3D Brain Atlas Research Articles

Developmental mouse brain common coordinate framework

3D brain atlases are key resources to understand the brain’s spatial organization and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of developing mouse brain 3D reference atlases hinders advancements in understanding brain development. Here, we present a 3D developmental common coordinate framework (DevCCF) spanning embryonic day (E)11.5, E13.5, E15.5, E18.5, and postnatal day (P)4, P14, and P56, featuring undistorted morphologically averaged atlas templates created from magnetic resonance imaging and co-registered high-resolution light sheet fluorescence microscopy templates. The DevCCF with 3D anatomical segmentations can be downloaded or explored via an interactive 3D web-visualizer. As a use case, we utilize the DevCCF to unveil GABAergic neuron emergence in embryonic brains. Moreover, we map the Allen CCFv3 and spatial transcriptome cell-type data to our stereotaxic P56 atlas. In summary, the DevCCF is an openly accessible resource for multi-study data integration to advance our understanding of brain development.

Enhancing neuro-ophthalmic surgical education: The role of neuroanatomy and 3D digital technologies - An overview.

Neuro-ophthalmology, bridging neurology and ophthalmology, highlights the nervous system's crucial role in vision, encompassing afferent and efferent pathways. The evolution of this field has emphasized the importance of neuroanatomy for precise surgical interventions, presenting educational challenges in blending complex anatomical knowledge with surgical skills. This review examines the interplay between neuroanatomy and surgical practices in neuro-ophthalmology, aiming to identify educational gaps and suggest improvements. A literature search across databases such as PubMed, Scopus, and Web of Science was conducted, focusing on the implications of neuroanatomy in neuro-ophthalmic surgery education and practice. The review synthesizes insights from both recent and foundational studies to highlight current understandings and future research directions, particularly in educational approaches. Findings indicate that 3D digital modeling and virtual reality have significantly enhanced neuroophthalmic surgical education by providing immersive and engaging learning experiences. For instance, detailed 3D brain atlases offer comprehensive resources for understanding the central nervous system's normal and pathological states. Although studies show that 3D and traditional 2D methods achieve similar post-test results, 3D methods notably improve engagement and motivation, suggesting a shift toward more interactive learning environments. Integrating both traditional and innovative educational tools is crucial for the progression of neuro-ophthalmic surgical training. This balance helps overcome educational hurdles and better prepare future surgeons. Continuous research and collaboration are essential to refine educational strategies, ultimately aiming to enhance patient care in neuro-ophthalmology.

The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases.

Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.

On the definition, construction, and presentation of the human cerebral sulci: A morphology-based approach.

