistency in the distribution and morphology of cells within the healthy prefrontal cortex of the rat. Journal of Neuroinflammation, 11, 182.
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3

Pyramidal Neuron Morphometrics in Irradiated Mice

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Neurons were manually traced and reconstructed in 3-dimensions with a 63×/1.4 N.A., Plan-Apochromat oil immersion objective on a Zeiss Axio Imager Vario microscope equipped with a motorized stage, video camera system, and Neurolucida morphometry software (MBF Bioscience, Williston, VT, USA). To be included in the analysis, a loaded neuron had to satisfy the following criteria: (1) reside within the pyramidal layer of the CA1 as defined by cytoarchitectural characteristics; (2) demonstrate complete filling of dendritic tree, as evidenced by well-defined endings; and (3) demonstrate intact tertiary branches, with the exception of branches that extended beyond 50 μm in radial distance from the cell soma [33 (link),34 (link),75 (link)].Using NeuroExplorer software (MBF Bioscience) total dendritic length, number of intersections, and the amount of dendritic material per radial distance from the soma, in 30-μm increments [34 (link)]. were analyzed in order to assess morphological cellular diversity and potential differences between the animal groups. A total of 50 cells were reconstructed for controls (~8 cells per animal) and a total of 49 cells were reconstructed for neutron irradiated mice (~8 cells per animal).
Krishnan B., Natarajan C., Bourne K.Z., Alikhani L., Wang J., Sowa A., Groen K., Perry B., Dickstein D.L., Baulch J.E., Limoli C.L, & Britten R.A. (2021). Chronic Low Dose Neutron Exposure Results in Altered Neurotransmission Properties of the Hippocampus-Prefrontal Cortex Axis in Both Mice and Rats. International Journal of Molecular Sciences, 22(7), 3668.
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4

Reconstruction of Hippocampal Pyramidal Neurons

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To be included in the analysis, a loaded neuron had to satisfy the following criteria: (1) reside within the pyramidal layer of the CA1 as defined by cytoarchitectural characteristics; (2) demonstrate complete filling of dendritic tree, as evidenced by well-defined endings; and (3) demonstrate intact tertiary branches, with the exception of branches that extended beyond 50 μm in radial distance from the cell soma42 (link)43 (link)44 (link). Neurons meeting these criteria were reconstructed in three-dimensions (3D) with a 40×/1.4 N.A., Plan-Apochromat oil immersion objective on a Zeiss Axiophot 2 microscope equipped with a motorized stage, video camera system, and Neurolucida morphometry software (MBF Bioscience). Using NeuroExplorer software (MBF Bioscience) total dendritic length, number of intersections, and the amount of dendritic material per radial distance from the soma, in 30 μm increments were analyzed in order to assess morphological cellular diversity and potential differences among animals45 (link).
Lazarczyk M.J., Kemmler J.E., Eyford B.A., Short J.A., Varghese M., Sowa A., Dickstein D.R., Yuk F.J., Puri R., Biron K.E., Leist M., Jefferies W.A, & Dickstein D.L. (2016). Major Histocompatibility Complex class I proteins are critical for maintaining neuronal structural complexity in the aging brain. Scientific Reports, 6, 26199.
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5

Dendritic Morphology Analysis of CA1 Pyramidal Neurons

Cited 3 times
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To be included in the analysis, a loaded neuron had to satisfy the following criteria: (1) reside within the pyramidal layer of the CA1 as defined by cytoarchitectural characteristics; (2) demonstrate complete filling of dendritic tree, as evidenced by well-defined endings; and (3) demonstrate intact tertiary branches, with the exception of branches that extended beyond 50 μm in radial distance from the cell soma
[75 (link), 76 (link), 78 (link)]. Neurons meeting these criteria were reconstructed in 3-dimensions (3D) with a 40×/1.4 N.A., Plan-Apochromat oil immersion objective on a Zeiss Axiophot 2 microscope equipped with a motorized stage, video camera system, and Neurolucida morphometry software (MBF Bioscience). Using NeuroExplorer software (MBF Bioscience) total dendritic length, number of intersections, and the amount of dendritic material per radial distance from the soma, in 30-μm increments
[79 (link)] were analyzed in order to assess morphological cellular diversity and potential differences between the animal groups.
Price K.A., Varghese M., Sowa A., Yuk F., Brautigam H., Ehrlich M.E, & Dickstein D.L. (2014). Altered synaptic structure in the hippocampus in a mouse model of Alzheimer’s disease with soluble amyloid-β oligomers and no plaque pathology. Molecular Neurodegeneration, 9, 41.
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6

Quantitative Analysis of Hippocampal CA1 Neuron Morphology

Cited 3 times
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In order for a loaded neuron to be included in the analysis, it had to satisfy the following criteria: (1) reside within the pyramidal layer of the CA1 as defined by cytoarchitectural characteristics; (2) demonstrate complete filling of dendritic tree, as evidenced by well-defined endings; and (3) demonstrate intact tertiary branches, with the exception of branches that extended beyond 50 μm in radial distance from the cell soma (Radley et al., 2006 (link); Radley et al., 2008 (link); Dickstein et al., 2010 (link); Midthune et al., 2012 (link); Tyan et al., 2012 (link)). Neurons meeting these criteria were reconstructed in 3-dimension (3D) with a 40x/1.4 N.A., Plan-Apochromat oil immersion objective on a Zeiss Axiophot 2 microscope equipped with a motorized stage, video camera system, and Neurolucida morphometry software (MBF Bioscience, Williston, VT). Using NeuroExplorer software (MBF Bioscience) total dendritic length, number of intersections, and the amount of dendritic material per radial distance from the soma, in 30-μm increments (Sholl, 1953 (link)) were analyzed in order to assess morphological cellular diversity and potential differences among animal groups.
Steele J.W., Brautigam H., Short J.A., Sowa A., Shi M., Yadav A., Weaver C.M., Westaway D., Fraser P.E., St George-Hyslop P.H., Gandy S., Hof P.R, & Dickstein D.L. (2014). Early Fear Memory Defects Are Associated with Altered Synaptic Plasticity and Molecular Architecture in the TgCRND8 Alzheimer's Disease Mouse Model. The Journal of comparative neurology, 522(10), 2319-2335.
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7

