Neurolucida 360

Manufactured by MBF Biosciences

Sourced in United States

Neurolucida 360 is a software application designed for 3D reconstruction and analysis of neuroanatomical structures. It allows users to capture and visualize detailed three-dimensional images of cells, tissues, and other biological samples.

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Lab products found in correlation

Neurolucida explorer, by MBF Biosciences (9 mentions) Fd rapid golgistain kit, by FD NeuroTechnologies (8 mentions) Neuroexplorer, by MBF Biosciences (5 mentions) Lsm 880, by Zeiss (4 mentions) Lsm 710 confocal microscope, by Zeiss (3 mentions) Water objective, by Nikon (2 mentions) Leica confocal microscope with 63x oil objective, by Nikon (2 mentions) Ar confocal microscope with, by Nikon (2 mentions) Tcs spe laser, by Leica camera (2 mentions) Neuroexplorer, by MicroBrightField (2 mentions) Huygens professional v16, by Scientific Volume Imaging (2 mentions) Vibratome, by Leica camera (2 mentions) Apotome 2 microscope, by Zeiss (2 mentions) Fv1200, by Olympus (2 mentions) Imager m2, by Zeiss (2 mentions) Lsm 800, by Zeiss (2 mentions) Mouse anti parvalbumin, by Merck Group (2 mentions) Rabbit anti ankyrin g, by Santa Cruz Biotechnology (2 mentions) Vt1000s vibratome, by Leica camera (2 mentions) Alexa fluor 647, by Thermo Fisher Scientific (2 mentions)

85 protocols using neurolucida 360

Whole-Brain Neuron Reconstruction from Fluorescence Imaging

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We manually reconstruct 42 neurons based on the whole brain fluorescence imaging dataset at 0.2 × 0.2 × 1 μm³ voxel resolution using Amira software (v6.1.1, FEI, France) with the TDat data accessing module^{46 (link)}. The brain imaging dataset used for the single neuron reconstruction contains more than ten thousand coronal slices at 1 μm axial resolution. The fibers can be separated clearly by their brightness and thickness at this resolution. We choose some somata with high fluorescent signals in motor cortex as the starting point for the whole neuron reconstruction. The neuron tracing process is similar to the approaches used by other researchers^{13 (link),18 (link),37 (link),47 (link)}. The annotators have been trained for neuron reconstruction for 6 months. Moreover, back-to-back verifications are performed for each reconstructed neuron.
To check the validity of the reconstructed neuron structure, we transform the file in the SWC format saved by Amira to the ASC format file using Neuronland software (Neuromorpho.org). In Neurolucida 360 software (Neurolucida 360, version 2.70.1, MBF Bioscience, Williston, VT), we subsequently label the fibers as axon, apical dendrite or basal dendrite according to the manual reconstruction result.

Jiang S., Guan Y., Chen S., Jia X., Ni H., Zhang Y., Han Y., Peng X., Zhou C., Li A., Luo Q, & Gong H. (2020). Anatomically revealed morphological patterns of pyramidal neurons in layer 5 of the motor cortex. Scientific Reports, 10, 7916.

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Neuronal Morphology Characterization in Transgenic Mice

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Brain slices from slice electrophysiology were subjected to histochemical analysis using NEUN antibody to confirm neuron identity and streptavidin Alex Fluor-568 (Invitrogen) to label injected biocytin for morphology assessment. Stained sections were mounted in cell gasket with SlowFade Diamond Antifade Mountant (Invitrogen). Images for neuronal body and dendrites were taken under Zeiss LSM 880 Airyscan Confocal Microscope. We used Neurolucida 360 (https://www.mbfbioscience.com/neurolucida360) to trace the neuronal body (15 neurons from 8 WT animals, 14 neurons from 8 Het animals) and dendrites (10 neurons from 5 WT animals, 10 neurons from 6 Het animals) and count different types of dendritic spines (10 neurons from 4 WT animals, 7 neurons from 4 Het animals). Branch analysis and Sholl analysis were performed using Neurolucida Explorer (https://www.mbfbioscience.com/neurolucida-explorer). Then we exported measurements for soma surface area, soma volume, total dendrite number, total dendritic length, average dendrite length, dendrite node number, and complexity ([Sum of the terminal orders + Number of terminals] * [Total dendritic length / Number of primary dendrites]), branch number, branch length, total spine density, and density of different spine subtypes to compare neuron morphological maturation between Hets and WTs.

