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Automatic dendrite spines detection from x-ray tomography volumes
2013
2013 IEEE 10th International Symposium on Biomedical Imaging
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We consider the problem of dendritic spine detection from X-ray micro-tomographic volumes that allow huge volume of tissue visualization. ...
To compensate for the noise in data that induces false positives in the spine detection process, we first segment the dendrites. ...
In this paper, we consider an alternative imaging protocol, namely the X-rays micro-tomography (XRMT). ...
doi:10.1109/isbi.2013.6556505
dblp:conf/isbi/DescombesMFNM13
fatcat:3g3qrnhuwzakhg3bcrvononbdq
Synchrotron radiation micro-tomography for high-resolution neurovascular network morphology investigation
2019
Journal of Synchrotron Radiation
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Synchrotron radiation X-ray imaging, which has emerged as a cutting-edge imaging technology with a high spatial resolution, provides a novel platform for the non-destructive imaging of microvasculature ...
When coupled with computed tomography, this technique allows the characterization of the 3D morphology of vasculature. ...
The variations in refractive index deviate the X-rays at angles that can be detected by adjusting the detector at a certain distance from the object. ...
doi:10.1107/s1600577519003060
pmid:31074423
fatcat:zzzdbhbhnncexaw7iol74vjmme
Front Matter: Volume 10578
2018
Medical Imaging 2018: Biomedical Applications in Molecular, Structural, and Functional Imaging
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outlier detection using hidden Markov model for cerebellar lobule segmentation 10578 0E Segmentation and assessment of structural plasticity of hippocampal dendritic spines from 3D confocal light microscopy ...
bioluminescence tomography [10578-33]
10578 0Z
Dynamic cone beam x-ray luminescence computed tomography with principal component
analysis [10578-34]
10578 10
A fast reconstruction algorithm for ...
doi:10.1117/12.2323952
fatcat:om4wezsn3vgr7mebecadzuy5ly
Imaging of Big and Messy Biological Structures Using Electron Tomography
2003
Microscopy Today
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cryomicroscopy and X-ray crystallography (5) . ...
These thicker sections have been used to measure dendritic spines In neuronal spiny dendrites (as seen in Figure 2C -E). ...
doi:10.1017/s1551929500053001
fatcat:bsklooqcxzfr5cqzddh3223v7a
Direct Visualization of Actin Filaments and Actin-Binding Proteins in Neuronal Cells
2020
Frontiers in Cell and Developmental Biology
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In dendrites, actin and ABPs are related to filopodia attenuation, spine formation, and synapse plasticity. ...
ABP phosphorylation or mutation changes ABP–actin binding, which regulates axon or dendritic plasticity. ...
X-ray crystallography gives highquality images of structures, but it is difficult to make crystals. ...
doi:10.3389/fcell.2020.588556
pmid:33324645
pmcid:PMC7726226
fatcat:b7h3n473ifhblgi6yrhmonyapa
Evaluation of different heavy-metal stains and embedding media for phase contrast tomography of neuronal tissue
2019
Developments in X-Ray Tomography XII
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In the present work, we evaluate and compare the contrast and resolution obtained on neuronal tissues, i.e. human and mouse cerebellar tissue, with propagation-based x-ray phase-contrast computed tomography ...
At this dedicated endstation developed and operated by our group, we utilize x-ray waveguide optics for high-resolution cone-beam scans at strong geometrical magnification. ...
X-ray phase-contrast tomography scans were recorded with 1001 angular positions at an acquisition time of 50s. ...
doi:10.1117/12.2528432
fatcat:ggv42kqw2jahlgxugwcbduqoki
Life Inside a Thin Section: Tomography
2008
Journal of Neuroscience
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We received invaluable help from David Mastronarde with reconstruction methods, and Maria Aronova tested the SIRT method. ...
Although typical of those used for tomography, through a dendritic spine from hippocampal culture prepared by freeze-substitution. Fine structural details are obscured by overlap within the section. ...
from high-resolution x-ray crystallography or NMR can be combined to estimate the size of PSD-95 (Doyle et al., 1996; McGee et al., 2001; Long et al., 2003) . ...
doi:10.1523/jneurosci.2992-08.2008
pmid:18799665
pmcid:PMC2716091
fatcat:pok7wgvubbby3etwfipt5p42ti
Automated and Accurate Detection of Soma Location and Surface Morphology in Large-Scale 3D Neuron Images
2013
PLoS ONE
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For the soma surface detection algorithm, the overlap of the volumes created by automatic detection of soma surfaces and manually segmenting soma volumes was more than 84% for 89% of all correctly detected ...
The method for soma surface detection will serve as a valuable tool for systematic studies of neuron types based on neuron structure. ...
