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Velká potřebnost koordinace standardů a osvědčených postupů v neurovědách souvisí s úsilím o to, aby se neurovědy staly disciplínou zaměřenou na data. Globální iniciativy a projekty ve výzkumu mozku jsou připraveny generovat obrovské množství neurovědeckých dat. Zároveň se neurovědy, stejně jako mnohé domény v biomedicíně, potýkají s otázkami transparentnosti, přesnosti a reprodukovatelnosti. Široce používané a validované standardy a osvědčené postupy jsou klíčem k řešení výzev ve výzkumu, který využívá velká i malá data, protože tyto standardy a postupy jsou nezbytné pro integraci různých dat a pro rozvoj robustní, efektivní a udržitelné infrastruktury podporující otevřené a reprodukovatelné neurovědy. Vypracování komunitních standardů a jejich přijetí je však obtížné. Současná situace se vyznačuje nedostatkem robustních, validovaných standardů a množstvím překrývajících se, nedostatečně rozvinutých, nevyzkoušených a nedostatečně využívaných standardů a osvědčených postupů. International Neuroinformatics Coordinating Facility (INCF), nezávislá organizace zaměřená na podporu sdílení dat prostřednictvím koordinace infrastruktury a standardů, nedávno zavedla formální proces pro hodnocení a schvalování komunitních standardů a osvědčených postupů podporující FAIR principy. Tím, že INCF formálně slouží jako standardizační organizace zaměřená na otevřené a FAIR neurovědy, pomáhá hodnotit, propagovat a koordinovat standardy a osvědčené postupy napříč neurovědami. Tento článek poskytuje přehled o tomto procesu a diskutuje o tom, jak můžou neurovědy těžit z existence specializované standardizačního orgánu. There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.

open access article This paper was produced by the International Brain Initiative Data Standards and Sharing Working Group's Taskforce on International Data Governance chaired by Damian Eke (from CCSR) As neuroscience projects increase in scale and cross international borders, different ethical principles, national and international laws, regulations, and policies for data sharing must be considered. These concerns are part of what is collectively called data governance. Whereas neuroscience data transcend borders, data governance is typically constrained within geopolitical boundaries. An international data governance framework and accompanying infrastructure can assist investigators, institutions, data repositories, and funders with navigating disparate policies. Here, we propose principles and operational considerations for how data governance in neuroscience can be navigated at an international scale and highlight gaps, challenges, and opportunities in a global brain data ecosystem. We consider how to approach data governance in a way that balances data protection requirements and the need for open science, so as to promote international collaboration through federated constructs such as the International Brain Initiative (IBI).

Axonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. Combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines, and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei.Summary statementCortical gradient expression of the area patterning gene Nr2f1 spatially and temporally controls corticopontine topographic connectivity in layer V projection neurons.

Summary The calcium-binding proteins parvalbumin and calbindin are expressed in neuronal populations regulating brain networks involved in spatial navigation, memory processes, and social interactions. Information about the numbers of these neurons across brain regions is required to understand their functional roles but is scarcely available. Employing semi-automated image analysis, we performed brain-wide analysis of immunohistochemically stained parvalbumin and calbindin sections and show that these neurons distribute in complementary patterns across the mouse brain. Parvalbumin neurons dominate in areas related to sensorimotor processing and navigation, whereas calbindin neurons prevail in regions reflecting behavioral states. We also find that parvalbumin neurons distribute according to similar principles in the hippocampal region of the rat and mouse brain. We validated our results against manual counts and evaluated variability of results among researchers. Comparison of our results to previous reports showed that neuron numbers vary, whereas patterns of relative densities and numbers are consistent., Graphical Abstract, Highlights • Brain-wide, semi-automatic quantification of parvalbumin and calbindin neurons • Largely complementary distribution of calbindin and parvalbumin neurons in mice • Comparison with several previous studies shows variable numbers but similar trends • Similar distribution of parvalbumin neurons in the rat and mouse hippocampal region, Histology; Imaging Anatomy; Optical Imaging; Molecular Neuroscience; Cellular Neuroscience

This editorial review of the Research Topic Appning describes several solutions to support the sharing of animal imaging data and processing tools. Appning promotes the federation of multiple sources of information, processing tools and shows how this contributes to the diffusion of knowledge distributed in various preclinical imaging centers.

With recent technological advances in microscopy and image acquisition of tissue sections, further developments of tools are required for viewing, transforming, and analyzing the ever-increasing amounts of high-resolution data produced. In the field of neuroscience, histological images of whole rodent brain sections are commonly used for investigating brain connections as well as cellular and molecular organization in the normal and diseased brain, but present a problem for the typical neuroscientist with no or limited programming experience in terms of the pre- and post-processing steps needed for analysis. To meet this need we have designed Nutil, an open access and stand-alone executable software that enables automated transformations, post-processing, and analyses of 2D section images using multi-core processing (OpenMP). The software is written in C++ for efficiency, and provides the user with a clean and easy graphical user interface for specifying the input and output parameters. Nutil currently contains four separate tools: (1) A transformation toolchain named “Transform” that allows for rotation, mirroring and scaling, resizing, and renaming of very large tiled tiff images. (2) “TiffCreator” enables the generation of tiled TIFF images from other image formats such as PNG and JPEG. (3) A “Resize” tool completes the preprocessing toolset and allows downscaling of PNG and JPEG images with output in PNG format. (4) The fourth tool is a post-processing method called “Quantifier” that enables the quantification of segmented objects in the context of regions defined by brain atlas maps generated with the QuickNII software based on a 3D reference atlas (mouse or rat). The output consists of a set of report files, point cloud coordinate files for visualization in reference atlas space, and reference atlas images superimposed with color-coded objects. The Nutil software is made available by the Human Brain Project (https://www.humanbrainproject.eu) at https://www.nitrc.org/projects/nutil/.

The International Brain Initiative (IBI) has been established to coordinate efforts across existing and emerging national and regional brain initiatives. This NeuroView describes how to be involved and the new opportunities for global collaboration that are emerging between scientists, scientific societies, funders, industry, government, and society.