Although the term sulcus is known for almost four centuries, its formal, precise, consistent, constructive, and quantitative definition is practically lacking. As the cerebral sulci (and gyri) are vital in cortical anatomy which, in turn, is central in neuroeducation and neuroimage processing, a new sulcus definition is needed. The contribution of this work is threefold, namely to (1) propose a new, morphology-based definition of the term sulcus (and consequently that of gyrus), (2) formulate a constructive method for sulcus calculation, and (3) provide a novel way for the presentation of sulci. The sulcus is defined here as a volumetric region on the cortical mantle between adjacent gyri separated from them at the levels of their gyral white matter crest lines. Consequently, the sulcal inner surface is demarcated by the crest lines of the gyral white matter of its adjacent gyri. Correspondingly, the gyrus is defined as a volumetric region on the cortical mantle separated from its adjacent sulci at the level of its gyral white matter crest line. This volumetric sulcus definition is conceptually simple, anatomy-based, educationally friendly, quantitative, and constructive. Considering the sulcus as a volumetric object is a major differentiation from other works. Based on the introduced sulcus definition, a method for volumetric sulcus construction is proposed in two, conceptually straightforward, steps, namely, sulcal intersection formation followed by its propagation which steps are to be repeated for every sulcal segment. These sulcal and gyral constructions can be automated by applying existing methods and public tools. As a volumetric sulcus forms an imprint into the white matter, this enables prominent sulcus presentation. Since this type of presentation is novel yet unfamiliar to the reader, also a dual surface presentation was proposed here by employing the spatially co-registered white matter and cortical surfaces. The results were presented as dual surface labeled sulci on eight standard orthogonal views, anterior, left lateral, posterior, right lateral, superior, inferior, medial left, and medial right by using a 3D brain atlas. Moreover, additional 108 labeled images were created with sulcus-oriented views for 27 individual left and right sulci forming 54 dual white matter-cortical surface images strengthening in this way the educational value of the proposed approach. These images were included for public use in the NOWinBRAIN neuroimage repository with over 7700 3D images available at www.nowinbrain.org. The results demonstrated the superiority of white matter surface sulci presentation over the standard cortical surface and cross-sectional presentations in terms of sulcal course, continuity, size, shape, width, depth, side branches, and pattern. To my best knowledge, this is the first work ever presenting the labeling of sulci on all cerebral white matter surfaces as well as on dual white matter-cortical surfaces. Additionally to neuroeducation, three other applications of the proposed approach were discussed, sulcal reference maps, sulcus quantification in terms of new parameters introduced here (sulcal volume, wall skewness, and the number of white matter basins), and an atlas-assisted tool for exploration and studying of cerebral sulci and gyri .

Spatial mapping of subcellular disease pathways and cytoarchitecture to anatomical brain regions for multi‐scale brain simulation with The Virtual Brain

AbstractBackgroundComprehensive knowledge bases as NeuroMMSig, a knowledge base of multimodal mechanistic signatures, catalog knowledge about Alzheimer's Disease (AD) and its underlying candidate mechanisms. Besides, digital atlases provide information about cytoarchitectonics and receptor densities, e.g. JuBrain at the EBRAINS platform of the Human Brain Project. However, a gap exists presently with respect to the integration of the various knowledge sources. The Virtual Brain (TVB) is a full brain simulation platform that integrates multimodal imaging data with mathematical brain networks. We present a methodology to map semantic information about AD to 3D brain atlases and to use it for simulations with TVB – increasing the biological plausibility of whole‐brain simulations and disease specificity.MethodOur framework allows topological assignment of brain‐related data from different sources to the Multimodal surface‐based cortical parcellation (MMP) of the Human Connectome Project. Our tool allows mapping of stochastic information from the literature database SCAIView to brain regions. The relevance score for a specific query is calculated for anatomy‐related words from the anatomic ontology Uberon, which we transfer by a unique matrix to MMP parcels. Re‐sampling by the fsaverage brain space of freesurfer allows interoperability with other atlases. In addition, atlas‐annotated data from EBRAINS and neuroimaging data are co‐registered with MMP, enabling knowledge integration into a standardized 3D brain space.ResultOur methodologic pipeline can be used as a software to map semantic information to the brain, which we demonstrate with NeuroMMSig pathways. We further demonstrate how the resulting maps constrain TVB simulations. Face validity is provided through reproducing group‐level (AD versus controls) results of simulations integrating subject‐specific positron emission tomography when semantic information about AD stages is integrated into TVB. We elucidate how brain maps derived from different semantic queries can change simulated brain dynamics fundamentally. Literature‐derived NMDA receptor densities show significant differences between AD and healthy controls. When used to constrain TVB models, this leads to an in silico disruption of functional subnetworks in AD.ConclusionWe developed a tool for mapping semantic knowledge to anatomical brain regions. This enables multi‐scale brain simulations with increases biological plausibility and disease‐specificity for translational research.

