Knife-Edge Scanning Microscope Mouse Brain Atlas in Vector Graphics for Enhanced Performance PDF Download

Author: Jinho Choi
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Book Description
The microstructure of the brain at the cellular level provides crucial information for the understanding of the function of the brain. A large volume of high-resolution brain image data from 3D microscopy is an essential resource to study detailed microstructures of the brain. Accordingly, we have worked on obtaining high-resolution image data of entire mouse brains using the Knife-Edge Scanning Microscope (KESM). Furthermore, to disseminate these high-resolution whole mouse brain data sets to the neuroscience research community, we developed a web-based brain atlas, the KESM Brain Atlas (KESMBA). To visualize the data sets in 3D while using only a standard web browser, we employed distance attenuation and Google Maps API. The KESMBA is a powerful tool to analyze and share the KESM mouse brain data sets, but the image loading was slow because of the number of raster image (PNG) tiles and the file size. Moreover, since Google Maps API is governed by a commercial license, it does not provide enough flexibility for customization, extension, and mirroring. To solve these issues, we designed and developed a new KESM mouse brain atlas that uses a vector graphics format called Scalable Vector Graphics (SVG) instead of PNG, and OpenLayers API instead of Google Maps API. The SVG-based KESMBA using OpenLayers allows faster navigation and exploration of the KESM data, and more overlay of layers with the 4 times reduced file size compared to PNG tiles. Due to the reduced file size, the SVG-based KESMBA using OpenLayers is 2.45 times faster than the original atlas. By enhancing the performance, the users can more easily access the KESM data. We expect the SVG-based KESMBA to accelerate new discoveries in neuroscience. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/151255

Author: Manisha Srivastava
Publisher:
ISBN:
Category :
Languages : en
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The study of the neurovascular network in the brain is important to understand brain functions as well as causes of several brain dysfunctions. Many techniques have been applied to acquire neurovascular data. The Knife-Edge Scanning Microscope (KESM), developed by the Brain Network Lab at Texas A&M University, can generate whole-brain-scale data at submicrometer resolution. The specimen can be stained with different stains, and depending on the type of stain used, the KESM can image different types of microstructures in the brain. The India ink stain allows the neurovascular network in the brain to be imaged. In order to visualize and analyze such large datasets (~ 1.5 TB per brain), a lightweight, web-based mouse brain atlas called the Knife-Edge Scanning Microscope Brain Atlas (KESMBA) was developed in the lab. The atlas serves several whole mouse brain data sets including India ink. The multi-section overlay technique used in the atlas enables 3D visualization of the structural information in the data. To solve the challenging issue of tracing micro-vessels in the brain, in this thesis a semi-automated tracing and analysis method is developed and integrated into the KESM brain atlas. Using the KESMBA interface developed in this thesis, the user can look at the 3D structure of the vessels on the brain atlas and can guide the tracing algorithm. In order to analyze the vasculature network traced by the user, a data analysis component is also added. This new KESMBA interface is expected to help in quickly tracing and analyzing the vascular network of the brain with minimal manual effort. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/155681

Author: Hong Wei Dong
Publisher: Wiley
ISBN: 9780470054086
Category : Medical
Languages : en
Pages : 0

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Book Description
“… this atlas acts not only as a key companion to the Allen Reference Atlas but also as a harbinger of things to come.” –Genes, Brain and Behavior, 2010 The best resource available for brain research! The Allen Reference Atlas is available for the first time in this lavishly produced, full-color print edition. This exciting new resource provides users with a meticulously selected and compiled collection of key information from the highly successful web-based Allen Brain Atlas, the now-famous online mouse brain anatomical atlas and gene expression database (www.brain-map.org). Including both coronal and sagittal mouse brain sectional views, these finely detailed brain map images have been carefully chosen for maximum utility and information content, and are presented as full-color plates on pages with corresponding text labels and lists of selected genetic markers. Every brain structure annotated in the Atlas is assigned a distinct color based on its hierarchical position in the brain, which not only provides stunning visual effects to emphasize brain organization, but also facilitates unique definition and segmentation, which is critical to informatics processing and computer-generated 3D reconstruction in the online Allen Brain Atlas. In addition, more than eighty genes showing unique expression patterns in the brain were carefully selected and are presented with the brain map images as molecular markers, for substantially increasing the accuracy of brain structure delineations. The brain map images are the heart and soul of the Allen Reference Atlas, but also included are extremely useful text materials such as thoughtfully annotated nomenclature tables, comprehensive indices, lists of abbreviations, and a thorough and up-to-date bibliography. A free accompanying CD-ROM contains all of the Atlas images in a black-and-white format, perfect for quick reference and use in presentations. The Allen Reference Atlas is a valuable addition to the reference libraries of millions of neuro-scientists, molecular biologists, genomicists, genomics researchers, informaticians, informatics researchers, and many other scientists for whom beautifully developed and perfectly accurate brain reference images are an indispensable tool. The Allen Institute for Brain Science is an independent, 501(c)(3) non-profit medical research organization dedicated to performing innovative basic research on the brain and distributing its discoveries to researchers around the world. Through its efforts, the Institute aims to advance understanding of the brain in health and disease and have a positive, long-lasting impact on brain science. The Institute was established by philanthropist Paul G. Allen and Jody Allen Patton. Available in print format (with CD-ROM), as DVD edition, and as comprehensive reference set.