Transgenic animal models are invaluable research tools for elucidating the pathways and mechanisms involved in the development of neurodegenerative diseases. Mechanistic clues can be revealed by applying labelling techniques such as immunohistochemistry or in situ hybridisation to brain tissue sections. Precision in both assigning anatomical location to the sections and quantifying labelled features is crucial for output validity, with either using a stereological approach or an image based feature extraction. However, both approaches are restricted by the need to manually delineate anatomical regions. To circumvent this limitation, we present the QUINT workflow for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases. The workflow is semi-automated, combining three open source software that can be operated without scripting knowledge, making it accessible to most researchers. As an example, a brain region specific quantification of amyloid plaques across whole transgenic Tg2576 mouse brain series, immunohistochemically labelled for three amyloid related antigens is demonstrated. Firstly, the whole brain image series were registered to the Allen Mouse Brain Atlas to produce customised atlas maps adapted to match the cutting plan and proportions of the sections (QuickNII software). Secondly, the labelling was segmented from the original images by the Random Forest Algorithm for supervised classification (ilastik software). Finally, the segmented images and atlas maps were used to generate plaque quantifications for each region in the reference atlas (Nutil software). The method yielded comparable results to manual delineations and to the output of a stereological method. While the use case demonstrates the QUINT workflow for quantification of amyloid plaques only, the workflow is suited to all mouse or rat brain series with labelling that is visually distinct from the background, for example for the quantification of cells or labelled proteins.

The Human Brain Project (HBP) is a European flagship project with a 10-year horizon aiming to understand the human brain and to translate neuroscience knowledge into medicine and technology. To achieve such aims, the HBP explores the multilevel complexity of the brain in space and time; transfers the acquired knowledge to brain-derived applications in health, computing, and technology; and provides shared and open computing tools and data through the HBP European brain research infrastructure. We discuss how the HBP creates a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating perspectives on societal benefits., This Community Page article presents the Human Brain Project; a European Flagship project with a ten-year horizon aiming to understand the human brain and translate neuroscience knowledge into medicine and technology.

The Human Brain Project (HBP) is one of two European flagship projects with a 10-year horizon. It aims to contribute to an integrated understanding of the human brain by providing a European brain research infrastructure that is intended for both neuroscience and neuro-inspired research as well as intense data sharing and collaboration on one of the most demanding scientific challenges of the 21st century. The human brain is an exceptional organ—it is the basis of our cognition, emotion, ability to act, language, memory, consciousness, and self-consciousness. Furthermore, due to its complexity, knowledge of the brain requires an integrative, multimodal, and multiscale approach—from signal molecules and genes, neuronal and glial cells, and microcircuits up to large networks with numerous, interconnected brain regions. The fact that approximately 86 billion nerve cells, each with approximately 10,000 synapses, interact in a dynamic manner with each other illustrates the challenge that the project faces.

The transgenic rat model of Huntington disease expressing a fragment of mutant HTT (tgHD rat) has been thoroughly characterized and reproduces hallmark symptoms of human adult-onset HD. Pursuing the optimization of this model for evaluation of translational therapeutic approaches, the F344 inbred rat strain was considered as advantageous genetic background for the expression of the HD transgenic construct. In the present study, a novel congenic line of the SPRDtgHD transgenic model of HD, carrying 51 CAG repeats, was generated on the F344 rat genetic background. To assess the behavioral phenotype, classical assays investigating motor function, emotion, and sensorimotor gating were applied, along with automated screening of metabolic and activity parameters as well as operant conditioning tasks. The neuropathological phenotype was analyzed by immunohistochemistry and ex vivo magnetic resonance imaging. F344tgHD rats displayed markedly reduced anxiety-like behavior in the social interaction test and elevated impulsivity traits already at 3 months of age. Neuropathologically, reduced striatal volume and pronounced aggregation of mutant huntingtin in several brain regions were detected at later disease stage. In conclusion, the congenic F344tgHD model reproduces key aspects of the human HD phenotype, substantiating its value for translational therapeutic approaches.

The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource.

Spinally projecting neurons in the rostral ventrolateral medulla (RVLM) play a critical role in the generation of vasomotor sympathetic tone and are thought to receive convergent input from neurons at every level of the neuraxis; the factors that determine their ongoing activity remain unresolved. In this study we use a genetically restricted viral tracing strategy to definitively map their spatially diffuse connectome. We infected bulbospinal RVLM neurons with a recombinant rabies variant that drives reporter expression in monosynaptically connected input neurons and mapped their distribution using an MRI-based volumetric atlas and a novel image alignment and visualization tool that efficiently translates the positions of neurons captured in conventional photomicrographs to Cartesian coordinates. We identified prominent inputs from well-established neurohumoral and viscero-sympathetic sensory actuators, medullary autonomic and respiratory subnuclei, and supramedullary autonomic nuclei. The majority of inputs lay within the brainstem (88-94%), and included putative respiratory neurons in the pre-Botzinger Complex and post-inspiratory complex that are therefore likely to underlie respiratory-sympathetic coupling. We also discovered a substantial and previously unrecognized input from the region immediately ventral to nucleus prepositus hypoglossi. In contrast, RVLM sympathetic premotor neurons were only sparsely innervated by suprapontine structures including the paraventricular nucleus, lateral hypothalamus, periaqueductal gray, and superior colliculus, and we found almost no evidence of direct inputs from the cortex or amygdala. Our approach can be used to quantify, standardize and share complete neuroanatomical datasets, and therefore provides researchers with a platform for presentation, analysis and independent reanalysis of connectomic data.

Modern high throughput brain wide profiling techniques for cells and their morphology, connectivity, and other properties, make the use of reference atlases with 3D coordinate frameworks essential. However, anatomical location of observations made in microscopic sectional images from rodent brains is typically determined by comparison with 2D anatomical reference atlases. A major challenge in this regard is that microscopic sections often are cut with orientations deviating from the standard planes used in the reference atlases, resulting in inaccuracies and a need for tedious correction steps. Overall, efficient tools for registration of large series of section images to reference atlases are currently not widely available. Here we present QuickNII, a stand-alone software tool for semi-automated affine spatial registration of sectional image data to a 3D reference atlas coordinate framework. A key feature in the tool is the capability to generate user defined cut planes through the reference atlas, matching the orientation of the cut plane of the sectional image data. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between experimental image and atlas is defined, without introducing distortions in the original experimental images. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of sectional images to reduce the amount of manual steps required. By having coordinates assigned to the experimental images, further analysis of the distribution of features extracted from the images is greatly facilitated. Copyright: © 2019 Puchades et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Glial cells in their plurality pervade the human brain and impact on brain structure and function. A principal component of the emerging glial doctrine is the hypothesis that astrocytes, the most abundant type of glial cells, trigger major molecular processes leading to brain ageing. Astrocyte biology has been examined using molecular, biochemical and structural methods, as well as 3D brain imaging in live animals and humans. Exosomes are extracelluar membrane vesicles that facilitate communication between glia, and have significant potential for biomarker discovery and drug delivery. Polymorphisms in DNA repair genes may indirectly influence the structure and function of membrane proteins expressed in glial cells and predispose specific cell subgroups to degeneration. Physical exercise may reduce or retard age-related brain deterioration by a mechanism involving neuro-glial processes. It is most likely that additional information about the distribution, structure and function of glial cells will yield novel insight into human brain ageing. Systematic studies of glia and their functions are expected to eventually lead to earlier detection of ageing-related brain dysfunction and to interventions that could delay, reduce or prevent brain dysfunction.