A micro-CT-based standard brain atlas of the bumblebee

In recent years, bumblebees have become a prominent insect model organism for a variety of biological disciplines, particularly to investigate learning behaviors as well as visual performance. Understanding these behaviors and their underlying neurobiological principles requires a clear understanding of brain anatomy. Furthermore, to be able to compare neuronal branching patterns across individuals, a common framework is required, which has led to the development of 3D standard brain atlases in most of the neurobiological insect model species. Yet, no bumblebee 3D standard brain atlas has been generated. Here we present a brain atlas for the buff-tailed bumblebee Bombus terrestris using micro-computed tomography (micro-CT) scans as a source for the raw data sets, rather than traditional confocal microscopy, to produce the first ever micro-CT-based insect brain atlas. We illustrate the advantages of the micro-CT technique, namely, identical native resolution in the three cardinal planes and 3D structure being better preserved. Our Bombus terrestris brain atlas consists of 30 neuropils reconstructed from ten individual worker bees, with micro-CT allowing us to segment neuropils completely intact, including the lamina, which is a tissue structure often damaged when dissecting for immunolabeling. Our brain atlas can serve as a platform to facilitate future neuroscience studies in bumblebees and illustrates the advantages of micro-CT for specific applications in insect neuroanatomy.

Mapping the Human Brain: What Is the Next Frontier?

Abstract The structure and function of the human brain have long been the topic of exploration by scientists. To understand how the brain works, researchers have created various brain navigation maps, i.e. brain atlases, which are still being developed and improved. To clarify the trend of human brain mapping and to achieve better applications in brain science and diseases, this commentary briefly traces the history of human brain mapping and describes insights into the next stage of building brain atlases.

Histology‐Based Average Template of the Marmoset Cortex With Probabilistic Localization of Cytoarchitectural Areas

The rapid adoption of marmosets in neuroscience has created a demand for three dimensional (3D) atlases of the brain of this species to facilitate data integration in a common reference space. We report on a new open access template of the marmoset cortex (the Nencki–Monash, or NM template), representing a morphological average of 20 brains of young adult individuals, obtained by 3D reconstructions generated from Nissl-stained serial sections. The method used to generate the template takes into account morphological features of the individual brains, as well as the borders of clearly defined cytoarchitectural areas. This has resulted in a resource which allows direct estimates of the most likely coordinates of each cortical area, as well as quantification of the margins of error involved in assigning voxels to areas, and preserves quantitative information about the laminar structure of the cortex. We provide spatial transformations between the NM and other available marmoset brain templates, thus enabling integration with magnetic resonance imaging (MRI) and tracer-based connectivity data. The NM template combines some of the main advantages of histology-based atlases (e.g. information about the cytoarchitectural structure) with features more commonly associated with MRI-based templates (isotropic nature of the dataset, and probabilistic analyses). The underlying workflow may be found useful in the future development of 3D brain atlases that incorporate information about the variability of areas in species for which it may be impractical to ensure homogeneity of the sample in terms of age, sex and genetic background.

Assessment of Brain Glucose Metabolism Following Cardiac Arrest by [18F]FDG Positron Emission Tomography.

Cardiac arrest (CA) patients who survived by cardiopulmonary resuscitation (CPR) can present different levels of neurological deficits ranging from minor cognitive impairments to persistent vegetative state and brain death. The pathophysiology of the resulting brain injury is poorly understood, and whether changes in post-CA brain metabolism contribute to the injury are unknown. Here we utilized [18F]fluorodeoxyglucose (FDG)-Positron emission tomography (PET) to study in vivo cerebral glucose metabolism 72h following CA in a murine CA model. Anesthetized and ventilated adult C57BL/6 mice underwent 12-min KCl-induced CA followed by CPR. Seventy-two hours following CA, surviving mice were intraperitoneally injected with [18F]FDG (~ 186µCi/200µL) and imaged on Molecubes preclinical micro-PET/computed tomography (CT) imaging systems after a 30-min awake uptake period. Brain [18F]FDG uptake was determined by the VivoQuant software on fused PET/CT images with the 3D brain atlas. Upon completion of Positron emission tomography (PET) imaging, remaining [18F]FDG radioactivity in the brain, heart, and liver was determined using a gamma counter. Global increases in brain [18F]FDG uptake in post-CA mice were observed compared to shams and controls. The median standardized uptake value of [18F]FDG for CA animals was 1.79 versus sham 1.25 (p < 0.05) and control animals 0.78 (p < 0.01). This increased uptake was consistent throughout the 60-min imaging period and across all brain regions reaching statistical significance in the midbrain, pons, and medulla. Biodistribution analyses of various key organs yielded similar observations that the median [18F]FDG uptake for brain was 7.04%ID/g tissue for CA mice versus 5.537%ID/g tissue for sham animals, p < 0.05). This study has successfully applied [18F]FDG-PET/CT to measure changes in brain metabolism in a murine model of asystolic CA. Our results demonstrate increased [18F]FDG uptake in the brain 72h following CA, suggesting increased metabolic demand in the case of severe neurological injury. Further study is warranted to determine the etiology of these changes.

