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Automatic dendrite spines detection from x-ray tomography volumes

Xavier Descombes, Gregoire Malandain, Caroline Fonta, Lazlo Negyessy, Rajmund Mosko
2013 2013 IEEE 10th International Symposium on Biomedical Imaging  
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

Yong Cao, Mengqi Zhang, Hui Ding, Zhuohui Chen, Bin Tang, Tianding Wu, Bo Xiao, Chunyue Duan, Shuangfei Ni, Liyuan Jiang, Zixiang Luo, Chengjun Li (+7 others)
2019 Journal of Synchrotron Radiation  
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

Barjor Gimi, Andrzej Krol
2018 Medical Imaging 2018: Biomedical Applications in Molecular, Structural, and Functional Imaging  
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

Gina E. Sosinsky, Maryann E. Martone
2003 Microscopy Today  
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

Minkyo Jung, Doory Kim, Ji Young Mun
2020 Frontiers in Cell and Developmental Biology  
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

Marina Eckermann, Mareike Töpperwien, Torben Ruhwedel, Wiebke Möbius, Tim Salditt, Bert Müller, Ge Wang
2019 Developments in X-Ray Tomography XII  
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

X. Chen, C. A. Winters, T. S. Reese
2008 Journal of Neuroscience  
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

Cheng Yan, Anan Li, Bin Zhang, Wenxiang Ding, Qingming Luo, Hui Gong, Giorgio F. Gilestro
2013 PLoS ONE  
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

Keun-Young Kim, Luis C. Rios, Hiep Le, Alex J. Perez, Sébastien Phan, Eric A. Bushong, Thomas J. Deerinck, Yu Hsin Liu, Maya A. Ellisman, Varda Lev-Ram, Suyeon Ju, Sneha A. Panda (+6 others)
2019 Cell Reports  
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

Charles Kervrann, Carlos Oscar Sanchez Sorzano, Scott T. Acton, Jean-Christophe Olivo-Marin, Michael Unser
2016 IEEE Journal on Selected Topics in Signal Processing  
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

Alberto A. Rasia-Filho
2022 Frontiers in Physiology  
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

Shawn Mikula, Winfried Denk
2015 Nature Methods  
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

Brian A. Wilt, Laurie D. Burns, Eric Tatt Wei Ho, Kunal K. Ghosh, Eran A. Mukamel, Mark J. Schnitzer
2009 Annual Review of Neuroscience  
Downloaded from 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

Tingwei Quan, Jing Li, Hang Zhou, Shiwei Li, Ting Zheng, Zhongqing Yang, Qingming Luo, Hui Gong, Shaoqun Zeng
2014 Scientific Reports  
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]

James F. Brinkley, Robert A. Greenes
2006 Health Informatics Series  
(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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