Axonal tracing techniques are powerful tools for exploring the structural organization of neuronal connections. Tracers such as biotinylated dextran amine (BDA) and Phaseolus vulgaris leucoagglutinin (Pha-L) allow brain-wide mapping of connections through analysis of large series of histological section images. We present a workflow for efficient collection and analysis of tract-tracing datasets with a focus on newly developed modules for image processing and assignment of anatomical location to tracing data. New functionality includes automatic detection of neuronal labeling in large image series, alignment of images to a volumetric brain atlas, and analytical tools for measuring the position and extent of labeling. To evaluate the workflow, we used high-resolution microscopic images from axonal tracing experiments in which different parts of the rat primary somatosensory cortex had been injected with BDA or Pha-L. Parameters from a set of representative images were used to automate detection of labeling in image series covering the entire brain, resulting in binary maps of the distribution of labeling. For high to medium labeling densities, automatic detection was found to provide reliable results when compared to manual analysis, whereas weak labeling required manual curation for optimal detection. To identify brain regions corresponding to labeled areas, section images were aligned to the Waxholm Space (WHS) atlas of the Sprague Dawley rat brain (v2) by custom-angle slicing of the MRI template to match individual sections. Based on the alignment, WHS coordinates were obtained for labeled elements and transformed to stereotaxic coordinates. The new workflow modules increase the efficiency and reliability of labeling detection in large series of images from histological sections, and enable anchoring to anatomical atlases for further spatial analysis and comparison with other data.

Water diffusion magnetic resonance imaging (dMRI) is a powerful tool for studying biological tissue microarchitectures in vivo. Recently, there has been increased effort to develop quantitative dMRI methods to probe both length scale and orientation information in diffusion media. Diffusion spectrum imaging (DSI) is one such approach that aims to resolve such information based on the three-dimensional diffusion propagator at each voxel. However, in practice, only the orientation component of the propagator function is preserved when deriving the orientation distribution function. Here, we demonstrate how a straightforward extension of the linear spherical deconvolution (SD) model can be used to probe tissue orientation structures over a range (or "spectrum") of length scales with minimal assumptions on the underlying microarchitecture. Using high b-value Cartesian q-space data on a rat brain tissue sample, we demonstrate how this "restriction spectrum imaging" (RSI) model allows for separating the volume fraction and orientation distribution of hindered and restricted diffusion, which we argue stems primarily from diffusion in the extraneurite and intraneurite water compartment, respectively. Moreover, we demonstrate how empirical RSI estimates of the neurite orientation distribution and volume fraction capture important additional structure not afforded by traditional DSI or fixed-scale SD-like reconstructions, particularly in gray matter. We conclude that incorporating length scale information in geometric models of diffusion offers promise for advancing state-of-the-art dMRI methods beyond white matter into gray matter structures while allowing more detailed quantitative characterization of water compartmentalization and histoarchitecture of healthy and diseased tissue.

The mammalian brain is characterized by orderly spatial distribution of its cellular components, commonly referred to as topographical organization. The topography of cortical and subcortical maps is thought to represent functional or computational properties. In the present investigation, we have studied map transformations and organizing principles in the projections from the cerebral cortex to the pontine nuclei, with emphasis on the mapping of the cortex as a whole onto the pontine nuclei. Following single or multiple axonal tracer injections into different cortical regions, three-dimensional (3-D) distributions of anterogradely labeled axons in the pontine nuclei were mapped. All 3-D reconstructed data sets were normalized to a standardized local coordinate system for the pontine nuclei and uploaded in a database application (FACCS, Functional Anatomy of the Cerebro-Cerebellar System, available via The Rodent Brain Workbench, http://www.rbwb.org). The database application allowed flexible use of the data in novel combinations, and use of a previously published data sets. Visualization of different combinations of data was used to explore alternative principles of organization. As a result of these analyses, a principal map of the topography of corticopontine projections was developed. This map followed the organization of early spatiotemporal gradients present in the cerebral cortex and the pontine nuclei. With the principal map for corticopontine projections, a fairly accurate prediction of pontine target area can be made for any site of origin in the cerebral cortex. The map and the underlying shared data sets represent a basis for modeling of topographical organization and structure-function relationships in this system.

The cerebral cortex conveys major input to the granule cell layer of the cerebellar hemispheres by way of the pontine nuclei. Cerebrocortical projections terminate in multiple, widely distributed clusters in the pontine nuclei. This clustered organization is thought to provide the transition between the different organizational principles of the cerebrum and cerebellum, and indicates that parallel processing occurs at multiple sites in the pontine nuclei. At a cellular level, however, it is unknown whether individual cerebropontine neurons target pontocerebellar cells located in different clusters or not. We have employed anterograde axonal tracing and 3D computerized reconstruction techniques to characterize the branching pattern and morphology of individual cerebropontine axons from the primary somatosensory cortex (SI). Our findings show that 43% of the cerebrobulbar fibers arising from SI whisker representations provide two or three fibers entering the pontine nuclei, whereas 39% have only one fiber, and the remaining 18% do not project to the pontine nuclei. Thus, it appears that a majority of cerebropontine axons originating in SI whisker representations diverge to contact multiple, separated pontocerebellar cells. Further, 84% of the somatosensory cerebropontine fibers are collateral branches from cerebrobulbar and/or cerebrospinal parent fibers, while 16% are direct cerebropontine projections without a further descending projection. A range of thicknesses of the fibers entering the pontine nuclei were observed, with collaterals of corticobulbar fibers having the smallest diameter. Taken together, these findings may be related to previously described separate cerebropontine transmission lines with different properties.

Integration of dispersed and complicated information collected from the brain is needed to build new knowledge. But integration may be hampered by rigid presentation formats, diversity of data formats among laboratories, and lack of access to lower level data. We have addressed some of the fundamental issues related to this challenge at the level of anatomical data, by producing a coordinate based digital atlas and database application for a major projection system in the rat brain: the cerebro-ponto-cerebellar system. This application, Functional Anatomy of the Cerebro-Cerebellar System in rat (FACCS), is available via the Rodent Brain WorkBench (http://www.rbwb.org/). The data included are x,y,z-coordinate lists describing exact distributions of tissue elements (axonal terminal fields of axons, or cell bodies) that are labeled with axonal tracing techniques. All data are translated to a common local coordinate system to facilitate across animal comparison. A search capability allows queries based on, e.g. location of tracer injection sites, tracer category, size of the injection sites, and contributing author. A graphic search tool allows the user to move a volume cursor inside a coordinate system to detect particular injection sites having connections to a specific tissue volume at chosen density levels. Tools for visualization and analysis of selected data are included, as well as an option to download individual data sets for further analysis. With this application, data and metadata from different experiments are mapped into the same information structure and made available for re-use and re-analysis in novel combinations. The application is prepared for future handling of data from other projection systems as well as other data categories.