Tracing and Quantifying MSN Spines

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Unobstructed MSNs of the NAc core or shell (2–6/subregion/mouse) were traced bilaterally (40X) using Neurolucida software (MBF Bioscience, Williston, VT). Spines were counted (100X) from a single 3rd-order or higher, complete terminal tip (≥20 uM) and categorized by type. Quantitative assessment was performed using NeuroExplorer software (MBF Bioscience).
Smith L.N., Jedynak J.P., Fontenot M.R., Hale C.F., Dietz K.C., Taniguchi M., Thomas F.S., Zirlin B.C., Birnbaum S.G., Huber K.M., Thomas M.J, & Cowan C.W. (2014). Fragile X mental retardation protein regulates synaptic and behavioral plasticity to repeated cocaine administration. Neuron, 82(3), 645-658.
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8

Dendritic Morphology and Spine Analysis

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Three dimensional (3D) dendritic morphology was assessed in Golgi-Cox stained material as previously described (Lima et al., 2014 (link)). mPFC layer V pyramidal neurons were analyzed for the following dendritic features: length, arborization, Sholl analysis and spine number and classification. Briefly, at least five neurons were analyzed for each animal by using a motorized microscope controlled by the Neurolucida software (MBF Bioscience, United States) under 100× magnification. Dendritic spine densities were assessed in randomly selected dendritic segments of 30 μm, in the proximal and distal portions of the apical dendrite and in the proximal portion of the basal dendrite. Moreover, spines were classified into four categories: thin, mushroom, thick, and ramified. The extraction of data for both reconstructed neurons and spines was performed by using NeuroExplorer software (MBF Bioscience, United States).
Guerra-Gomes S., Viana J.F., Nascimento D.S., Correia J.S., Sardinha V.M., Caetano I., Sousa N., Pinto L, & Oliveira J.F. (2018). The Role of Astrocytic Calcium Signaling in the Aged Prefrontal Cortex. Frontiers in Cellular Neuroscience, 12, 379.
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9

Golgi Staining and 3D Neuron Analysis

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Fourteen days after sham-CHI or CHI, mice were anesthetized with urethane (0.1 mL 40%) and whole brains were stained as described in the FD Rapid Golgi Stain kit (FD Neurotechnologies, Columbia, MD, USA). Coronal sections (180μm) were prepared on a vibratome (Leica VT 100M), mounted and stained. Z-stacks of Golgi-stained dorsal hippocampus (from Bregma −1.3 to −2.7) were obtained with a Nikon DS-U3 camera on a Nikon Eclipse Ci-L microscope and processed with NIS-Elements D 4.40.00 software. Individual CA3 and CA1 pyramidal neurons were analyzed that had a fully impregnated dendritic tree that was minimally obscured by the dendrites of nearby neurons. CA1 and CA3 pyramidal cells meeting these criteria (10 cells per region) in each group (n=5 animals/group) were reconstructed into 3-dimensional traces using Neurolucida 360 software (Version 11.03, MBF Bioscience). NeuroExplorer software (MBF Bioscience) measured the reconstructed neurons for surface area and volume, branch morphology (total number, length, surface area and volume), and node number. Basal and apical dendritic trees were analyzed separately. Built-in convex hull analysis (NeuroExplorer, MBF Bioscience) measured neuronal volume and dendritic field size. Built-in Sholl analysis measured dendritic intersection number at 10μm intervals from the neuronal soma.
Whitney K., Nikulina E., Rahman S.N., Alexis A, & Bergold P.J. (2021). Delayed dosing of Minocycline plus N-acetylcysteine reduces neurodegeneration in distal brain regions and restores spatial memory after experimental traumatic brain injury. Experimental neurology, 345, 113816.
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10

Golgi-Cox Staining and 3D Morphometric Analysis

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Three-dimensional morphometric analysis was performed on Golgi-Cox stained material obtained from rats that had been transcardially perfused with 0.9% saline and further processed, as previously described.22 (link) For each animal, at least eight neurons (randomly selected) were analyzed in the hippocampal dentate gyrus and PFC. For each selected neuron, dendritic branches were reconstructed at × 1000 (oil) magnification (× 100 objective × × 10 ocular) using a motorized microscope (Axioplan 2; Carl Zeiss, Oberkochen, Germany) and the Neurolucida software (MBF Bioscience, Williston, VT, USA). Three-dimensional analysis of the reconstructed neurons was performed using the NeuroExplorer software (MBF Bioscience). Measurements from individual neurons from each animal were averaged. Total dendritic length was compared among the experimental groups. Branching of the neurons was evaluated using 3D Sholl analysis; for this, the number of dendritic intersections with concentric circles positioned at radial intervals of 20 μm was determined. To minimize bias, each slide was coded to keep the experimenter blind to the experimental group.
Morais M., Patrício P., Mateus-Pinheiro A., Alves N.D., Machado-Santos A.R., Correia J.S., Pereira J., Pinto L., Sousa N, & Bessa J.M. (2017). The modulation of adult neuroplasticity is involved in the mood-improving actions of atypical antipsychotics in an animal model of depression. Translational Psychiatry, 7(6), e1146-.
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