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Internet-enabled high-resolution brain mapping and virtual microscopy

Shawn Mikula, Issac Trotts, James M. Stone, Edward G. Jones
2007 NeuroImage  
We describe a method utilizing virtual microscopy for generation of internet-enabled, high-resolution brain maps and atlases.  ...  Virtual microscopy involves the conversion of histological sections mounted on glass microscope slides to high-resolution digital images.  ...  Supported by Human Brain Project Grant Number MH60975 from the National Institutes of Health, United States Public Health Service.  ... 
doi:10.1016/j.neuroimage.2006.11.053 pmid:17229579 pmcid:PMC1890021 fatcat:zqfiqrp33zem3lgjswvfqjrb74 - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy

Shawn Mikula, James M Stone, Edward G Jones
2008 Brains is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate  ...  brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.  ...  For purposes of brain mapping, current virtual microscopy scanners achieve resolutions of digitized slides of more than 100,000 dpi, enabling the generation of brain atlases at microscopic resolutions  ... 
pmid:19129928 pmcid:PMC2614326 fatcat:hlhafljarnfzvbytrfqprtwdiu

Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas

Ji Ryang Chung, Chul Sung, David Mayerich, Jaerock Kwon, Daniel E. Miller, Todd Huffman, John Keyser, Louise C. Abbott, Yoonsuck Choe
2011 Frontiers in Neuroinformatics  
Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown  ...  (e.g., serial sectioning electron microscopy).  ... is an internet-enabled, high-resolution brain map (Mikula et al., 2007) .  ... 
doi:10.3389/fninf.2011.00029 pmid:22275895 pmcid:PMC3254184 fatcat:4amvlcja2fee3iavoukmihfo24

Integrating anatomy and function for zebrafish circuit analysis

Aristides B. Arrenberg, Wolfgang Driever
2013 Frontiers in Neural Circuits  
Due to its transparency, virtually every brain structure of the larval zebrafish is accessible to light-based interrogation of circuit function.  ...  To comprehensively understand circuit function, these functional maps need to be placed into the proper context of morphological features and projection patterns, neurotransmitter phenotypes, and key anatomical  ...  The authors are supported by the Excellence Initiative of the German Federal and State Governments (Centre for Biological Signalling Studies EXC 294, Wolfgang Driever) and the German Research Foundation  ... 
doi:10.3389/fncir.2013.00074 pmid:23630469 pmcid:PMC3632786 fatcat:bio4ejsirrgo3dl2ghx43bsboy

Online histological atlas of the Göttingen minipig brain

Dariusz Orlowski, Andreas N. Glud, Nicola Palomero-Gallagher, Jens Christian H. Sørensen, Carsten R. Bjarkam
2019 Heliyon  
One set was photographed in high resolution and labelled, the other set in low resolution (resized first set) was used for reference on the computer screen.  ...  allowed magnifying of the base image (low-resolution image) up to the maximum resolution of the high-resolution image.  ...  Bech and Mr. A. Meier.  ... 
doi:10.18154/rwth-conv-241766 fatcat:ig2z5xrzyngkvaqv2ccy4jkudq

Building retinal connectomes

Robert E Marc, Bryan W Jones, J. Scott Lauritzen, Carl B Watt, James R Anderson
2012 Current Opinion in Neurobiology  
References and annotations  ...  Acknowledgments We thank the National Institutes of Health (EY02576, EY015128, and EY014800), the National Science Foundation (0941717) , the Calvin and JeNeal Hatch Presidential Endowed Chair, and Research  ...  Internet-enabled high-resolution brain mapping and virtual microscopy. Neuroimage. 2007; 35:9-15. [PubMed: 17229579] 46. Curr Opin Neurobiol.  ... 
doi:10.1016/j.conb.2012.03.011 pmid:22498714 pmcid:PMC3415605 fatcat:ciigo2xprngqznvaq7rgpiwmw4

Visualization of image data from cells to organisms

Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider (+2 others)
2010 Nature Methods  
Second, the availability of high-throughput techniques enables experiments on a large scale, generating large sets of image data, and even though the readout of each single experiment may be easily visualized  ...  By their very nature, microscopy and magnetic resonance imaging (MRI) ( Fig. 1 and Boxes 1 and 2) are dependent on data visualization.  ...  Iterating this process and combining the acquired raw images yields a high-resolution image.  ... 
doi:10.1038/nmeth.1431 pmid:20195255 pmcid:PMC3650473 fatcat:b6nnwhe3t5fjnhxue3ghu4mjoy

Erratum: Visualization of image data from cells to organisms

Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider (+2 others)
2010 Nature Methods  
By their very nature, microscopy and magnetic resonance imaging (MRI) (Fig. 1 and Boxes 1 and 2) are dependent on data visualization.  ...  Advances in imaging techniques and high-throughput technologies are providing scientists with unprecedented possibilities to visualize internal structures of cells, organs and organisms and to collect  ...  Super-resolution fluorescence microscopy groups several recently developed methods in light microscopy capable of significantly increasing resolution and visualizing details at the nanometer scale.  ... 
doi:10.1038/nmeth0610-479a fatcat:mimxo5gqnrf6zpu2uhfh7iinxm

The OptIPuter: high-performance, QoS-guaranteed network service for emerging E-science applications