The magnetic resonance imaging (MRI)-detectable T1 contrast agent manganese (Mn2+) has recently been introduced as a neural tracer in rodents, birds, and monkeys. We have tested to what extent this in vivo method is useful for three-dimensional (3-D) survey of connectivity patterns in the rat somatosensory system. A commonly available 3 T human clinical MRI scanner was used to trace neural pathways following focal injection of manganese chloride (MnCl2) in the somatosensory cortex. Six to 10 h after MnCl2 injection, we found significant signal enhancement in major projection systems, including corticocortical, corticostriatal, corticothalamic, corticotectal, corticopontine, and corticospinal pathways. To facilitate the assignment of anatomic localization to the observed Mn2+ signal enhancement, we registered the MRI data with a 3-D digital reconstruction of a stereotaxic rat brain atlas. Across-animal comparison using the digital model allowed demonstration of a corticothalamic 3-D topographic organization in agreement with previously published two-dimensional topographic schemes based on classical neural tracing data. We conclude that anterograde MnCl2/MRI tracing allows rapid analysis of topographic organization across multiple brain regions. The method allows a higher data throughput for 3-D studies of large-scale brain connectivity than conventional methods based on tissue sectioning.

Anatomical and electrophysiological evidence has raised the possibility that corelease of GABA and glutamate occurs at hippocampal mossy fibre synapses which, however, lack the vesicular GABA transporter VGAT. Here, we apply immunogold cytochemistry to show that GABA, like glutamate, has a close spatial relation to synaptic vesicles in rat mossy fibre terminals, implying that a mechanism exists to package GABA in synaptic vesicles. We also show that GABAA and AMPA receptors are colocalized at mossy fibre synapses. The expression of GABA and GABAA receptors is, however, weaker than in inhibitory synapses. Electrical stimuli that recruit mossy fibres evoke monosynaptic GABAA receptor-mediated signals in post-synaptic targets that show marked frequency-dependent facilitation and sensitivity to group II metabotropic receptors, two features that are characteristic of mossy fibre transmission. These results provide further evidence for GABA and glutamate cotransmission at mossy fibre synapses, although paired pre- and post-synaptic recordings will be required to determine the role of GABA at this unusual synapse.

Neuroanatomy is in need of high throughput methods for reliably recording the distribution of tissue elements across large brain regions. We compared two methods for recording the spatial distribution of identified neuronal elements such as tracer labelled cell bodies or axonal plexuses. The methods compared were computerized image-combining microscopy (semi-automatic method), which is a user controlled method providing feedback during digitization, and digital camera technology with image analysis software (automatic method). Both methods were applied to biotinylated dextran amine labelled axonal plexuses and FluoroRuby labelled neuronal cell bodies, in the pontine nuclei of the rat. Coordinates were assigned to the labelled elements using both methods. The ensuing distribution patterns were compared, section by section, and in three-dimensional reconstruction. The experienced investigator, using th es emi-automatic method, could detect individual axons, fragments of axons, weakly labelled elements, and overlapping cell bodies, better than the automatic system. Nevertheless, both methods detected the overall distribution of the labelled axons and cells investigated. Automatic methods provide opportunities fo re fficient large-scale data acquisition of labelled neuronal elements.

The entorhinal cortex (EC) plays a central role in episodic memory and is among the earliest sites of neurodegeneration and neurofibrillary tangle formation in Alzheimer's disease. Given its importance in memory and dementia, the ability to selectively modulate gene expression or neuronal function in the EC is of widespread interest. To this end, several recent studies have taken advantage of a transgenic line in which the tetracycline transactivator (tTA) was placed under control of the neuropsin (Nop) promoter to limit transgene expression within the medial EC and pre-/parasubiculum. Although the utility of this driver is contingent on its spatial specificity, no detailed neuroanatomical analysis of its expression has yet been conducted. We therefore undertook a systematic analysis of Nop-tTA expression using a lacZ reporter and have made the complete set of histological sections available through the Rodent Brain Workbench tTA atlas, www.rbwb.org. Our findings confirm that the highest density of tTA expression is found in the EC and pre-/parasubiculum, but also reveal considerable expression in several other cortical areas. Promiscuous transgene expression may account for the appearance of pathological protein aggregates outside of the EC in mouse models of Alzheimer's disease using this driver, as we find considerable overlap between sites of delayed amyloid deposition and regions with sparse (β-galactosidase reporter labeling. While different tet-responsive lines can display individual expression characteristics, our results suggest caution when designing experiments that depend on precise localization of gene products controlled by the Nop-tTA or other spatially restrictive transgenic drivers.

Comparisons of microscopical neuroanatomic data from different experiments and investigators are typically hampered by the use of different section planes and dissimilar techniques for data documentation. We have developed a framework for visualization and comparison of section-based, spatial distribution data, in brain stem nuclei. This framework provides opportunities for harmonized data presentation in neuroinformatics databases. Three-dimensional computerized reconstructions of the rat brain stem and precerebellar nuclei served as a basis for establishing internal coordinate systems for the pontine nuclei and the precerebellar divisions of the sensory trigeminal nuclei. Coordinate based diagrams were used for presentation of experimental data (spatial distribution of labelled neurons and axonal plexuses) from standard angles of view. Each nuclear coordinate system was based on a cuboid bounding box with a defined orientation. The bounding box was size-adjusted to touch cyto- and myeloarchitectonically defined boundaries of the individual nuclei, or easily identifiable nearby landmarks. We exemplify the use of these internal coordinate systems with dual retrograde neural tracing data from pontocerebellar and trigeminocerebellar systems. The new experimental data were combined, in the same coordinate based diagrams, with previously published data made available via a neuroinformatics data repository (www.nesys.uio.no/Database, see also www.cerebellum.org). Three-dimensional atlasing, internal nuclear coordinate systems, and consistent formats for presentation of neuroanatomic data in web-based data repositories, offer new opportunities for efficient analysis and re-analysis of neuroanatomic data.