Author: Peter W. Hawkes
Publisher: Springer Nature
ISBN: 3030000699
Category : Technology & Engineering
Languages : en
Pages : 1561

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Book Description
This book features reviews by leading experts on the methods and applications of modern forms of microscopy. The recent awards of Nobel Prizes awarded for super-resolution optical microscopy and cryo-electron microscopy have demonstrated the rich scientific opportunities for research in novel microscopies. Earlier Nobel Prizes for electron microscopy (the instrument itself and applications to biology), scanning probe microscopy and holography are a reminder of the central role of microscopy in modern science, from the study of nanostructures in materials science, physics and chemistry to structural biology. Separate chapters are devoted to confocal, fluorescent and related novel optical microscopies, coherent diffractive imaging, scanning probe microscopy, transmission electron microscopy in all its modes from aberration corrected and analytical to in-situ and time-resolved, low energy electron microscopy, photoelectron microscopy, cryo-electron microscopy in biology, and also ion microscopy. In addition to serving as an essential reference for researchers and teachers in the fields such as materials science, condensed matter physics, solid-state chemistry, structural biology and the molecular sciences generally, the Springer Handbook of Microscopy is a unified, coherent and pedagogically attractive text for advanced students who need an authoritative yet accessible guide to the science and practice of microscopy.

Author: Matt Carter
Publisher: Academic Press
ISBN: 0323915612
Category : Medical
Languages : en
Pages : 416

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Book Description
Modern neuroscience research is inherently multidisciplinary, with a wide variety of cutting edge new techniques to explore multiple levels of investigation. This Third Edition of Guide to Research Techniques in Neuroscience provides a comprehensive overview of classical and cutting edge methods including their utility, limitations, and how data are presented in the literature. This book can be used as an introduction to neuroscience techniques for anyone new to the field or as a reference for any neuroscientist while reading papers or attending talks. - Nearly 200 updated full-color illustrations to clearly convey the theory and practice of neuroscience methods - Expands on techniques from previous editions and covers many new techniques including in vivo calcium imaging, fiber photometry, RNA-Seq, brain spheroids, CRISPR-Cas9 genome editing, and more - Clear, straightforward explanations of each technique for anyone new to the field - A broad scope of methods, from noninvasive brain imaging in human subjects, to electrophysiology in animal models, to recombinant DNA technology in test tubes, to transfection of neurons in cell culture - Detailed recommendations on where to find protocols and other resources for specific techniques - "Walk-through" boxes that guide readers through experiments step-by-step

Author: Carolyn A. Staton
Publisher: John Wiley & Sons
ISBN: 047002934X
Category : Medical
Languages : en
Pages : 410

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Book Description
Angiogenesis, the development of new blood vessels from the existing vasculature, is essential for physiological growth and over 18,000 research articles have been published describing the role of angiogenesis in over 70 different diseases, including cancer, diabetic retinopathy, rheumatoid arthritis and psoriasis. One of the most important technical challenges in such studies has been finding suitable methods for assessing the effects of regulators of eh angiogenic response. While increasing numbers of angiogenesis assays are being described both in vitro and in vivo, it is often still necessary to use a combination of assays to identify the cellular and molecular events in angiogenesis and the full range of effects of a given test protein. Although the endothelial cell - its migration, proliferation, differentiation and structural rearrangement - is central to the angiogenic process, it is not the only cell type involved. the supporting cells, the extracellular matrix and the circulating blood with its cellular and humoral components also contribute. In this book, experts in the use of a diverse range of assays outline key components of these and give a critical appraisal of their strengths and weaknesses. Examples include assays for the proliferation, migration and differentiation of endothelial cells in vitro, vessel outgrowth from organ cultures, assessment of endothelial and mural cell interactions, and such in vivo assays as the chick chorioallantoic membrane, zebrafish, corneal, chamber and tumour angiogenesis models. These are followed by a critical analysis of the biological end-points currently being used in clinical trials to assess the clinical efficacy of anti-angiogenic drugs, which leads into a discussion of the direction future studies should take. This valuable book is of interest to research scientists currently working on angiogenesis in both the academic community and in the biotechnology and pharmaceutical industries. Relevant disciplines include cell and molecular biology, oncology, cardiovascular research, biotechnology, pharmacology, pathology and physiology.