The SIGMA rat brain templates and atlases for multimodal MRI data analysis and visualization

Preclinical imaging studies offer a unique access to the rat brain, allowing investigations that go beyond what is possible in human studies. Unfortunately, these techniques still suffer from a lack of dedicated and standardized neuroimaging tools, namely brain templates and descriptive atlases. Here, we present two rat brain MRI templates and their associated gray matter, white matter and cerebrospinal fluid probability maps, generated from ex vivo {mathrm{T}}_2^ ast-weighted images (90 µm isotropic resolution) and in vivo T2-weighted images (150 µm isotropic resolution). In association with these templates, we also provide both anatomical and functional 3D brain atlases, respectively derived from the merging of the Waxholm and Tohoku atlases, and analysis of resting-state functional MRI data. Finally, we propose a complete set of preclinical MRI reference resources, compatible with common neuroimaging software, for the investigation of rat brain structures and functions.

P02-Brain-mapping on animal models

Electroencephalography (EEG) is a method that reflects the electrical activity of the brain. Changes in electrical activity can be reflected also in 2D or 3D maps Measurements of brain electrical activity in animals are essential for the validation of the pharmaco-effect on the brain. The translational approach using similar methods for quantitative EEG needs to be analysed in animal models. We measured nine brains of Wistar rats using dental X-ray. We compared these values with the model from atlas (3d Brain Atlas Reconstructor). To validate the brain model, we used the descriptive statistics. Wistar’s and human EEG were mapped using spherical spline curves and 3D spline curves. Both methods have the lowest error values – root mean squared error (RMS). By validating the model, we obtained the following statistical values: maximal upper deviation 1.466 mm, maximal lower deviation −1.660 mm, average deviation 0.091/0.300 mm, standard deviation 0.239 mm. Created module was implemented in MATLAB R2015a and allows you to record different kind of brain models. The way to evaluate these records should be comparable to that of EEG on humans. We have validated the rat brain model. Implemented module can be used for further studies in animals and humans.

