scholarly journals A robust image registration interface for large volume brain atlas

2018 ◽  
Author(s):  
Hong Ni ◽  
Chaozhen Tan ◽  
Zhao Feng ◽  
Shangbin Chen ◽  
Zoutao Zhang ◽  
...  
Keyword(s):  
Large Volume ◽  
Three Dimensional ◽  
Brain Structures ◽  
Cellular Level ◽  
Brain Atlas ◽  
Biological Images ◽  
Brain Functions ◽  
Streak Image ◽  
Dataset Size ◽  
The Brain

AbstractMapping the brain structures in three-dimensional accurately is critical for an in-depth understanding of the brain functions. By using the brain atlas as a hub, mapping detected datasets into a standard brain space enables efficiently use of various datasets. However, because of the heterogeneous and non-uniform characteristics of the brain structures at cellular level brought with the recently developed high-resolution whole-brain microscopes, traditional registration methods are difficult to apply to the robust mapping of various large volume datasets. Here, we proposed a robust Brain Spatial Mapping Interface (BrainsMapi) to address the registration of large volume datasets at cellular level by introducing the extract regional features of the anatomically invariant method and a strategy of parameter acquisition and large volume transformation. By performing validation on model data and biological images, BrainsMapi can not only achieve robust registration on sample tearing and streak image datasets, different individual and modality datasets accurately, but also are able to complete the registration of large volume dataset at cellular level which dataset size reaches 20 TB. Besides, it can also complete the registration of historical vectorized dataset. BrainsMapi would facilitate the comparison, reuse and integration of a variety of brain datasets.

Anisotropic Modeling of Fibrous White Matter

2008 ◽  
Author(s):  
Rika M. Wright ◽  
K. T. Ramesh
Keyword(s):  
White Matter ◽  
Experimental Studies ◽  
Diffuse Axonal Injury ◽  
Strain Energy Function ◽  
Brain Structures ◽  
The United States ◽  
Cellular Level ◽  
Brain Deformation ◽  
Injury Mechanisms ◽  
The Brain

Traumatic brain injury (TBI) is a debilitating injury that affects more than 1.4 million people in the United States each year. Of the incidences of TBI, diffuse axonal injury (DAI) accounts for the second largest percentage of deaths. DAI is caused by inertial loads to the head, and it is characterized by damage to neurons. Despite the extensive research on DAI, the injury mechanisms associated with the pathology are still poorly understood. The crucial link between the inertial forces to the head at the macroscale and the resulting damage at the cellular level has yet to be explained. An integral step to understanding this coupling between mechanical forces and the functional damage of neurons is the development of an analytical model that accurately represents the mechanics of brain deformation under inertial loads. It has been noted in clinical and experimental studies that the most common injury location of DAI is within the deep white matter of the brain. Structures such as the splenium of the corpus callosum are cited as being highly susceptible to damage [1]. Although numerous brain tissue models have been proposed, few models account for the anisotropic nature of white matter in the brain. As a first step in developing an anisotropic model for white matter, the effect of the invariant terms in a strain energy function for white matter is analyzed.

scholarly journals Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging

2012 ◽  
Vol 44 (15) ◽  
pp. 778-785 ◽  
Author(s):  
Jacqueline A. Gleave ◽  
Michael D. Wong ◽  
Jun Dazai ◽  
Maliha Altaf ◽  
R. Mark Henkelman ◽  
...  
Keyword(s):  
Optical Imaging ◽  
Mouse Brain ◽  
Imaging Techniques ◽  
Three Dimensional ◽  
Brain Structures ◽  
Small Scale ◽  
Specimen Preparation ◽  
Normal Brain ◽  
Autofluorescence Imaging ◽  
The Brain

The structural organization of the brain is important for normal brain function and is critical to understand in order to evaluate changes that occur during disease processes. Three-dimensional (3D) imaging of the mouse brain is necessary to appreciate the spatial context of structures within the brain. In addition, the small scale of many brain structures necessitates resolution at the ∼10 μm scale. 3D optical imaging techniques, such as optical projection tomography (OPT), have the ability to image intact large specimens (1 cm3) with ∼5 μm resolution. In this work we assessed the potential of autofluorescence optical imaging methods, and specifically OPT, for phenotyping the mouse brain. We found that both specimen size and fixation methods affected the quality of the OPT image. Based on these findings we developed a specimen preparation method to improve the images. Using this method we assessed the potential of optical imaging for phenotyping. Phenotypic differences between wild-type male and female mice were quantified using computer-automated methods. We found that optical imaging of the endogenous autofluorescence in the mouse brain allows for 3D characterization of neuroanatomy and detailed analysis of brain phenotypes. This will be a powerful tool for understanding mouse models of disease and development and is a technology that fits easily within the workflow of biology and neuroscience labs.