Author: Trygve B. Leergaard
Publisher: Frontiers E-books
ISBN: 2889191079
Category :
Languages : en
Pages : 251

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Author: Matt Pearson
Publisher: Simon and Schuster
ISBN: 1638352437
Category : Computers
Languages : en
Pages : 352

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Book Description
Summary Generative Art presents both the technique and the beauty of algorithmic art. The book includes high-quality examples of generative art, along with the specific programmatic steps author and artist Matt Pearson followed to create each unique piece using the Processing programming language. About the Technology Artists have always explored new media, and computer-based artists are no exception. Generative art, a technique where the artist creates print or onscreen images by using computer algorithms, finds the artistic intersection of programming, computer graphics, and individual expression. The book includes a tutorial on Processing, an open source programming language and environment for people who want to create images, animations, and interactions. About the Book Generative Art presents both the techniques and the beauty of algorithmic art. In it, you'll find dozens of high-quality examples of generative art, along with the specific steps the author followed to create each unique piece using the Processing programming language. The book includes concise tutorials for each of the technical components required to create the book's images, and it offers countless suggestions for how you can combine and reuse the various techniques to create your own works. Purchase of the print book comes with an offer of a free PDF, ePub, and Kindle eBook from Manning. Also available is all code from the book. What's Inside The principles of algorithmic art A Processing language tutorial Using organic, pseudo-random, emergent, and fractal processes ========================================​========= Table of Contents Part 1 Creative Coding Generative Art: In Theory and Practice Processing: A Programming Language for ArtistsPart 2 Randomness and Noise The Wrong Way to Draw A Line The Wrong Way to Draw a Circle Adding Dimensions Part 3 Complexity Emergence Autonomy Fractals

Author:
Publisher: DIANE Publishing
ISBN: 1428990488
Category :
Languages : en
Pages : 228

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Book Description
In February 1999, only a few weeks before the U.S. Air Force spearheaded NATO's Allied Force air campaign against Serbia, Col. C.R. Anderegg, USAF (Ret.), visited the commander of the U.S. Air Forces in Europe. Colonel Anderegg had known Gen. John Jumper since they had served together as jet forward air controllers in Southeast Asia nearly thirty years earlier. From the vantage point of 1999, they looked back to the day in February 1970, when they first controlled a laser-guided bomb strike. In this book Anderegg takes us from "glimmers of hope" like that one through other major improvements in the Air Force that came between the Vietnam War and the Gulf War. Always central in Anderegg's account of those changes are the people who made them. This is a very personal book by an officer who participated in the transformation he describes so vividly. Much of his story revolves around the Fighter Weapons School at Nellis Air Force Base (AFB), Nevada, where he served two tours as an instructor pilot specializing in guided munitions.

Author: George Paxinos
Publisher: Academic Press
ISBN: 9780124158184
Category : Science
Languages : en
Pages : 0

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Book Description
The Marmoset Brain in Stereotaxic Coordinates is the most comprehensive atlas of the brain of this animal available. The atlas is constructed in the style of The Rat Brain in Stereotaxic Coordinates, the most-cited book in neuroscience. It represents a collaboration between world leaders in neuroanatomy of the primate cortex and subcortex. It will be an indispensible tool for neuroanatomists, behavioral neuroscientists, and molecular biologists trying to understand the primate brain. ENDORSED BY SOCIETY FOR BRAIN MAPPING AND THERAPEUTICS (SBMT) - SBMT is a non-profit society organized for the purpose of encouraging basic and clinical scientists who are interested in areas of Brain Mapping, engineering, stem cell, nanotechnology, imaging and medical device to improve the diagnosis, treatment and rehabilitation of patients afflicted with neurological disorders. This society promotes the public welfare and improves patient care through the translation of new technologies/therapies into life saving diagnostic and therapeutic procedures. The Society is focused in breaking boundaries of science, technology, medicine, art and healthcare policy. For more information about how to become a member or participate in SBMT programs please visit: www.WorldBrainMapping.org