Online repository of three-dimensional models of brain structures

Event Abstract Back to Event Online repository of three-dimensional models of brain structures Piotr Majka1*, Jakub M. Kowalski1, Natalia Chlodzinska1 and Daniel K. Wójcik1 1 Nencki Institute of Experimental Biology, Poland Brain atlases provide key reference frameworks for neuroscience. With the advancement of technology traditional 2D atlases are being complemented by digital 3D atlases, which are more flexible and better adapted to address modern computational, analytical and visualisation challenges of neuroscience. Although the number of available brain atlases grows, the set of tools facilitating systematic access to these data is limited. To provide an easy access to a range of neuroanatomical data we created the 3D Brain Atlas Reconstructor web service ( http://service.3dbar.org ) – an on-line repository of brain atlases and 3D models of brain structures. The essential part of the 3dBAR service is a browser-based interface providing a wide range of functionalities including: - Browsing and downloading of reconstructed 3D models of brain structures in form of polygonal mesh or a volumetric dataset; - Previewing and manipulating the models within the browser window using WebGL technology, without necessity of installing additional software; - Accessing and downloading brain atlas packages consisting of a series of SVG slices or labelled NIfTI volumes; - Generation and management of custom reconstructions (e.g. processed with non-standard pipeline or generating result in an additional file format) using on-line reconstruction wizard. Currently, there are several atlases available through the service, including various delineations of the INCF Waxholm Space mouse brain reference, Allen Brain Institute mouse reference atlas, and a collection of atlases distributed by the Scalable Brain Atlas project ( http://scalablebrainatlas.incf.org ). Some of them are intrinsically 3D atlases based on MRI scans while others are reconstructed from collections of 2D delineations. We can also host additional atlases. Modern data repository should provide a convenient interface for data exchange and allow integration of its services with other systems or software. To facilitate interoperability with third-party applications we offer a complete application programming interface consisting of a set of HTTP queries providing the developers with programmatic access to resources we provide. Currently this mechanism is used by ScalableBrainAtlas, Neurolex.org website and WaxML services developed by INCF DAI. The project is supported by an infrastructural grant from the Polish Ministry of Regional Development POIG.02.03.00-00-003/09. Keywords: digital atlasing, 3D models, computational neuroscience, Brain Atlas, web services Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012. Presentation Type: Poster Topic: Neuroinformatics Citation: Majka P, Kowalski J, Chlodzinska N and Wójcik D (2014). Online repository of three-dimensional models of brain structures. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2014.08.00107 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 21 Mar 2013; Published Online: 27 Feb 2014. * Correspondence: Dr. Piotr Majka, Nencki Institute of Experimental Biology, Warsaw, Poland, p.majka@nencki.edu.pl Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik Google Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik Google Scholar Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik PubMed Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user’s point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.Electronic Supplementary MaterialThe online version of this article (doi:10.1007/s12021-013-9199-9) contains supplementary material, which is available to authorized users.

New 3D Brain Atlas Takes Neuroimaging to Next Level

New 3D Brain Atlas Takes Neuroimaging to Next Level

Common atlas format and 3D brain atlas reconstructor: infrastructure for constructing 3D brain atlases.

One of the challenges of modern neuroscience is integrating voluminous data of diferent modalities derived from a variety of specimens. This task requires a common spatial framework that can be provided by brain atlases. The first atlases were limited to two-dimentional presentation of structural data. Recently, attempts at creating 3D atlases have been made to offer navigation within non-standard anatomical planes and improve capability of localization of different types of data within the brain volume. The 3D atlases available so far have been created using frameworks which make it difficult for other researchers to replicate the results. To facilitate reproducible research and data sharing in the field we propose an SVG-based Common Atlas Format (CAF) to store 2D atlas delineations or other compatible data and 3D Brain Atlas Reconstructor (3dBAR), software dedicated to automated reconstruction of three-dimensional brain structures from 2D atlas data. The basic functionality is provided by (1) a set of parsers which translate various atlases from a number of formats into the CAF, and (2) a module generating 3D models from CAF datasets. The whole reconstruction process is reproducible and can easily be configured, tracked and reviewed, which facilitates fixing errors. Manual corrections can be made when automatic reconstruction is not sufficient. The software was designed to simplify interoperability with other neuroinformatics tools by using open file formats. The content can easily be exchanged at any stage of data processing. The framework allows for the addition of new public or proprietary content. Electronic supplementary material The online version of this article (doi:10.1007/s12021-011-9138-6) contains supplementary material, which is available to authorized users.