In the primary somatosensory cortex (SI), the body surface is mapped in a relatively continuous fashion, with adjacent body regions represented in adjacent cortical domains. In contrast, somatosensory maps found in regions of the cerebellar hemispheres, which are influenced by the SI through a monosynaptic link in the pontine nuclei, are discontinuous ("fractured") in organization. To elucidate this map transformation, the authors studied the organization of the first link in the SI-cerebellar pathway, the SI-pontine projection. After injecting anterograde axonal tracers into electrophysiologically defined parts of the SI, three-dimensional reconstruction and computer-graphic visualization techniques were used to analyze the spatial distribution of labeled fibers. Several target regions in the pontine nuclei were identified for each major body representation. The labeled axons formed sharply delineated clusters that were distributed in an inside-out, shell-like fashion. Upper lip and other perioral representations were located in a central core, whereas extremity and trunk representations were found more externally. The multiple clusters suggest that the pontine nuclei contain several representations of the SI map. Within each representation, the spatial relationships of the SI map are largely preserved. This corticopontine projection pattern is compatible with recently proposed principles for the establishment of subcortical topographic patterns during development. The largely preserved spatial relationships in the pontine somatotopic map also suggest that the transformation from an organized topography in SI to a fractured map in the cerebellum takes place primarily in the mossy fiber pontocerebellar projection.

The dorsal nucleus of the lateral lemniscus (DNLL) is an auditory structure of the brainstem. It plays an important role in binaural processing and sound localization and it provides the inferior colliculus with an inhibitory projection. The DNLL is a highly conserved auditory structure across mammals, but differences among species in its detailed organization have been reported. The main goal of this study was to analyze the topographic organization of the cat DNLL. Single, small iontophoretic injections of biotinylated dextran amine were made at different loci in the central nucleus of the inferior colliculus (CNIC). The distribution of the labeled structures in the ipsi- and contralateral DNLL was computer reconstructed in three dimensions. In individual sections, a band of labeling is seen in the DNLL on both sides. These two labeled bands occupy symmetric locations and are made of retrogradely labeled neurons with flattened dendritic arbors oriented parallel to each other. Moreover, the ipsilateral labeled band contains labeled terminal fibers parallel to the labeled dendrites. With three-dimensional reconstructions, it becomes evident that the labeled band seen in each individual DNLL section represents a slice through a rostrocaudally oriented lamina. The shape, size, orientation, and location of this lamina change as the injection site is shifted along the tonotopic axis of the CNIC. An injection in the low-frequency region of the CNIC, produces a lamina that resembles a flattened tube located in the dorsolateral corner of the DNLL. An injection in the high-frequency region of the CNIC, by contrast, results in a lamina that is an elongated sheet located at the ventromedial surface of the DNLL. The laminae of the DNLL might constitute the structural basis for its tonotopical organization. Previous studies (Merchan MA, et al. 1994. J Comp Neurol 342:259–278) in conjunction with our current results suggest that the laminar organization in the DNLL might be common among mammals. J. Comp. Neurol. 407:349–366, 1999. © 1999 Wiley-Liss, Inc.

We have studied the anatomic organization of corticopontine neurons in the monkey cytoarchitectonic areas 3a, 3b, 1, and 2. The purpose was to provide information about the composition of somatosensory cortical influence on cerebellar operations. Large tracer injections were made in the pontine nuclei. Retrogradely labeled neurons were confined to cortical layer 5, with the largest cell bodies located in area 3a and the smallest in area 3b. The distribution of labeled cells was quantitatively recorded and displayed in three-dimensional reconstructions and in flat maps. We have: (1) compared the average densities of labeled cells among the cytoarchitectonic areas, and (2) outlined the distribution of labeled cells within the cortical map of the body surface representation. The average density of labeled cells was considerably higher in areas 3a, 1, and 2, compared to area 3b. This finding suggests that areas 3a, 1, and 2 are more engaged in cerebellar operations than area 3b. We found marked density gradients of labeled cells within areas 3b, 1, and 2, but not within area 3a. When the density maps from areas 3b, 1, and 2 were superimposed on previously published somatotopic maps, we found higher average densities of corticopontine neurons in regions representing the trunk and proximal limbs, than in regions representing the distal forelimb. Thus, the distal forelimb representation, which is known to be strongly emphasized in terms of cortical volume, appears not to be correspondingly emphasized in the corticopontine projection. J. Comp. Neurol. 406:109–128, 1999. © 1999 Wiley-Liss, Inc.

The grand challenge in neuroscience is—it would seem—the effort of understanding the structure, function, and development of the nervous system in health and disease. Such understanding requires the integration of huge amounts of heterogeneous and complex data collected at multiple levels of investigation. The interdisciplinary field of neuroinformatics combines neuroscience with information science/technology and deals with the creation of the data systems that will be required to achieve such integration. The grand challenge in neuroinformatics is to achieve advanced, ultimately seamless, integration of all data needed to understand the nervous system. Integration of neuroscience data may be compared to a multi-dimensional puzzle. One dimension of the puzzle is time. Thus, the adult brain and each developmental stage hold their own set of structural and functional data. Another dimension is the multiple levels of investigation. The levels span from genes and molecules through synapses, cells, networks, regions, and whole brain, to cognition and behavior. Fitting data together across time and within and across the many levels of investigation is a gigantic challenge. From a neuroinformatics perspective, the challenge may be described as related to 1) accumulation, storage, management, and sharing of data—the “databasing challenge”, 2) development and sharing of tools for data analyses—the “tools challenge”, and 3) creation and validation of computational models of brain structure and function built on the available data—the “modeling challenge”. The databasing challenge: Each of the multiple levels of investigation generates vast amounts of primary data of many different formats. Challenges for database developments include the establishment of standards for ontologies, metadata descriptions, and data formats, and the creation of mechanisms (from technical to sociological and legal) for sharing the vast amount of data among researchers (Amari et al, 2002; Koslow, 2002; Eckersley et al., 2003). Ontology is more than terminology. The ontology of a database is the definition of the elements and the relationships between the elements included in the database. It is difficult to arrive at a standard ontology but important to strive towards clarification of definitions and concepts, allowing data to be more easily compared and interpreted. Metadata, “data about data”, are made up by data describing the primary research data. Data collected in an experiment are only meaningful if a number of experimental conditions and parameters are provided. Research articles contain metadata but not in a structured format. Standards for minimal sets of metadata for experimental data are needed and can realistically be developed. Many types of data formats are used in neuroscience. Standardized formats allow easier use of shared tools and comparison of data produced by different communities and laboratories. Standard practices for sharing of data are also important for the development of large databases. With an increasing number of large databases, data sharing in neuroscience may gradually become as common and useful as it is in genomics, where the existence of very large bodies of data is leading to increased knowledge as well as products and services linked to the improvement of human health. The tools challenge: Many techniques for visualization and analysis of data have been developed by other fields. But the neuroscience community is in need of special-purpose, optimized tools and algorithms. Data only make sense in the context of tools. Navigation and manipulation of data requires a multitude of tools. Integration builds not only on the accumulation of data within and across the many levels of investigation, but also on the tools used to compare data, create higher order representations, and extract principles. Over time, some of these tools may even benefit researchers in branches of the information sciences as they deal with issues related to brain function such as machine learning and robotic task planning. The modeling challenge: As in all of science, the understanding of the systems and phenomena under study involves the development of models that are descriptive as well as predictive and explanatory. In neuroscience, the systems and phenomena are among the most difficult to model due to the many levels of investigation required to understand function and the complexities present at each level (Grillner et al. 2005). The only way to validate models of the sophisticated functions carried out by the nervous system is through confrontation with the data sets of neuroscience, using tools developed via neuroinformatics. All of the above outlined challenges are demanding. Few neuroscience laboratories have the combined expertise to deal with all aspects of neuroinformatics: databasing, tools development and sharing, and modeling. Most neuroscience laboratories have only a few experienced researchers and carry a responsibility to train younger researchers. Data and tools sharing in the context of training is not an easy task. Performing the experiments, collecting the data, carrying out the initial analyses, and completing reports and publications often take most of the available time and resources. Standardization at all levels of investigation, additional data acquisition for completeness, and sharing may not be on the agenda. With the establishment of larger consortia of multiple research groups, as well as the establishment of new data production oriented institutions and services, neuroscience research is gradually changing. Such larger enterprises are developing an increasing number of data systems, standards, and requirements for populating the systems. With a growing number of available data systems covering one or several levels of investigation, it is to be expected that the neuroscience field will gradually move towards the use of such systems. The field of neuroinformatics will deal with the further development of the data systems and the challenge of making the systems work together—becoming interoperable. Recently, new opportunities for international coordination in the field of neuroinformatics have emerged. With an international science policy mandate, multi-disciplinary and multi-national panels have analyzed the field and provided recommendations for its further development (OECD, 1999, 2002). This effort has provided a basis for global coordinated actions (for review, see Bjaalie and Grillner, 2007) within all of the three legs of neuroinformatics (databasing, tools development and sharing, and modeling), as outlined above. Neuroinformatics is a large area of multidisciplinary research poised to play an important role in supporting neuroscience in the information age.