Chen J., Lambo M.E., Ge X., Dearborn J.T., Liu Y., McCullough K.B., Swift R.G., Tabachnick D.R., Tian L., Noguchi K., Garbow J.R., Constantino J.N., Gabel H.W., Hengen K.B., Maloney S.E, & Dougherty J.D. (2021). A MYT1L syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation. Neuron, 109(23), 3775-3792.e14.

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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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3D Viral Expression Mapping in Monkey Striatum

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Following image collection, the sections were aligned and compiled into stacks using BrainMaker (MBF Bioscience), with 400 µm in between sections. A stack was created for each brain hemisphere of each monkey. The image stacks were then imported into Neurolucida360 (MBF Bioscience) for analysis. The striatal region of interest (caudate or putamen) was outlined using the Contour mode of the program. Area measurements of striatal regions and treated regions were calculated from these outlines by the program. While only visualizing the ChAT channel, markers were used to count and categorize the ChAT positive cells as either strong, medium, or weak. The injection region was similarly outlined using only the relevant channels. ChAT cells within the injection region were also counted and categorized as either having strong, medium, weak, or no viral expression. This process was repeated for all sections within the stacks. 3D reconstructions of each brain hemisphere were created using the 3D environment of Neurolucida360 to visualize the viral expression in the monkey striatum. Movies of the reconstructions are available at: 10.35092/yhjc.12616832.

Lerchner W., Adil A.A., Mumuney S., Wang W., Falcone R., Turchi J, & Richmond B.J. (2021). RNAi and chemogenetic reporter co-regulation in primate striatal interneurons. Gene Therapy, 29(1-2), 69-80.

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Dendritic Spine Analysis Using Neurolucida

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The dendrites were manually traced, and the dendritic spines were traced using a point-and-click method within neurolucida-360 in neurolucida software [52] (link). Neurolucida explorer software was used to manually edit the spines. The spine density was analysed by the number of spines present in the 10 µm length of the dendritic processes. The spine classification was performed in neurolucida-360 (MBF Bioscience). Neurolucida categorized spine into three classes; mushroom, stubby and thin. Neurolucida software does not have any feature to classify filopodia, which may be due to the structural similarity between filopodia and thin spines.

Al-Amin M.M., Sullivan R.K., Alexander S., Carter D.A., Bradford D, & Burne T.H. (2022). Impaired spatial memory in adult vitamin D deficient BALB/c mice is associated with reductions in spine density, nitric oxide, and neural nitric oxide synthase in the hippocampus. AIMS Neuroscience, 9(1), 31-56.

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3D Astrocyte Reconstruction from Confocal Imaging

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Confocal z stack images were captured using either a Leica confocal microscope with 63X oil objective with frame size at 1024× 1024 and bit depth at 8 or a Nikon AR Confocal Microscope with 40x water objective with frame size at 2048× 2048 and a bit depth of 12 (Nikon Instruments Inc., USA). The z stack (1 μm step size) images were taken encompassing the whole section or the regions of interest. Images were imported to Neurolucida 360 (MBF Bioscience). Orthogonal review for individual cells in z-projected images was generated with 3D overview module. The 3D objects of tdT + astrocytes were then analyzed with the 3D reconstruction using tdT and DAPI fluorescence. Cells’ processes were manually traced with the use of the dendrite tracing.

Wei H., Wu X., Withrow J., Duran R.C., Singh S., Chaboub L.S., Rakshit J., Mejia J., Rolfe A., Herrera J.J., Horner P.J, & Wu J.Q. (2023). Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury. Cell reports, 42(5), 112486.

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Pyramidal Neuron-Microglia Interactions in Premotor Cortex

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We assessed the interaction between filled L3 pyramidal neurons and immuno-labeled microglia in the perilesional ventral premotor cortex. Dual channel imaging was conducted using a Leica TCS SPE laser scanning confocal microscope with 488 nm and 546 nm laser under 63x/1.4 N.A. oil objective lens at a resolution of 0.04*0.04*0.3μm. One apical dendrite and one basal dendrite of each filled cell were followed and scanned from base to tip. Confocal scanned images were montaged, and the dendritic segments were traced and reconstructed in Neurolucida 360 (RRID: SCR_016788; MBF Bioscience). The appositions of microglia (P2RY12/Iba-1+) on dendrites and dendritic spines were counted and categorized as contacts and neighboring. Contacts required overlap of saturated signal from the two channels, while neighboring was identified when the signal of two channels were adjacent and the distance was ~ 0.3μm to ~ 1μm. The traced dendrites with markers of microglial apposition were analyzed and exported using Neuroexplorer (v11.01, Microbrightfield). The density of appositions (# of appositions/total length of dendrite imaged) was calculated for each dendrite.

