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Neurolucida software

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Neurolucida is a software application designed for three-dimensional reconstruction and analysis of neuroanatomical structures. It provides tools for tracing and digitizing microscopic images, allowing users to create detailed models of neurons, blood vessels, and other biological features.

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Lab products found in correlation

Neuroexplorer, by MicroBrightField (11 mentions) Fd rapid golgistain kit, by FD NeuroTechnologies (11 mentions) Neuroexplorer software, by MicroBrightField (10 mentions) Bx51 microscope, by Olympus (5 mentions) Neurolucida explorer, by MicroBrightField (4 mentions) Stereoinvestigator system, by MicroBrightField (4 mentions) Hematoxylin, by Bio-Optica (3 mentions) Eukitt, by Bio-Optica (3 mentions) Bv61 microscopy, by Olympus (3 mentions) Vibratome, by Leica camera (3 mentions) E800 microscope, by Nikon (3 mentions) Cryostat, by Leica camera (2 mentions) Vt1000s vibrating microtome, by Leica camera (2 mentions) Abc kit, by Vector Laboratories (2 mentions) Ds u3 camera, by Nikon (2 mentions) Vt1200, by Leica camera (2 mentions) Bx 51 upright light microscope, by Olympus (2 mentions) Eclipse ci l microscope, by Nikon (2 mentions) Bz9000 bright field microscopic, by Keyence (2 mentions) Axioplan 2, by Zeiss (2 mentions)

112 protocols using neurolucida software

1

Golgi-Cox Staining and 3D Neuron Analysis

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Animals were transcardially perfused with 0.9% saline under deep pentobarbital anesthesia and processed as described previously.23 (link) In summary, brains were immersed in Golgi–Cox solution24 (link) for 14 days, processed and cut on a vibratome at 200 μm thick coronal sections. For each selected neuron, all branches of the dendritic tree were reconstructed at × 1000 magnification, using a motorized microscope (Zeiss, Thornwood, NY, USA) attached to a camera (Sony, Tokyo, Japan) and Neurolucida software (Microbrightfield, Williston, VT, USA). A three-dimensional analysis of the reconstructed neurons was performed using NeuroExplorer software (Microbrightfield). Ten neurons were analyzed for each animal.
Soares-Cunha C., Coimbra B., Borges S., Carvalho M.M., Rodrigues A.J, & Sousa N. (2014). The motivational drive to natural rewards is modulated by prenatal glucocorticoid exposure. Translational Psychiatry, 4(6), e397-.
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2

Quantifying Microglial and Astrocytic Responses

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We used a computer-based tracing system (Neurolucida software, MicroBrightfield, Colchester, VT) (Niv et al., 2012 (link)) to trace and analyze dendrites and cell bodies of microglia and astrocytes in the peri-lesional APTw-hyperintense brain areas. We analyzed cell body area, cell volume, number of branches and trees, and total surface and length of dendrites for Iba1- and GFAP-positive cells on each immunofluorescence image under 40 × objective. We analyzed three to four cells per field from four fields per section and three sections per rat.
Wang W., Zhang H., Lee D.H., Yu J., Cheng T., Hong M., Jiang S., Fan H., Huang X., Zhou J, & Wang J. (2017). Using functional and molecular MRI techniques to detect neuroinflammation and neuroprotection after traumatic brain injury. Brain, behavior, and immunity, 64, 344-353.
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3

Analyzing Dendritic Elongation in Cultured Hippocampal Neurons

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Dendritic elongation of cultured hippocampal neurons was analyzed in accordance with a previous study [18 (link)]. Axons were identified by double immunostaining in terms of tau-positive (axonal marker) and MAP2-negative (dendritic marker), and only MAP2-positive neurites were defined as dendrites. Neurons that clearly had tau- or MAP2-positive neurites were selected randomly by an expert researcher who was blinded to the experimental groups. Dendrites were traced automatically with the same configuration using Neurolucida software (MicroBrightField, Williston, VT) and total dendritic length in a single neuron was calculated using Neuroexplorer (MicroBrightField). This assay was performed for three independent experiments.
Yamada S., Itoh N., Nagai T., Nakai T., Ibi D., Nakajima A., Nabeshima T, & Yamada K. (2018). Innate immune activation of astrocytes impairs neurodevelopment via upregulation of follistatin-like 1 and interferon-induced transmembrane protein 3. Journal of Neuroinflammation, 15, 295.
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4