There is a growing awareness in the neuroscience community of the need for databases extending from genes to cognition and disease mechanisms. Such databases are important for data sharing as well as for modeling and use of computational tools at different levels. The development of this area

The somatotopically organized whisker barrel field of the rat primary somatosensory (S1) cortex is a commonly used model system for anatomical and physiological investigations of sensory processing. The neural connections of the barrel cortex have been extensively mapped. But most investigations have focused on connections to limited regions of the brain, and overviews in the literature of the connections across the brain thus build on a range of material from different laboratories, presented in numerous publications. Furthermore, given the limitations of the conventional journal article format, analyses and interpretations are hampered by lack of access to the underlying experimental data. New opportunities for analyses have emerged with the recent release of an online resource of experimental data consisting of collections of high-resolution images from 6 experiments in which anterograde tracers were injected in S1 whisker or forelimb representations. Building on this material, we have conducted a detailed analysis of the brain wide distribution of the efferent projections of the rat barrel cortex. We compare our findings with the available literature and reports accumulated in the Brain Architecture Management System (BAMS2) database. We report well-known and less known intracortical and subcortical projections of the barrel cortex, as well as distinct differences between S1 whisker and forelimb related projections. Our results correspond well with recently published overviews, but provide additional information about relative differences among S1 projection targets. Our approach demonstrates how collections of shared experimental image data are suitable for brain-wide analysis and interpretation of connectivity mapping data.

We have explored basic rules guiding the early development of topographically organized projections, employing the rat corticopontine projection as a model system. Using anterograde in vivo tracing with 1,1',dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI), we studied the distribution of labelled fibers in the pontine nuclei in relation to cortical site of origin during the first postnatal week. Labelled corticopontine fibers enter the pontine nuclei in distinct, sharply defined zones. The putative terminal fibers typically occupy lamella-like subspaces. Related to changes in cortical site of origin, we describe mediolateral, internal to external, and caudorostral distribution gradients in the pontine nuclei. Fibers originating in the anterolateral cortex occupy an internal central core, while implantations at increasing distance from the anterolateral cortex produce 1) more externally located lamellae, and 2) a caudal to rostral shift in fiber location. Previous investigations have shown that pontocerebellar neurons migrate into the ventral pons in a temporal sequence (Altman and Bayer [1987] J. Comp. Neurol. 257:529). The earliest arriving neurons occupy the central core and later arriving neurons settle in more externally and rostrally located subspaces. We hypothesize that the earliest arriving corticopontine fibers grow into the then only available zone of pontocerebellar neurons (central core), attracted by a diffusible chemotropic cue. Later arriving fibers grow into correspondingly later and more externally and rostrally located contingents of pontocerebellar neurons. Thus, we propose that the topographical organization in the early postnatal corticopontine projection is determined by simple temporal and spatial gradients operative within source (cerebral cortex) and target region (pontine nuclei).

Detailed knowledge about the anatomical organization of axonal connections is important for understanding normal functions of brain systems and disease-related dysfunctions. Such connectivity data are typically generated in neuroanatomical tract-tracing experiments in which specific axonal connections are visualized in histological sections. Since journal publications typically only accommodate restricted data descriptions and example images, literature search is a cumbersome way to retrieve overviews of brain connectivity. To explore more efficient ways of mapping, analyzing, and sharing detailed axonal connectivity data from the rodent brain, we have implemented a workflow for data production and developed an atlas system tailored for online presentation of axonal tracing data. The system is available online through the Rodent Brain WorkBench (www.rbwb.org; Whole Brain Connectivity Atlas) and holds experimental metadata and high-resolution images of histological sections from experiments in which axonal tracers were injected in the primary somatosensory cortex. We here present the workflow and the data system, and exemplify how the online image repository can be used to map different aspects of the brain-wide connectivity of the rat primary somatosensory cortex, including not only presence of connections but also morphology, densities, and spatial organization. The accuracy of the approach is validated by comparing results generated with our system with findings reported in previous publications. The present study is a contribution to a systematic mapping of rodent brain connections and represents a starting point for further large-scale mapping efforts. © 2011 Zakiewicz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