In Rayburst Sampling, the spine surface is detected by casting discrete rays from a certain point inside the spine. ...
doi:10.1371/journal.pone.0062579
pmid:23638117
pmcid:PMC3634810
fatcat:yltxalpjfzdonn6odeht5aa2om
Synaptic Specializations of Melanopsin-Retinal Ganglion Cells in Multiple Brain Regions Revealed by Genetic Label for Light and Electron Microscopy
2019
Cell Reports
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A network of dendro-dendritic chemical synapses (DDCSs) was also revealed in the SCN, with ipRGC axon terminals preferentially synapsing on the DDCS-linked cells. ...
We also received support from NIH R01GM086197. We thank Dr. ...
This labeling strategy was also aided by combining X-ray micro-computed tomography (microCT) to "visualize" a larger sample, enabling selection of a sub-region with suitable staining and location for subsequent ...
doi:10.1016/j.celrep.2019.09.006
pmid:31618632
pmcid:PMC7045601
fatcat:xvrskbagbvf6horpfcaep33zae
A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy
2016
IEEE Journal on Selected Topics in Signal Processing
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microscopy (TXM), scanning transmission X-ray microscopy (STXM), scanning photoelectron microscopy, micro-X-ray fluorescence, synchrotron radiation X-ray tomographic microscopy (SRXTM), etc. ...
Spine detection is often performed after detecting the dendritic branch, since spines are attached to the filaments. ...
He is the recipient of several international prizes including three IEEE-SPS Best Paper Awards and two Technical Achievement Awards from the IEEE (2008 SPS and EMBS 2010). ...
doi:10.1109/jstsp.2015.2505402
fatcat:fgbrxtuhsfbobluogllqll6q2e
Unraveling Brain Microcircuits, Dendritic Spines, and Synaptic Processing Using Multiple Complementary Approaches
2022
Frontiers in Physiology
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C., Xia, X., Li, X., et al. (2014). Integration of multi scale dendritic spine structure and function data into systems biology models. Front. ...
R., Bhat, A., Ray, B., Mahalakshmi, A. M., et al. (2019). Dendritic spines: revisiting the physiological role. Prog. Neuropsychopharmacol. Biol. ...
doi:10.3389/fphys.2022.831568
pmid:35295578
pmcid:PMC8918670
fatcat:6prvq2eqk5dqdlpwxeuhhl56ku
High-resolution whole-brain staining for electron microscopic circuit reconstruction
2015
Nature Methods
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Using serial block-face electron microscopy (SBEM), we tested human annotator ability to follow neural 'wires' reliably and over long distances as well as the ability to detect synaptic contacts. ...
X-ray microCT imaging. ...
X-rays from a microfocus X-ray source were passed through the epoxy-embedded BROPA-prepared brain, and projections were collected by a high-resolution chargecoupled device (CCD) detector. ...
doi:10.1038/nmeth.3361
pmid:25867849
fatcat:gttvrut2rvhcrenxb7t53tij7a
Advances in Light Microscopy for Neuroscience
2009
Annual Review of Neuroscience
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Downloaded from arjournals.annualreviews.org by Stanford University -Main Campus -Robert Crown Law Library on 06/26/09. For personal use only. ...
Other progress permits functional imaging at faster speeds, at greater depths in brain tissue, and over larger tissue volumes than previously possible. ...
ACKNOWLEDGMENTS This review greatly benefited from critical feedback on portions of the text and contributions of images generously provided by many neuroscientists and microscopists. ...
doi:10.1146/annurev.neuro.051508.135540
pmid:19555292
pmcid:PMC2820375
fatcat:iihdajrrmramtibudjt66tvroe
Digital reconstruction of the cell body in dense neural circuits using a spherical-coordinated variational model
2014
Scientific Reports
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However, automatic reconstruction of the dense neural connections from microscopic image still remains a challenge. ...
the volumetric images in the spherical coordinate system, the reconstruction of somas with variational model is no longer sensitive to the interference of the complicated neuronal morphology, and could automatically ...
, and even spines. ...
doi:10.1038/srep04970
pmid:24829141
pmcid:PMC4021323
fatcat:u4b6ktdvbrdmlneqf3dvimsshm
Imaging and Structural Informatics
[chapter]
2006
Health Informatics Series
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(A) Front view; (B) side view; (C) detail on dendritic branches; (D) detail on dendritic spines. ...
We produce a typical X-ray image by projecting an X-ray beamone form of ionizing radiation-from an X-ray source through a patient's body (or other object) and onto an X-ray-sensitive film. ...
The resulting dendritic models capture a large set of dendritic morphologic classes from only a small set of variables. ...
doi:10.1007/0-387-36278-9_9
fatcat:qvv7drjnirfszb4iqbyfozuzyi
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