scholarly journals Neuronal morphology and projection analysis by multispectral tracing in densely labeled mouse brain

2017 ◽  
Author(s):  
Douglas H. Roossien ◽  
John M. Webb ◽  
Benjamin V. Sadis ◽  
Yan Yan ◽  
Lia Y. Min ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Long Range ◽  
Mouse Brain ◽  
Cell Morphology ◽  
Brain Function ◽  
Neuronal Morphology ◽  
Neuronal Populations ◽  
Sparse Labeling ◽  
Projection Analysis ◽  
Imagej Plugin

AbstractAccurate and complete neuronal wiring diagrams are necessary for understanding brain function at many scales from long-range interregional projections to microcircuits. Traditionally, light microscopy-based anatomical reconstructions use monochromatic labeling and therefore necessitate sparse labeling to eliminate tracing ambiguity between intermingled neurons. Consequently, our knowledge of neuronal morphology has largely been based on averaged estimations across many samples. Recently developed second-generation Brainbow tools promise to circumvent this limitation by revealing fine anatomical details of many unambiguously identifiable neurons in densely labeled samples. Yet, a means to quantify and analyze the information is currently lacking. Therefore, we developed nTracer, an ImageJ plugin capable of rapidly and accurately reconstructing whole-cell morphology of large neuronal populations in densely labeled brains.

scholarly journals Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain

2019 ◽  
Author(s):  
Johan Winnubst ◽  
Erhan Bas ◽  
Tiago A. Ferreira ◽  
Zhuhao Wu ◽  
Michael N. Economo ◽  
...  
Keyword(s):  
Long Range ◽  
Mouse Brain ◽  
Neuronal Cell ◽  
Cell Types ◽  
Neuronal Morphology ◽  
Projection Neurons ◽  
Axonal Arbor ◽  
Flow Of Information ◽  
Organizational Principles ◽  
The Brain

SummaryNeuronal cell types are the nodes of neural circuits that determine the flow of information within the brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of cell type and reveals how individual neurons route their output across the brain. Despite the importance of morphology, few projection neurons in the mouse brain have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the brain. We used this platform to reconstruct more than 1,000 projection neurons in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed neurons comprise more than 75 meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of projection neurons and suggest organizational principles of long-range connectivity.

High-Resolution Fiber and Fiber Tract Imaging Using Polarized Light Microscopy in the Human, Monkey, Rat, and Mouse Brain

2016 ◽  
pp. 369-389 ◽  
Author(s):  
Karl Zilles ◽  
Nicola Palomero-Gallagher ◽  
David Gräßel ◽  
Philipp Schlömer ◽  
Markus Cremer ◽  
...  
Keyword(s):  
High Resolution ◽  
Light Microscopy ◽  
Mouse Brain ◽  
Polarized Light ◽  
Polarized Light Microscopy ◽  
Fiber Tract

scholarly journals Rapid Reconstruction of 3D Neuronal Morphology from Light Microscopy Images with Augmented Rayburst Sampling

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e84557 ◽  
Author(s):  
Xing Ming ◽  
Anan Li ◽  
Jingpeng Wu ◽  
Cheng Yan ◽  
Wenxiang Ding ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Neuronal Morphology ◽  
Microscopy Images

scholarly journals Imaging Sterols and Oxysterols in Mouse Brain Reveals Distinct Spatial Cholesterol Metabolism

2018 ◽  
Author(s):  
Eylan Yutuc ◽  
Roberto Angelini ◽  
Mark Baumert ◽  
Natalia Mast ◽  
Irina Pikuleva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mouse Brain ◽  
Brain Function ◽  
Mass Spectrometry Imaging ◽  
Cholesterol Metabolism ◽  
Biologically Active ◽  
Wild Type ◽  
Tissue Slices ◽  
The Brain

AbstractDysregulated cholesterol metabolism is implicated in a number of neurological disorders. Many sterols, including cholesterol and its precursors and metabolites, are biologically active and important for proper brain function. However, spatial cholesterol metabolism in brain and the resulting sterol distributions are poorly defined. To better understand cholesterol metabolism in situ across the complex functional regions of brain, we have developed on-tissue enzyme-assisted derivatisation in combination with micro-liquid-extraction for surface analysis and liquid chromatography - mass spectrometry to image sterols in tissue slices (10 µm) of mouse brain. The method provides sterolomic analysis at 400 µm spot diameter with a limit of quantification of 0.01 ng/mm2. It overcomes the limitations of previous mass spectrometry imaging techniques in analysis of low abundance and difficult to ionise sterol molecules, allowing isomer differentiation and structure identification. Here we demonstrate the spatial distribution and quantification of multiple sterols involved in cholesterol metabolic pathways in wild type and cholesterol 24S-hydroxylase knock-out mouse brain. The technology described provides a powerful tool for future studies of spatial cholesterol metabolism in healthy and diseased tissues.SignificanceThe brain is a remarkably complex organ and cholesterol homeostasis underpins brain function. It is known that cholesterol is not evenly distributed across different brain regions, however, the precise map of cholesterol metabolism in the brain remains unclear. If cholesterol metabolism is to be correlated with brain function it is essential to generate such a map. Here we describe an advanced mass spectrometry imaging platform to reveal spatial cholesterol metabolism in situ at 400 µm resolution on 10 µm tissue slices from mouse brain. We mapped, not only cholesterol, but also other biologically active sterols arising from cholesterol turnover in both wild type and mice lacking cholesterol 24-hydroxylase (Cyp46a1), the major cholesterol metabolising enzyme.