scholarly journals Diagnosis of brain death

2010 ◽  
Vol 2 (1) ◽  
pp. 2 ◽  
Author(s):  
Calixto Machado
Keyword(s):  
Brain Death ◽  
Perfusion Pressure ◽  
Cellular Level ◽  
Irreversible Loss ◽  
Clinical Expression ◽  
Neuronal Tissue ◽  
Brain Functions ◽  
The Mean ◽  
The Brain ◽  
Signs Of Death

Brain death (BD) should be understood as the ultimate clinical expression of a brain catastrophe characterized by a complete and irreversible neurological stoppage, recognized by irreversible coma, absent brainstem reflexes, and apnea. The most common pattern is manifested by an elevation of intracranial pressure to a point beyond the mean arterial pressure, and hence cerebral perfusion pressure falls and, as a result, no net cerebral blood flow is present, in due course leading to permanent cytotoxic injury of the intracranial neuronal tissue. A second mechanism is an intrinsic injury affecting the nervous tissue at a cellular level which, if extensive and unremitting, can also lead to BD. We review here the methodology of diagnosing death, based on finding any of the signs of death. The irreversible loss of cardio-circulatory and respiratory functions can cause death only when ischemia and anoxia are prolonged enough to produce an irreversible destruction of the brain. The sign of such loss of brain functions, that is to say BD diagnosis, is fully reviewed.

scholarly journals A Review of Publicly Available Automatic Brain Segmentation Methodologies, Machine Learning Models, Recent Advancements, and Their Comparison

2021 ◽  
pp. 097275312199017
Author(s):  
Mahender Kumar Singh ◽  
Krishna Kumar Singh
Keyword(s):  
Machine Learning ◽  
Automatic Segmentation ◽  
Three Dimensional ◽  
Brain Structures ◽  
Magnetic Resonance Images ◽  
Learning Models ◽  
Convolutional Network ◽  
Research Perspective ◽  
The Brain ◽  
Machine Learning Models

Background: The noninvasive study of the structure and functions of the brain using neuroimaging techniques is increasingly being used for its clinical and research perspective. The morphological and volumetric changes in several regions and structures of brains are associated with the prognosis of neurological disorders such as Alzheimer’s disease, epilepsy, schizophrenia, etc. and the early identification of such changes can have huge clinical significance. The accurate segmentation of three-dimensional brain magnetic resonance images into tissue types (i.e., grey matter, white matter, cerebrospinal fluid) and brain structures, thus, has huge importance as they can act as early biomarkers. The manual segmentation though considered the “gold standard” is time-consuming, subjective, and not suitable for bigger neuroimaging studies. Several automatic segmentation tools and algorithms have been developed over the years; the machine learning models particularly those using deep convolutional neural network (CNN) architecture are increasingly being applied to improve the accuracy of automatic methods. Purpose: The purpose of the study is to understand the current and emerging state of automatic segmentation tools, their comparison, machine learning models, their reliability, and shortcomings with an intent to focus on the development of improved methods and algorithms. Methods: The study focuses on the review of publicly available neuroimaging tools, their comparison, and emerging machine learning models particularly those based on CNN architecture developed and published during the last five years. Conclusion: Several software tools developed by various research groups and made publicly available for automatic segmentation of the brain show variability in their results in several comparison studies and have not attained the level of reliability required for clinical studies. The machine learning models particularly three dimensional fully convolutional network models can provide a robust and efficient alternative with relation to publicly available tools but perform poorly on unseen datasets. The challenges related to training, computation cost, reproducibility, and validation across distinct scanning modalities for machine learning models need to be addressed.

scholarly journals High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology

2021 ◽  
Author(s):  
Kadharbatcha S Saleem ◽  
Alexandru V Avram ◽  
Daniel Glen ◽  
Cecil Chern-Chyi Yen ◽  
Frank Q Ye ◽  
...  
Keyword(s):  
High Resolution ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Brain Structures ◽  
Macaque Monkey ◽  
Three Dimensions ◽  
Brain Atlas ◽  
Fiber Tracts ◽  
Subcortical Regions ◽  
Deep Brain