Service.3dbar.org – online reconstruction of three-dimensional brain structures

Event Abstract Back to Event service.3dbar.org – online reconstruction of three-dimensional brain structures Jakub M. Kowalski1*, Piotr Majka1 and Daniel K. Wójcik1 1 Nencki Instytute of Experimental Biology, Department of Neurophysiology, Poland The knowledge of brain anatomy has been one of the foundations of neuroscience since its beginning. Traditionally the reference for brain structures has been provided by printed brain atlases containing at least one series of planar parallel brain sections containing a map of the intersected structures. However, the brain structure is three-dimensional and it is much more convenient to use three-dimensional brain atlases if possible. In order to make precious anatomical information from two-dimensional atlases available in 3D, we have developed 3D Brain Atlas Reconstructor (3dBAR) software – a free, open source solution for performing automatic reconstruction of brain structure models from two-dimensional atlases. The 3dBAR consists of a reconstructor software, a set of tools to perform conversion of existing atlases to Common Atlas Format (CAF) and a Python module for reconstructing structures from CAF data. As 3dBAR is a complex offline package we provide some of its functionality as an online service. First, we provide a repository of free atlases (derived mainly from Scalable Brain Atlas – http://scalablebrainatlas.incf.org and Waxholm Space atlases) in CAF format, available to download and use with our software with no further conversion necessary. One can also download already reconstructed models of basic structures of different quality and format. It is also possible to request customized reconstructions (e.g. processed with non-standard pipeline or generating result in an additional file format) using on-line reconstruction wizard. The service facilities are available to the user via a browser based interface. We also provide an interface for communication with external services and third-party applications. The mechanism provided is so flexible that the user web interface can be realized as a javascript-based client application and so is compatible with most of modern web browsers. Currently, Scalable Brain Atlas contains a plugin using our service to visualize particular structures and download their reconstructions. The service functionality is also shared with WaxML services developed by the INCF DAI. Our plans include also combining the service facilities with neurosimulation software. Acknowledgements The project is supported from POIG.02.03.00-00-003/09 grant. Keywords: 3d Brain Atlas Reconstructor, 3d brain structures, 3dBAR, anatomical information, Online, reconstruction, repository, Service Conference: Bernstein Conference 2012, Munich, Germany, 12 Sep - 14 Sep, 2012. Presentation Type: Poster Topic: Data analysis, machine learning, neuroinformatics Citation: Kowalski JM, Majka P and Wójcik DK (2012). service.3dbar.org – online reconstruction of three-dimensional brain structures. Front. Comput. Neurosci. Conference Abstract: Bernstein Conference 2012. doi: 10.3389/conf.fncom.2012.55.00004 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 07 May 2012; Published Online: 12 Sep 2012. * Correspondence: Mr. Jakub M Kowalski, Nencki Instytute of Experimental Biology, Department of Neurophysiology, Warsaw, województwo Mazowieckie, 02-093, Poland, j.kowalski@nencki.gov.pl Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Jakub M Kowalski Piotr Majka Daniel K Wójcik Google Jakub M Kowalski Piotr Majka Daniel K Wójcik Google Scholar Jakub M Kowalski Piotr Majka Daniel K Wójcik PubMed Jakub M Kowalski Piotr Majka Daniel K Wójcik Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain

Rats are widely used in experimental neurobiological research, and rat brain atlases are important resources for identifying brain regions in the context of experimental microsurgery, tissue sampling, and neuroimaging, as well as comparison of findings across experiments. Currently, most available rat brain atlases are constructed from histological material derived from single specimens, and provide two-dimensional or three-dimensional (3D) outlines of diverse brain regions and fiber tracts. Important limitations of such atlases are that they represent individual specimens, and that finer details of tissue architecture are lacking. Access to more detailed 3D brain atlases representative of a population of animals is needed. Diffusion tensor imaging (DTI) is a unique neuroimaging modality that provides sensitive information about orientation structure in tissues, and is widely applied in basic and clinical neuroscience investigations. To facilitate analysis and assignment of location in rat brain neuroimaging investigations, we have developed a population-averaged three-dimensional DTI atlas of the normal adult Sprague Dawley rat brain. The atlas is constructed from high resolution ex vivo DTI images, which were nonlinearly warped into a population-averaged in vivo brain template. The atlas currently comprises a selection of manually delineated brain regions, the caudate-putamen complex, globus pallidus, entopeduncular nucleus, substantia nigra, external capsule, corpus callosum, internal capsule, cerebral peduncle, fimbria of the hippocampus, fornix, anterior commisure, optic tract, and stria terminalis. The atlas is freely distributed and potentially useful for several purposes, including automated and manual delineation of rat brain structural and functional imaging data.