scholarly journals Light microscopy based approach for mapping connectivity with molecular specificity

2020 ◽  
Author(s):  
Fred Y. Shen ◽  
Margaret M. Harrington ◽  
Logan A. Walker ◽  
Hon Pong Jimmy Cheng ◽  
Edward S. Boyden ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Brain Function ◽  
Inhibitory Neuron ◽  
Cell Types ◽  
Synaptic Connections ◽  
Connectivity Analysis ◽  
Brain Section ◽  
Molecular Specificity ◽  
Molecular Information ◽  
Genetic Labeling

AbstractMapping neuroanatomy is a foundational goal towards understanding brain function. Electron microscopy (EM) has been the gold standard for connectivity analysis because nanoscale resolution is necessary to unambiguously resolve chemical and electrical synapses. However, molecular information that specifies cell types is often lost in EM reconstructions. To address this, we devised a light microscopy approach for connectivity analysis of defined cell types called spectral connectomics. We combined multicolor genetic labeling (Brainbow) of neurons with a multi-round immunostaining Expansion Microscopy (miriEx) strategy to simultaneously interrogate morphology, molecular markers, and connectivity in the same brain section. We applied our multimodal profiling strategy to directly link inhibitory neuron cell types with their network morphologies. Furthermore, we showed that correlative Brainbow and endogenous synaptic machinery immunostaining can be used to define putative synaptic connections between spectrally unique neurons, as well as map putative inhibitory and excitatory inputs. We envision that spectral connectomics can be applied routinely in neurobiology labs to gain insights into normal and pathophysiological neuroanatomy across multiple animals and time points.

scholarly journals Multispectral tracing in densely labeled mouse brain with nTracer

2019 ◽  
Vol 35 (18) ◽  
pp. 3544-3546 ◽  
Author(s):  
Douglas H Roossien ◽  
Benjamin V Sadis ◽  
Yan Yan ◽  
John M Webb ◽  
Lia Y Min ◽  
...  
Keyword(s):  
Image Processing ◽  
Cell Morphology ◽  
Supplementary Information ◽  
Source Image ◽  
Supplementary Data ◽  
Tissue Samples ◽  
Neuronal Populations ◽  
Processing Software ◽  
Image Processing Software ◽  
Automated Tracing

Abstract Summary This note describes nTracer, an ImageJ plug-in for user-guided, semi-automated tracing of multispectral fluorescent tissue samples. This approach allows for rapid and accurate reconstruction of whole cell morphology of large neuronal populations in densely labeled brains. Availability and implementation nTracer was written as a plug-in for the open source image processing software ImageJ. The software, instructional documentation, tutorial videos, sample image and sample tracing results are available at https://www.cai-lab.org/ntracer-tutorial. Supplementary information Supplementary data are available at Bioinformatics online.

Three-dimensional inversion recovery manganese-enhanced MRI of mouse brain using super-resolution reconstruction to visualize nuclei involved in higher brain function

2014 ◽  
Vol 27 (7) ◽  
pp. 749-759 ◽  
Author(s):  
Dana S. Poole ◽  
Esben Plenge ◽  
Dirk H. J. Poot ◽  
Egbert A. J. F. Lakke ◽  
Wiro J. Niessen ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Brain Function ◽  
Three Dimensional ◽  
Super Resolution ◽  
Inversion Recovery ◽  
Enhanced Mri ◽  
Manganese Enhanced Mri

L23 Effects of peripheral (co-)administration of liraglutide and ghrelin in the R6/2 mouse brain function

2016 ◽  
Vol 87 (Suppl 1) ◽  
pp. A98.1-A98
Author(s):  
Ana I Duarte ◽  
Marie Sjögren ◽  
Maria S Santos ◽  
Catarina R Oliveira ◽  
Paula I Moreira ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Brain Function
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