Subcortical nuclei and other deep brain structures are known to play an important role in the regulation of the central and peripheral nervous systems. It can be difficult to identify and delineate many of these nuclei and their finer subdivisions in conventional MRI due to their small size, buried location, and often subtle contrast compared to neighboring tissue. To address this problem, we applied a multi-modal approach in ex vivo non-human primate (NHP) brain that includes high-resolution mean apparent propagator (MAP)-MRI and five different histological stains imaged with high-resolution microscopy in the brain of the same subject. By registering these high-dimensional MRI data to high-resolution histology data, we can map the location, boundaries, subdivisions, and micro-architectural features of subcortical gray matter regions in the macaque monkey brain. At high spatial resolution, diffusion MRI in general, and MAP-MRI in particular, can distinguish a large number of deep brain structures, including the larger and smaller white matter fiber tracts as well as architectonic features within various nuclei. Correlation with histology from the same brain enables a thorough validation of the structures identified with MAP-MRI. Moreover, anatomical details that are evident in images of MAP-MRI parameters are not visible in conventional T1-weighted images. We also derived subcortical template SC21 from segmented MRI slices in three-dimensions and registered this volume to a previously published anatomical template with cortical parcellation (Reveley et al., 2017; Saleem and Logothetis, 2012), thereby integrating the 3D segmentation of both cortical and subcortical regions into the same volume. This newly updated three-dimensional D99 digital brain atlas (V2.0) is intended for use as a reference standard for macaque neuroanatomical, functional, and connectional imaging studies, involving both cortical and subcortical targets. The SC21 and D99 digital templates are available as volumes and surfaces in standard NIFTI and GIFTI formats.

scholarly journals Large-scale calcium imaging with a head-mount axial scanning 3D fluorescence microscope

2021 ◽  
Author(s):  
Yuichiro Hayashi ◽  
Ko Kobayakawa ◽  
Reiko Kobayakawa
Keyword(s):  
Calcium Imaging ◽  
Large Scale ◽  
Low Cost ◽  
3D Structure ◽  
Three Dimensional ◽  
Brain Structures ◽  
Volumetric Imaging ◽  
Brain Functions ◽  
Local Circuits ◽  
Axial Scanning

AbstractMiniaturized fluorescence microscopes are becoming more important for deciphering the neural codes underlying various brain functions. Using gradient index (GRIN) lenses, these devices enable the recording of neuronal activity in deep brain structures. However, to minimize any damage to brain tissue and local circuits, the diameter of the GRIN lens should be 0.5–1 mm, which results in a small field of view. Considering the three-dimensional (3D) structure of neural circuits in the brain, volumetric imaging capability would increase the number of neurons imaged through the lenses. To observe 3D calcium dynamics, we developed a miniaturized microscope with an electrically tunable lens. Using this microscope, we performed 3D calcium imaging in behaving mice and were able to image approximately twice the number of cells as could be recorded using a 2D imaging technique. This simple low-cost 3D microscope will improve the efficiency of calcium imaging in behaving animals.

scholarly journals Το νευροεπιστημονικό υπόβαθρο της ψυχοθεραπείας: μηχανισμοί και εγκεφαλικές δομές που επηρεάζονται από την ψυχοθεραπευτική διαδικασία

2020 ◽  
Vol 22 (2) ◽  
pp. 1
Author(s):  
Θεοδώρα Σεληνιωτάκη ◽  
Ιωάννης Νέστορος
Keyword(s):  
Mental Health ◽  
Psychiatric Disorders ◽  
Learning And Memory ◽  
Large Volume ◽  
Recent Literature ◽  
General Tendency ◽  
Brain Functions ◽  
Ancient Times ◽  
The Brain

Recently we witness a general tendency to synthesize psychotherapeutic models, as well as, a tendency to explore the effects of psychotherapy on the brain. This article summarizes a large volume of literature on the neuroscientific substrate of psychotherapy starting with scientific findings located in Ancient times till recent literature. The published literature that deals with the effects of psychotherapy on the brain includes studies, usually neuroimaging ones, which examine the neurological aspects of the most popular models of psychotherapy and pharmacotherapy. All researchers draw the conclusion that psychotherapy affects the brain functions, such as neuroplasticity,learning and memory, neurogenesis, mood and emotions, thus leading to an improvement of mental health. The discussion leads to the constitution of a new discipline, the Neuropsychotherapy, whichis promising for the liberation from the grip of psychiatric disorders.

Brain shift during bur hole–based procedures using interventional MRI

2014 ◽  
Vol 121 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Michael E. Ivan ◽  
Jay Yarlagadda ◽  
Akriti P. Saxena ◽  
Alastair J. Martin ◽  
Philip A. Starr ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Brain Biopsy ◽  
Brain Structures ◽  
Interventional Mri ◽  
Preoperative Imaging ◽  
Brain Shift ◽  
Stereotactic Brain Biopsy ◽  
Electrode Implantation ◽  
The Brain ◽  
Deep Brain