FEASIBILITY STUDY OF A CLINICAL BLOOD-BRAIN BARRIER OPENING ULTRASOUND SYSTEM.

In this paper, we investigate the focalization properties of single-element transducers at intermediate frequencies (500 kHz) through primate and human skulls. The study addresses the transcranial targeting involved in ultrasound-induced blood brain barrier (BBB) opening with clinically relevant targets such as the hippocampus and the basal ganglia, which are typically affected by early Alzheimer's and Parkinson's disease, respectively. The targeted brain structures were extracted from three-dimensional (3D) brain atlases registered with the skulls and used to virtually position and orient the transducers. The frequency dependence is first investigated and the capability of targeting of different structures is explored. Preliminary in vivo feasibility is investigated in mice at this frequency. A simple, affordable and convenient system is found to be feasible for BBB opening in primates and humans capable of successfully targeting the hippocampus, putamen and substantia nigra and could thus allow for its broader impact and applications.

3D standard brain of the red flour beetle Tribolium castaneum: a tool to study metamorphic development and adult plasticity

The red flour beetle Tribolium castaneum is emerging as a further standard insect model beside Drosophila. Its genome is fully sequenced and it is susceptible for genetic manipulations including RNA-interference. We use this beetle to study adult brain development and plasticity primarily with respect to the olfactory system. In the current study, we provide 3D standard brain atlases of freshly eclosed adult female and male beetles (A0). The atlases include eight paired and three unpaired neuropils including antennal lobes (ALs), optic lobe neuropils, mushroom body calyces and pedunculi, and central complex. For each of the two standard brains, we averaged brain areas of 20 individual brains. Additionally, we characterized eight selected olfactory glomeruli from 10 A0 female and male beetles respectively, which we could unequivocally recognize from individual to individual owing to their size and typical position in the ALs. In summary, comparison of the averaged neuropil volumes revealed no sexual dimorphism in any of the reconstructed neuropils in A0 Tribolium brains. Both, the female and male 3D standard brain are also used for interspecies comparisons, and, importantly, will serve as future volumetric references after genetical manipulation especially regarding metamorphic development and adult plasticity.

Stereotactic neurosurgical planning, recording, and visualization for deep brain stimulation in non-human primates

Methodologies for stereotactic neurosurgery and neurophysiological microelectrode recordings (MER) in non-human primate research typically rely on brain atlases that are not customized to the individual animal, and require paper records of MER data. To address these limitations, we developed a software tool (Cicerone) that enables simultaneous interactive 3D visualization of the neuroanatomy, neurophysiology, and neurostimulation data pertinent to deep brain stimulation (DBS) research studies in non-human primates. Cicerone allows for analysis of co-registered magnetic resonance images (MRI), computed tomography (CT) scans, 3D brain atlases, MER data, and DBS electrode(s) with predictions of the volume of tissue activated (VTA) as a function of the stimulation parameters. We used Cicerone to aid the implantation of DBS electrodes in two parkinsonian rhesus macaques, targeting the subthalamic nucleus in one monkey and the globus pallidus in the other. Cicerone correctly predicted the anatomical position of 79% and 73% of neurophysiologically defined MER sites in the two animals, respectively. In contrast, traditional 2D print atlases achieved 61% and 48% accuracy. Our experience suggests that Cicerone can improve anatomical targeting, enhance electrophysiological data visualization, and augment the design of stimulation experiments.