Identifying PTEN Knockout Cells in Hippocampus

Cited 2 times
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Biocytin-filled cells were imaged using a Nikon A1Rsi inverted microscope (software RRID:SCR_014329) equipped with a 40× Plan Apo water immersion objective (NA=1.15; field size 317 × 317 μm; 0.5 μm z-step). Confocal z-series image stacks were imported to Neurolucida software (Microbrightfield Inc., RRID: SCR_001775) for whole cell tracing. Overlapping image stacks were three-dimensionally montaged into a single image for reconstruction. Reconstructions encoded soma area, dendritic length and branch points. Image stacks were also used to encode the location of the hilar-granule cell body layer border, the granule cell body layer-molecular layer border, and the location of the hippocampal fissure, as described in prior work (Santos et al. 2011 (link)). Since KO animals are mosaics, the blind patch approach yielded both PTEN KO and PTEN-expressing cells. Cells were categorized as either PTEN KO or PTEN-expressing only after reconstruction using soma area as a criterion. Cells with soma areas that exceeded two standard deviations of the control cell mean for biocytin-filled cells (107.8±18.3) were defined as KOs; and were not included in the present study. Cells below this size threshold were defined as PTEN-expressing for the current work. This criteria has been previously validated to distinguish >95% of KO cells from control cells (Santos et al. 2017 (link)).
LaSarge C.L., Pun R.Y., Gu Z., Santos V.R, & Danzer S.C. (2019). Impact of mTOR hyperactive neurons on the morphology and physiology of adjacent neurons: Do PTEN KO cells make bad neighbors?. Experimental neurology, 321, 113029.
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5

Golgi Staining and Neurolucida Analysis

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Golgi staining was performed on freshly dissected brains using a FD Rapid GolgiStain kit (FD NeuroTechnologies, Columbia, Maryland). Dendrites and dendritic spines in L6 of S1 were traced using Neurolucida software (MicroBrightField, Williston, Vermont).
Bruining H., Matsui A., Oguro-Ando A., Kahn R.S., Van't Spijker H.M., Akkermans G., Stiedl O., van Engeland H., Koopmans B., van Lith H.A., Oppelaar H., Tieland L., Nonkes L.J., Yagi T., Kaneko R., Burbach J.P., Yamamoto N, & Kas M.J. (2015). Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development. Biological psychiatry, 78(7).
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6

Histological Analysis of Skeletal Muscles

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For hematoxylin/eosin (H/E) staining, sections of fresh triceps and gastrocnemius muscles were sliced using the cryostat (Leica) in cross section at the thickness of 30 μm, and directly mounted on 4% gelatin-coated slides and air-dried overnight. Sections were then hydrated in distilled water, and stained firstly with hematoxylin, then with eosin (Bio-Optica), dehydrated in ascending series of ethanol (95–100%) and cleared in xylene (98.5%). Finally, sections were cover-slipped with Eukitt (Bio-Optica). The sections were drawn and analyzed by Neurolucida software (MicroBrightField Inc., Williston, VT, USA), and data were obtained by the associated data analysis software Neurolucida Explorer (MicroBrightField).
Schellino R., Besusso D., Parolisi R., Gómez-González G.B., Dallere S., Scaramuzza L., Ribodino M., Campus I., Conforti P., Parmar M., Boido M., Cattaneo E, & Buffo A. (2023). hESC-derived striatal progenitors grafted into a Huntington’s disease rat model support long-term functional motor recovery by differentiating, self-organizing and connecting into the lesioned striatum. Stem Cell Research & Therapy, 14, 189.
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7

Grafting and Muscle Morphology Analysis

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Grafted cell body area and Feret’s diameter were measured on HuNu/DARPP32-positive cells, on confocal images using ImageJ software. 30 human striatal cells per animal per group were analyzed, and the average values calculated. The distance between HuNu+ grafted cells was measured by the nearest neighbor distance calculation on ImageJ. About 150 measurements were evaluated for each group.
After H/E staining, gastrocnemius and triceps muscles were morphologically evaluated in terms of mean fiber area and Feret’s diameter, by drawing the section with Neurolucida software (MicroBrightField Inc., Williston, VT, USA), and data were obtained by the associated data analysis software NeuroExplorer (MicroBrightField). More than 100 fibers were drawn and analyzed for each animal of each group (sham and transplanted animals maintained in SE or EE); we then averaged the means obtained from a single animal. Both contralesional and ipsilesional muscles were analyzed.
Schellino R., Besusso D., Parolisi R., Gómez-González G.B., Dallere S., Scaramuzza L., Ribodino M., Campus I., Conforti P., Parmar M., Boido M., Cattaneo E, & Buffo A. (2023). hESC-derived striatal progenitors grafted into a Huntington’s disease rat model support long-term functional motor recovery by differentiating, self-organizing and connecting into the lesioned striatum. Stem Cell Research & Therapy, 14, 189.
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8