Object Brain shift during minimally invasive, bur hole–based procedures such as deep brain stimulation (DBS) electrode implantation and stereotactic brain biopsy is not well characterized or understood. We examine shift in various regions of the brain during a novel paradigm of DBS electrode implantation using interventional imaging throughout the procedure with high-field interventional MRI. Methods Serial MR images were obtained and analyzed using a 1.5-T magnet prior to, during, and after the placement of DBS electrodes via frontal bur holes in 44 procedures. Three-dimensional coordinates in MR space of unique superficial and deep brain structures were recorded, and the magnitude, direction, and rate of shift were calculated. Measurements were recorded to the nearest 0.1 mm. Results Shift ranged from 0.0 to 10.1 mm throughout all structures in the brain. The greatest shift was seen in the frontal lobe, followed by the temporal and occipital lobes. Shift was also observed in deep structures such as the anterior and posterior commissures and basal ganglia; shift in the pallidum and subthalamic region ipsilateral to the bur hole averaged 0.6 mm, with 9% of patients having over 2 mm of shift in deep brain structures. Small amounts of shift were observed during all procedures; however, the initial degree of shift and its direction were unpredictable. Conclusions Brain shift is continual and unpredictable and can render traditional stereotactic targeting based on preoperative imaging inaccurate even in deep brain structures such as those used for DBS.

scholarly journals Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis

2021 ◽  
Vol 22 (16) ◽  
pp. 8802
Author(s):  
Anastasia N. Vaganova ◽  
Ramilya Z. Murtazina ◽  
Taisiia S. Shemyakova ◽  
Andrey D. Prjibelski ◽  
Nataliia V. Katolikova ◽  
...  
Keyword(s):  
Brain Structures ◽  
Gene Expression Omnibus ◽  
Brain Atlas ◽  
Potential Contribution ◽  
Brain Functions ◽  
Neuropsychiatric Diseases ◽  
Human Protein Atlas ◽  
Olfactory Input ◽  
Socially Relevant ◽  
Novel Target

Trace amine-associated receptors (TAAR) recognize organic compounds, including primary, secondary, and tertiary amines. The TAAR5 receptor is known to be involved in the olfactory sensing of innate socially relevant odors encoded by volatile amines. However, emerging data point to the involvement of TAAR5 in brain functions, particularly in the emotional behaviors mediated by the limbic system which suggests its potential contribution to the pathogenesis of neuropsychiatric diseases. TAAR5 expression was explored in datasets available in the Gene Expression Omnibus, Allen Brain Atlas, and Human Protein Atlas databases. Transcriptomic data demonstrate ubiquitous low TAAR5 expression in the cortical and limbic brain areas, the amygdala and the hippocampus, the nucleus accumbens, the thalamus, the hypothalamus, the basal ganglia, the cerebellum, the substantia nigra, and the white matter. Altered TAAR5 expression is identified in Down syndrome, major depressive disorder, or HIV-associated encephalitis. Taken together, these data indicate that TAAR5 in humans is expressed not only in the olfactory system but also in certain brain structures, including the limbic regions receiving olfactory input and involved in critical brain functions. Thus, TAAR5 can potentially be involved in the pathogenesis of brain disorders and represents a valuable novel target for neuropsychopharmacology.

Information Processing in the Mammalian Olfactory System

2005 ◽  
Vol 85 (1) ◽  
pp. 281-317 ◽  
Author(s):  
Pierre-Marie Lledo ◽  
Gilles Gheusi ◽  
Jean-Didier Vincent
Keyword(s):  
Olfactory System ◽  
Cellular Level ◽  
Adult Brain ◽  
Organizational Strategies ◽  
Cellular Mechanisms ◽  
Brain Functions ◽  
Olfactory Systems ◽  
And Behavior ◽  
High Degree ◽  
The Brain

Recently, modern neuroscience has made considerable progress in understanding how the brain perceives, discriminates, and recognizes odorant molecules. This growing knowledge took over when the sense of smell was no longer considered only as a matter for poetry or the perfume industry. Over the last decades, chemical senses captured the attention of scientists who started to investigate the different stages of olfactory pathways. Distinct fields such as genetic, biochemistry, cellular biology, neurophysiology, and behavior have contributed to provide a picture of how odor information is processed in the olfactory system as it moves from the periphery to higher areas of the brain. So far, the combination of these approaches has been most effective at the cellular level, but there are already signs, and even greater hope, that the same is gradually happening at the systems level. This review summarizes the current ideas concerning the cellular mechanisms and organizational strategies used by the olfactory system to process olfactory information. We present findings that exemplified the high degree of olfactory plasticity, with special emphasis on the first central relay of the olfactory system. Recent observations supporting the necessity of such plasticity for adult brain functions are also discussed. Due to space constraints, this review focuses mainly on the olfactory systems of vertebrates, and primarily those of mammals.

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