Zhou Y., Bhatt H., Mojica C.A., Xin H., Pessina M., Rosene D.L., Moore T.L, & Medalla M. (2023). Mesenchymal-Derived Extracellular Vesicles Enhance Microglia-mediated Synapse Remodeling after Cortical Injury in Rhesus Monkeys. Research Square.

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Hippocampal Dendritic Spine Density Analysis

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The captured images were coded, and an investigator blinded to the experimental conditions measured the numbers of spines per dendritic length using Zen Blue 2.5 (Zeiss, Oberkochen, Germany) and Neurolucida 360, version 2018.1.1 (MBF Bioscience, Williston, VT, USA). software, which provides an automatic unbiased quantitative 3D analysis of identified neurons [41 (link)]. The spine detection threshold was set an outer range of 2.5 μm, the minimal height was 0.3 μm, the sensitivity was 100%, and the minimum count was 10 voxels.
The spine density was analyzed in each hemisphere of each murine brain. Two hippocampal pyramidal cells, with soma located in the center of 150-μm corresponding sections, were selected for the analysis (24 neurons per experimental group). The spine density on a secondary oblique dendritic branch localized in the stratum radiatum of the CA1 hippocampal pyramidal neurons was also quantified.

Polis B., Srikanth K.D., Elliott E., Gil-Henn H, & Samson A.O. (2018). L-Norvaline Reverses Cognitive Decline and Synaptic Loss in a Murine Model of Alzheimer’s Disease. Neurotherapeutics, 15(4), 1036-1054.

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Imaging and Quantifying Adult Neurogenesis

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Whole dentate gyri of 3 coronal sections per animals (n = 5–6 animals/group) were imaged on a Nikon/Spectral Spinning Disk confocal microscope in mosaics using a 40× oil-immersion objective (NA 1.35), with a z-step of 0.5 μm. Four-channel mosaic images (.nd2) were deconvolved using Huygens professional v16.10 (Scientific Volume Imaging, The Netherlands) with iteration number set at 100, quality threshold at 0.001, signal to noise ratio at 15 for the 4 channels and converted in .tif for subsequent quantification in Neurolucida 360 (MBF Bioscience). Counting of BrdU+, DCX+, Ki67+, BrdU/Ki67+ and BrdU/Ki67/DCX+ cells was performed by an experimenter blind to the treatment, averaged per animal and plot as mean ± SEM for each group. Density of counted cells was normalized to the volume of granular cell layer sampled in each group. Representative images were taken on a Olympus FV1200 confocal microscope using a 60× oil-objective (NA 1.35), x3.0 numerical zoom and 0.5 z-step.

Belmer A., Patkar O.L., Lanoue V, & Bartlett S.E. (2018). 5-HT1A receptor-dependent modulation of emotional and neurogenic deficits elicited by prolonged consumption of alcohol. Scientific Reports, 8, 2099.

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Dendritic Spine Analysis in HSV-GFP Mice

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See Supplementary Methods for details. Briefly, animals were transcardially
perfused three days after HSV-GFP injections, and tissue was processed for
immunohistochemical detection of GFP. Z-stack projections were acquired on a
laser-scanning confocal microscope, and dendritic branches were
three-dimensional-reconstructed using Neurolucida 360 (version 2017.01.1; MBF
Biosciences, Williston, VT). Automatic classification of spine type (thin,
stubby, and mushroom type) was based on established parameters.^{28 (link)} Data are presented as number of spines per 10 µm of dendrite segment.

Wright K.N., Hagarty D.P., Strong C.E., Schoepfer K.J, & Kabbaj M. (2019). Sex-Dependent Ketamine Addiction-Like Behavior Profile Following Exposure to Chronic Mild Stress. Chronic Stress, 3, 2470547019832613.

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