N. Taesombot, F. Uyeda, A.A. Chien, L. Smarr, T.A. DeFanti, P. Papadopoulos, J. Leigh, M. Ellisman, J. Orcutt
2006 IEEE Communications Magazine  
Emerging large-scale scientific applications have a critical need for high bandwidth and predictableperformance network service.  ...  These private optical paths are set up on-demand, and combined with end resources to form a Distributed Virtual Computer (DVC).  ...  from NIH/NCRR for the National Center for Microscopy and Imaging Research (P41RR004050) and BIRN (U24 RR019701).  ... 
doi:10.1109/mcom.2006.1637945 fatcat:uoxx42zccfeutbu3vmkisq7xmy

Stereo Pseudo 3D Rendering for Web-based Display of Scientific Volumetric Data [article]

Daniel Chern-Yeow Eng, Yoonsuck Choe
2008 International Workshop on Volume Graphics, Proceedings of the  
Advancement in high-throughput microscopy technology such as the Knife-Edge Scanning Microscopy (KESM) is enabling the production of massive amounts of high-resolution volumetric data of biological microstructures  ...  Google Maps and Google Maps-like interfaces such as allow users to pan and zoom 2D images efficiently.  ...  Mayerich, and J. Kwon for KESM data acquisition, and J. Keyser for valuable feedback.  ... 
doi:10.2312/vg/vg-pbg08/073-080 fatcat:mngnd7zxonbqxn3pconmqcn3vu

Visible rodent brain-wide networks at single-neuron resolution

Jing Yuan, Hui Gong, Anan Li, Xiangning Li, Shangbin Chen, Shaoqun Zeng, Qingming Luo
2015 Frontiers in Neuroanatomy  
of neuron and vessels and tracing long-distant circuit at axonal resolution in the whole brain of mammals.  ...  In this review, we summarize brain-wide optical tomography techniques, review the progress on visible brain neuronal/vascular networks benefit from these novel techniques, and prospect the future technical  ...  Acknowledgments We appreciate Jie Peng, Congdi Guo, Benyi Xiong and Hang Lu for image processing, Prof. Tonghui Xu for valuable discussion, and the financial supports from the Science  ... 
doi:10.3389/fnana.2015.00070 pmid:26074784 pmcid:PMC4446545 fatcat:ha7wxtug3nhzvbopailzptt5ju

Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics [article]

Adam H Marblestone, Evan R Daugharthy, Reza Kalhor, Ian D Peikon, Justus M Kebschull, Seth L Shipman, Yuriy Mishchenko, Je Hyuk Lee, David A Dalrymple, Bradley M Zamft, Konrad P Kording, Edward S Boyden (+2 others)
2013 bioRxiv   pre-print
An optical approach to whole mouse brain connectomics may be achievable for less than $10 million and could be enabled by emerging technologies to sequence nucleic acids in-situ in fixed tissue via fluorescent  ...  microscopy.  ...  We focus here on techniques for dense, cellular-resolution circuit mapping of individual brains: we do not consider sparse mapping (e.g., viral tracers), low-resolution mapping (e.g., diffusion MRI) or  ... 
doi:10.1101/001214 fatcat:qlpnmobhkjeulauwlggt7tn474

Virtual microscopy enhances the reliability and validity in histopathology curriculum: Practical guidelines [Version 2]

Samal Nauhria, Lee Hangfu
2019 MedEdPublish  
The new technology of virtual microscopy is a proven reliable and valid pedagogy method for histopathology learning objectives, and assessments.  ...  This paper emphasises the practical tips and guidelines for cost-effective implementation and the successful use of Virtual Microscope technology to enhance the histopathology curriculum in a medical school  ...  Virtual/Digital microscopy is the computerized conversion of light microscopic images in full resolution and their presentation over a computer network.  ... 
doi:10.15694/mep.2019.000028.2 fatcat:vji6cakyw5cmpem6ov6nb2mofq

Automated generation of massive image knowledge collections using Microsoft Live Labs Pivot to promote neuroimaging and translational research

Teeradache Viangteeravat, Matthew N Anyanwu, Venkateswara Ra Nagisetty, Emin Kuscu
2011 Journal of Clinical Bioinformatics  
The metadata along with high-resolution images were automatically extracted using the Allen Brain Atlas API.  ...  , explore or analyze the massive image data sets of high-resolution images and their associated meta information, such as neuro-imaging databases from the Allen Brain Atlas.  ...  All authors read and approved the final manuscript.  ... 
doi:10.1186/2043-9113-1-18 pmid:21884637 pmcid:PMC3164611 fatcat:5ai2eszqkrc4fotpnxcp7xwq5q

LIFE SCIENCE TECHNOLOGIES: This Is Your Brain: Mapping the Connectome

J. M. Perkel
2013 Science  
Neuroscientists would like to navigate the brain in virtual space as modern travelers do on the Internet: by zooming in and out and panning at will, from entire brain regions down to individual cells and  ...  Wedeen invented and uses one form of diffusion MRI, called diffusion spectrum imaging (DSI); the WashU and Minnesota teams use HARDI, or high-angular resolution diffusion imaging.  ... 
doi:10.1126/science.339.6117.350 fatcat:3kbcladsojb4tbjma46ovzrzk4
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