It has been suggested that spinal cord long-term potentiation (LTP) may contribute to hypersensitivity and hyperalgesia. We have investigated if noxious stimulus-induced spinal cord LTP might have a long lasting effect on supraspinal neuronal activity. First, we verified that spinal LTP was induced by electrical high frequency stimuli (HFS) conditioning applied to the sciatic nerve. The C-fibre response in the dorsal horn reached a twofold increase 150 min after HFS (t-test, p0.01, n=6). Then, to study the metabolic supraspinal activity following the same stimulation protocol, we used small animal positron emission tomography (PET) and the glucose analog [(18)F]-fluorodeoxyglucose (FDG). With this combined approach we measured changes in regional supraspinal activity at two time points in HFS conditioned and in sham animals; acute (immediately after HFS/sham, n=4) and late phase (150 min after HFS/sham, n=10). Comparisons between HFS and sham groups revealed that induction of spinal LTP was followed by an acute metabolic response in the primary somatosensory cortex (S1), but also various slower metabolic adaptations in brain regions involved in modulation of nociceptive signaling and descending inhibition, i.e., amygdala, periaqueductal gray (PAG), rostral ventromedial medulla (RVM), and the dorsolateral pontomesencephalic tegmentum (DLPT) (t-test, p0.05). The study demonstrates that PET may be used as an in vivo method to study regional brain metabolic activity between different conditions. It is concluded that noxious sciatic stimuli which induce spinal cord LTP also affect supraspinal metabolic activity. We suggest that these changes might illustrate a supraspinal maladaptive dysfunction involved in pain hypersensitivity and hyperalgesia.

The spatial organization of visual corticopontine neurons was studied both at a “large scale” (in relation to cortical visual field maps) and at a “small scale” (in relation to cortical modular organization). Large injections of horseradish peroxidase-wheat germ agglutinin were made in the pontine nuclei. In complete series of sections from parts of areas 17, 18, and 19, the position of each retrogradely labeled neuron was recorded with an x-y plotter connected to the microscope stage. Each cell was thus given a set of x, y, and z coordinates. After alignment of the sections, three-dimensional computer reconstructions of the distribution of the labeled cells were made. With program RPOP (developed by Blackstad and Bjaalie, ′88), the reconstructions were studied with different rotations, scaling, etc. In addition, section-independent parts of reconstructions were isolated („windows”) and further analyzed. Curved parts were automatically unfolded for inspection of distribution patterns and determination of cell densities. The spatial distribution of the labeled cells was analyzed within small windows, where density gradients are negligible. We confirm and extend previous demonstrations of a large-scale aggregation of visual corticopontine cells due to density gradients by showing that densities of corticopontine neurons increase linearly as a function of distance from paracentral to lower visual field representations in area 17 (and partly in areas 18 and 19). We demonstrate that density gradients are steeper in area 17 than in area 18. For example, clear-cut differences between the areas in mediolateral density gradients are found. These findings are discussed in relation to the different visual field maps of the areas and the existence of a similar visual field representation in corticopontine projections from different visual areas. The type of small-scale distribution (randomness or non-randomness, aggregation into clusters, bands, etc.) was studied with statistical methods. Such analysis shows that the labeled cells within small zones are non-randomly distributed in all three areas. In most cases, the analysis indicates an aggregated spatial distribution. A possible relationship to the cortical map of direction selectivity is discussed. To our knowledge, this study is the first to combine the use of three-dimensional computer reconstructions of a population of labeled neurons, with subsequent statistical analysis of apatial point (cell distribution) patterns.

The granule cell layer of the cerebellar hemispheres contains a patchy and noncontinuous map of the body surface, consisting of a complex mosaic of multiple perioral tactile representations. Previous physiological studies have shown that cerebrocerebellar mossy fibre projections, conveyed through the pontine nuclei, are mapped in registration with peripheral tactile projections to the cerebellum. In contrast to the fractured cerebellar map, the primary somatosensory cortex (SI) is somatotopically organized. To understand better the map transformation occurring in cerebrocerebellar pathways, we injected axonal tracers in electrophysiologically defined locations in Sprague-Dawley rat folium crus IIa, and mapped the distribution of retrogradely labelled neurons within the pontine nuclei using three-dimensional (3-D) reconstructions. Tracer injections within the large central upper lip patch in crus IIa-labelled neurons located centrally in the pontine nuclei, primarily contralateral to the injected side. Larger injections (covering multiple crus IIa perioral representations) resulted in labelling extending only slightly beyond this region, with a higher density and more ipsilaterally labelled neurons. Combined axonal tracer injections in upper lip representations in SI and crus IIa, revealed a close spatial correspondence between the cerebropontine terminal fields and the crus IIa projecting neurons. Finally, comparisons with previously published three-dimensional distributions of pontine neurons labelled following tracer injections in face receiving regions in the paramedian lobule (downloaded from http://www.rbwb.org) revealed similar correspondence. The present data support the coherent topographical organization of cerebro-ponto-cerebellar networks previously suggested from physiological studies. We discuss the present findings in the context of transformations from cerebral somatotopic to cerebellar fractured tactile representations.

The Global Science Forum (GSF) of the OECD has initiated a new international organization, INCF, to further the development of Neuroinformatics as a global effort with the support of all ministers of research within OECD. This presentation explains the background for the establishment of the INCF, outlines some of the goals, and defines the operations of the INCF Secretariat in relation the INCF National nodes and the general neuroscience community.

International audience; The cerebropontocerebellar mossy fiber system is a major CNS sensorimotor pathway. We used a double-retrograde axonal tracing technique (red and green beads) to chart in rats the pontocerebellar projection to different electrophysiologically defined climbing fiber zones in the posterior lobe (face-receiving A2 zone and forelimb-and hindlimb-receiving parts of the C1 zone in the paramedian lobule and copula pyramidis, respectively). Individual cortical injection sites were verified as located in a given zone by mapping the pattern of cell labeling in the inferior olive, whereas labeled cells in the pontine nuclei were mapped using computer-aided three-dimensional reconstruction techniques. A number of topographical differences were found for the pontine projection to the individual zones. Projections to the A2 zone were bilateral, whereas to both parts of the C1 zone, the inputs were mainly contralateral. Furthermore, the A2 (face), C1 (forelimb), and C1 (hindlimb) zone projections were centered in progressively more caudal parts of the pontine nuclei with little or no overlap between them. The areas occupied by cell labeling for each zone corresponded closely to territories in the pontine nuclei shown previously to receive projections from somatotopically equivalent regions of the somatosensory cortex. This precise cerebropontocer-ebellar topography, defined by climbing fiber somatotopy, is a new principle of organization for linking somatosensory and cerebellar cortices. The convergence of direct and indirect sensory projections is likely to have important implications for cerebellar cortical processing.