Grafting and Muscle Morphology Analysis

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Grafted cell body area and Feret’s diameter were measured on HuNu/DARPP32-positive cells, on confocal images using ImageJ software. 30 human striatal cells per animal per group were analyzed, and the average values calculated. The distance between HuNu+ grafted cells was measured by the nearest neighbor distance calculation on ImageJ. About 150 measurements were evaluated for each group.
After H/E staining, gastrocnemius and triceps muscles were morphologically evaluated in terms of mean fiber area and Feret’s diameter, by drawing the section with Neurolucida software (MicroBrightField Inc., Williston, VT, USA), and data were obtained by the associated data analysis software NeuroExplorer (MicroBrightField). More than 100 fibers were drawn and analyzed for each animal of each group (sham and transplanted animals maintained in SE or EE); we then averaged the means obtained from a single animal. Both contralesional and ipsilesional muscles were analyzed.
Schellino R., Besusso D., Parolisi R., Gómez-González G.B., Dallere S., Scaramuzza L., Ribodino M., Campus I., Conforti P., Parmar M., Boido M., Cattaneo E, & Buffo A. (2023). hESC-derived striatal progenitors grafted into a Huntington’s disease rat model support long-term functional motor recovery by differentiating, self-organizing and connecting into the lesioned striatum. Stem Cell Research & Therapy, 14, 189.
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9

Histological Analysis of Skeletal Muscles

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For hematoxylin/eosin (H/E) staining, sections of fresh triceps and gastrocnemius muscles were sliced using the cryostat (Leica) in cross section at the thickness of 30 μm, and directly mounted on 4% gelatin-coated slides and air-dried overnight. Sections were then hydrated in distilled water, and stained firstly with hematoxylin, then with eosin (Bio-Optica), dehydrated in ascending series of ethanol (95–100%) and cleared in xylene (98.5%). Finally, sections were cover-slipped with Eukitt (Bio-Optica). The sections were drawn and analyzed by Neurolucida software (MicroBrightField Inc., Williston, VT, USA), and data were obtained by the associated data analysis software Neurolucida Explorer (MicroBrightField).
Schellino R., Besusso D., Parolisi R., Gómez-González G.B., Dallere S., Scaramuzza L., Ribodino M., Campus I., Conforti P., Parmar M., Boido M., Cattaneo E, & Buffo A. (2023). hESC-derived striatal progenitors grafted into a Huntington’s disease rat model support long-term functional motor recovery by differentiating, self-organizing and connecting into the lesioned striatum. Stem Cell Research & Therapy, 14, 189.
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10

Retroviral Tracing and Dendritic Analysis

Cited 4 times
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Retrovirus production was performed as described previously [26 (link)–29 (link), 32 (link), 34 (link)]. In vivo retroviral grating was performed based on published methods with modifications [28 (link), 29 (link), 32 (link), 34 (link)]. Confocal imaging analysis was carried out as described [28 (link), 29 (link), 32 (link), 34 (link)]. 200-μm thick floating brain sections containing eGFP+ or RFP+ cells were selected. For dendritic branching analysis, fluorescent protein (FP)-positive (GFP+ or RFP+) cells were imaged on an ApoTome confocal with a 20x objective. The dendrites and the cell body of single expression of FP+ neurons were analyzed by Neurolucida software (MicroBrightField, Inc.). Roughly 30–50 neurons per DG were traced. Data were extracted for Scholl analysis, total dendritic length for each GFP+ neuron, and both GFP+ and RFP+ neurons.
Gao Y., Su J., Guo W., Polich E.D., Magyar D.P., Xing Y., Li H., Smrt R.D., Chang Q, & Zhao X. (2015). Inhibition of miR-15a promotes BDNF expression and rescues dendritic maturation deficits in MeCP2-deficient neurons. Stem cells (Dayton, Ohio), 33(5), 1618-1629.
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