Journal: Frontiers in Neuroanatomy

Article Title: Neuronize: a tool for building realistic neuronal cell morphologies

doi: 10.3389/fnana.2013.00015

Figure Lengend Snippet: (A) Confocal microscopy image of an intracellularly injected layer III pyramidal neuron of the human cingulate cortex. (B) High magnification image showing basal dendrites and spines (inset). (C) Computer-aided tracing in 3D (Neurolucida) of the neuron shown in (A) . (D) Same image illustrated in (B) showing a superimposed 3D tracing of the positions of the dendritic spines. (E) Digital representation of the pyramidal neuron shown in (A) and (C) . Left: the neuron definition where each row represents a morphological point (identifier, type of point, (X,Y,Z) coordinates, radius at that point, and parent identifier). Right: depiction of the morphological skeleton defined on the left. Scale bar in (D) : 50 μm in (A) , 10 μm in ( B, D ) (4.5 μm inset).

Article Snippet: Data points of neuron morphology were extracted using Neurolucida Confocal package (MicroBrightField; Figures ).

Techniques: Confocal Microscopy, Injection

Journal: Frontiers in Neuroanatomy

Article Title: Neuronize: a tool for building realistic neuronal cell morphologies

doi: 10.3389/fnana.2013.00015

Figure Lengend Snippet: Comparison of the same neuron using different 3D representations . Models generated using NeuroConstruct (A,D) , Neurolucida (B,E) and our proposed method (C,F) . Note the unconnected elements and the absence of a realistic soma in (A,B). (D–F) Close-up view of the same bifurcation with the three different technologies.

Article Snippet: Data points of neuron morphology were extracted using Neurolucida Confocal package (MicroBrightField; Figures ).

Techniques: Comparison, Generated

Journal: The Journal of Neuroscience

Article Title: Tumor Necrosis Factor α But Not Interleukin 1β Mediates Neuroprotection in Response to Acute Nitric Oxide Excitotoxicity

doi: 10.1523/JNEUROSCI.4032-05.2006

Figure Lengend Snippet: Three-dimensional representation of the volume of neuronal cell death, as measured by FJB-positive staining in wild-type (WT), IL-1β, TNF-α, and IL-1β/TNF-α double (Dbl) KO mice killed 4 d after an intraparenchymal injection of the excitotoxin SNP. A, These 3D reconstructions of FJB-positive regions were performed using a C-80 Nikon microscope and super-high-pressure mercury lamp (Nikon) fitted with a Retiga EXi Fast digital camera (QImaging) feeding to a Precision 660 workstation (Dell Computer). The FJB-positive regions were traced on a Wacom pen tablet using the Neurolucida stereological software package (version 6.02.1; MicroBrightField), and 3D reconstruction and volume determination were compiled using Neuroexplorer software (version 4.01.1; MicroBrightField). Please note the larger volumes of FJB in the TNF and Dbl KO animals compared with that of wild-type and IL-1 KO mice. B, Quantitative analysis of the FJB volume in the brains of wild-type, IL-1, TNF, and Dbl KO mice over time. Please note the rapid appearance of neuronal cell death 6 h after SNP injection and the marked spread of FJB staining (**p < 0.01 compared with wild type and IL-1 KO; data presented as mean ± SEM) in the CNS of TNF and Dbl KO 4 d after the single SNP infusion. For photomicrographs of the FJB staining, refer to Figures ​Figures11 and ​and88.

Article Snippet: The FJB-positive regions were traced on a Wacom (Vancouver, WA) pen tablet using the Neurolucida stereological software package (version 6.02.1; MicroBrightField, Williston, VT), and three-dimensional (3D) reconstruction and volume determination were compiled using Neuroexplorer software (version 4.01.1; MicroBrightField).

Techniques: Staining, Injection, Microscopy, Software

Journal: Nature Communications

Article Title: An injectable hydrogel enhances tissue repair after spinal cord injury by promoting extracellular matrix remodeling

doi: 10.1038/s41467-017-00583-8

Figure Lengend Snippet: MMP-9 mediates fibrotic ECM remodeling. a Gelatinase activity of MMP-9 and MMP-2 in the PBS ( N = 5) and the I-5 group ( N = 4) examined by zymography. b , c Graphs showing quantification of MMP-2 ( b ) and MMP-9 ( c ) activity. ** indicates p < 0.01 by two-tailed Student’s t -test. Error bars represent the SEM. d , e Representative images of transverse spinal cord sections from animals injected with either PBS ( d ) or I-5 ( e ). Asterisks indicate cystic cavities. A yellow dotted line indicates the boundary of the FN-rich matrix. The boxed regions in the middle panels were magnified in dʹ, eʹ. Scale bars represent 100 µm. f MMP-9 immunoreactive granules were bounded by CD11b positive membrane-like circular structures. Scale bars represent 50 µm. g , j Representative images of transverse spinal cord sections stained with eriochrome cyanine and eosin from animals with I-5 mixed with non-targeting control siRNA (NC) ( g ) or MMP-9 siRNA ( j ). Adjacent sections were stained with antibodies against FN ( h , k ). Scale bars represent 200 μm. i , l 3D reconstruction of the spinal cord tissue using the Neurolucida software. Scale bars represent 1 mm. Asterisks indicate cystic cavities. m Quantification graph of cavity volume. ** indicates p < 0.01 by two-tailed Student’s t -test. N = 5 for each group. Error bars represent the SEM

Article Snippet: Three-dimensional reconstruction of the lesion cavity was done using the Neurolucida tracing software equipped with the 3D Slide Scanning Module (MBF bioscience).

Techniques: Activity Assay, Zymography, Two Tailed Test, Injection, Membrane, Staining, Control, Software

Journal: Nature Communications

Article Title: An injectable hydrogel enhances tissue repair after spinal cord injury by promoting extracellular matrix remodeling

doi: 10.1038/s41467-017-00583-8

Figure Lengend Snippet: Interaction between macrophages and I-5 hydrogel. a Representative images of Nile Red fluorescence in a macrophage cell line. Cultured macrophages were treated with Nile Red (NR) alone or nanoparticles consisting of NR and either CP-2 or I-5. In addition, JNJ7777120, a histamine receptor 4 inhibitor, or mepyramine maleate, a histamine receptor 1 inhibitor, was added to the culture medium 30 min before treatment with I-5 polymer nanoparticles. Scale bar represents 50 µm. b Graph showing quantification of NR fluorescence intensity. *** indicates p < 0.001 by one-way ANOVA followed by Tukey’s post hoc analysis. N = 4 replicate experiments per group. Error bars represent the SEM. c , d Representative images of transverse spinal cord sections from animals injected with CP-2 hydrogel lacking the imidazole group. c Eriochrome cyanine and eosin staining revealed prominent cystic cavities (*) at the center of the lesion ( c ). d FN staining showed a smaller area of FN-rich matrix. Scale bars represent 200 μm. e 3D reconstruction of the spinal cord tissue from an animal injected with CP-2 hydrogel using the Neurolucida software. Scale bar represents 1 mm. f Graph showing the quantification of the cavity volumes. The data set for the I-5 group was the same as the one used in Fig. . ** indicates p < 0.01 by two-tailed Student’s t -test. N = 8 for the I-5 group and N = 5 for the CP-2 group. Error bars represent the SEM

Article Snippet: Three-dimensional reconstruction of the lesion cavity was done using the Neurolucida tracing software equipped with the 3D Slide Scanning Module (MBF bioscience).

Techniques: Fluorescence, Cell Culture, Polymer, Injection, Staining, Software, Two Tailed Test