The major cortical–subcortical re-entrant pathways through the basal ganglia and cerebellum are considered to represent anatomically segregated channels for information originating in different cortical areas. A capacity for integrating unique combinations of cortical inputs has been well documented in the basal ganglia circuits but is largely undefined in the precerebellar circuits. To compare and quantify the amount of overlap that occurs in the first link of the cortico–ponto–cerebellar pathway, a dual tracing approach was used to map the spatial relationship between projections originating from the primary somatosensory cortex (SI), the secondary somatosensory cortex (SII), and the primary motor cortex (MI). The anterograde tracers biotinylated dextran amine and Fluoro-Ruby were injected into homologous whisker representations of either SI and SII, or SI and MI. The ensuing pontine labeling patterns were analyzed using a computerized three-dimensional reconstruction approach. The results demonstrate that whisker-related projections from SI and MI are largely segregated. At some locations, the two projections are adjoining and partly overlapping. Furthermore, SI contributes significantly more corticopontine projections than MI. By comparison, projections from corresponding representations in SI and SII terminate in similar parts of the pontine nuclei and display considerable amounts of spatial overlap. Finally, comparison of corticopontine and corticostriatal projections in the same experimental animals reveals that SI–SII overlap is significantly larger in the pontine nuclei than in the neostriatum. These structural differences indicate a larger capacity for integration of information within the same sensory modality in the pontocerebellar system compared to the basal ganglia. J. Comp. Neurol. 478:306–322, 2004. © 2004 Wiley-Liss, Inc.

To understand the relationship between structure and function in specific brain regions, it is necessary to ascertain which anatomical features are physiologically relevant. Physiological studies of brain function traditionally have been set in the context of anatomical features based on cytoarchitectonics and myeloarchitectonics, but the relationship between structure and function in this context can be complex. Alternative schemes of anatomical organization, such as that based on hodology (the mapping of projections) may provide greater insight. Here, we make a direct comparison of the hodological and the cytoarchitectonic organization of the vestibular complex in the mid-term chicken embryo, using retrograde tracing and three-dimensional reconstruction. In one set of experiments, vestibulospinal and vestibulo-ocular neuron groups were selectively labeled with biotin dextran-amines and aligned with the cytoarchitectonically defined vestibular nuclei in alternating sections that were then combined into intercalated three-dimensional models. This allowed a semiquantitative analysis of the apportionment of individual hodological groups among cytoarchitectonic nuclei. In another set of experiments, vestibulospinal and vestibulo-ocular neuron groups were labeled differentially with fluorescent dextran-amines, three-dimensionally reconstructed, and subjected to a quantitative analysis of spatial overlap. Our results provide the first three-dimensional representation and quantitative analysis of the hodological compartmentalization of the vestibular complex (the "hodological mosaic"). They also show directly how each hodologically defined neuron group relates to the conventional vestibular nuclei, underscoring the fact that the units of the hodological mosaic do not bear a one-to-one correspondence to the cytoarchitectonic nuclear divisions. Some hodologically defined groups are localized to restricted portions of a nucleus, whereas others overlap multiple nuclei. Thus, hodology and cytoarchitectonic features appear to be separately regulated in the vestibular complex of the chicken embryo, possibly through different sets of positional specification mechanisms. The three-dimensional representations we present here provide a foundation for integrating anatomical, physiological, developmental, and evolutionary studies of the vestibular system.

Publisher Summary This chapter discusses that mossy fiber input to the cerebellum is coded primarily in spatial patterns, as reflected by the fractured: somatotopy of the receptive fields in the granular layer. A new theory of how information is coded along the parallel fibers in the cerebellar cortex is explained in the chapter. Feedback inhibition by Golgi cells loosely synchronizes granule cell firing along the parallel fiber beam. Simultaneous activation of granular layer patches causes synchronized firing of the activated granule cells and transforms the spatial code into a temporal code onto the parallel fiber beam. The corticopontine projection contributes by distributing a renormalized copy of cortical activity to multiple patches and possibly by equalizing activity across fibers.

We have compared the band-like distribution of the Purkinje cell-specific polypeptides zebrin I and zebrin II with the spatial organization of tactile projections to crus IIa in the cerebellar hemisphere of the rat. Maps of tactile responses in the granular layer of the cerebellar hemispheres are fractured into discontinuous regions, termed "patches". High-density micromapping was used to identify specific patches and their boundaries within this fractured somatotopic map. In one series of experiments, medial and lateral boundaries of the large central ipsilateral upper lip-related patch were identified and labeled with either Fast Blue or India Ink. Following immunocytochemical processing, the band-like distribution of immunostained Purkinje cells (zebrin-positive bands) and the identified patch boundaries were digitized and reconstructed in three dimensions. Comparisons between these two features demonstrate a spatial correspondence between zebrin transitions and the boundaries of the electrophysiologically defined upper lip-related patch. In another series of experiments, we outlined the boundaries or centers of several smaller patches consistently located in the medial portion of the folium. Again, we found a correspondence between the distribution of granule cell layer tactile patches and the zebrin staining pattern. The correspondence between tactile projection patterns and molecular features demonstrated in the present study implies that there is a distinct and largely fixed spatial pattern of organization in the cerebellar hemispheres. We discuss possible causal connections and developmental determinates, as well as the physiological significance of the correspondence between the two features.

The ventral complex of the lateral lemniscus (VCLL, i.e., the ventral and intermediate nuclei) is composed of cells embedded in the fibers of the lateral lemniscus. These cells are involved in the processing of monaural information and receive input from the collaterals of the fibers ascending to the inferior colliculus. Whereas tonotopic organization is a feature of all other nuclei of the auditory system, this functional principle is debated in the VCLL. We have made focal injections of the tracer biotinylated dextran amine into different frequency band representations of the inferior colliculus in cat. Retrogradely labeled cells and terminal fibers (collaterals of efferent local axons and other ascending lemniscal fibers) were found in the ipsilateral VCLL. The spatial distribution of the labeling was analyzed using three-dimensional (3-D) reconstruction and computer graphical visualization techniques. A complex topographic organization was found. In all cases, labeled fibers and cells were distributed in multiple clusters throughout the dorsoventral extent of the VCLL. The shape, size, and location of the labeled clusters suggest an interdigitation of clusters assigned to different frequency-band representations. But an overall mediolateral distribution gradient was observed, with high frequencies represented medially and lower frequencies progressively more laterally.We conclude that the clusters may represent discontinuous frequency-band compartments as a counterpart to the continuous laminar compartments in the remaining auditory nuclei. The 3-D orderly mosaic pattern indicates that the VCLL preserves the spectral decomposition originated in the cochlea in a way that facilitates across-frequency integration.

A unique feature of the auditory brainstem is the divergent/convergent nature of the path- ways from the auditory nerve to the inferior colliculus (IC, reviewed in Irvine, 1992). Some of the projections from the cochlear nucleus complex to the IC are direct while others are indirect via the superior olivary complex and the nuclei of the lateral lemniscus (NLL). In these nuclei, sig- nificant monaural and binaural information are extracted from the auditory signal.