117 research outputs found
INCF -- new capability for global coordination in neuroinformatics
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
Topography of the complete corticopontine projection: From experiments to principal Maps
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
PENGEMBANGAN JOBSHEET TRAINER PLC SEBAGAI SUMBER PEMBELAJARAN PRAKTIKUM OTOMASI INDUSTRI
Penelitian ini bertujuan untuk mengembangkan sebuah media pembelajaran sebagai sumber belajar mahasiswa berupa jobsheet praktikum Otomasi Industri. Selain itu, penelitian ini bertujuan untuk mengetahui kelayakan dari jobsheet yang telah dikembangkan serta melihat hasil implementasi jobsheet setelah digunakan oleh para mahasiswa. Penelitian ini dirasa perlu dilakukan untuk membuat sebuah sumber belajar yang layak serta dapat memberikan manfaat lebih khususnya mahasiswa Elektronika Indsutri. Metodologi yang digunakan oleh penulis pada penelitian ini menggunakan penelitian campuran dengan model rancangan campuran sekuensial eksploratori, menggunakan pendekatan penelitian dan pengembangan (Research and Development). Berdasarkan hasil penelitian yang telah dilakukan didapatkan hasil bahwa jobsheet trainer PLC Phoenix Contact ILC 130/131 Starterkit telah dikembangkan sesuai tahapan penelitian dan layak digunakan serta dapat diimplementasikan dalam praktikum Otomasi Industri.---This study aims to develop learning media as a source of students learning in form of practical Industrial Automation jobsheet. Besides, this study aims to prove the feasibility of jobsheet that has been developed and the result of jobsheet implementation by students. This study is considered important to create a decent learning resource and provide benefits, especially for Electronics Industries Students, Department of Electrical Engineering Education, Faculty of Technology and Vocational Skills Education. The methodology used by the authors in this study is mixed research model with exploratory sequences, using a research and development approach (research and development). Based on study results, trainer jobsheet of PLC Phoenix Contact ILC 130/131 Starterkit feasible to be used and can be implemented in practice Industrial Automation
Digital Atlas of Anatomical Subdivisions and Boundaries of the Rat Hippocampal Region
The rat hippocampal region is frequently studied in relation to learning and memory processes and brain diseases. The region is complex, consisting of multiple subdivisions that are challenging to delineate anatomically. Published atlases of the rat brain typically lack the underlying histological criteria necessary to identify boundaries, and textbooks descriptions of the region are often inadequately illustrated and thus difficult to relate to experimental data. An overview of both anatomical features and criteria used to delineate boundaries is required to assign location to experimental material from the hippocampal region. To address this issue, we have developed a web-based atlas application in which images of histological sections are integrated with new and up-to-date criteria for subdividing the rat hippocampus formation, fasciola, and associated parahippocampal regions. The atlas application consists of an interactive image viewer with high-resolution images of an extensive series of sections stained for NeuN, calbindin, and parvalbumin, and an index of structures with detailed descriptions of the criteria used to define the boundaries. Images can be inspected with a graphical overlay of selected subregions. Bi-directional links between images and the index of structures are provided. In summary, we provide a novel content-rich digital atlas resource facilitating identification of morphological features relevant for delineating the anatomical subdivisions of the rat hippocampal region. The atlas application is available at http://www.rbwb.org
Three-Dimensional Atlas System for Mouse and Rat Brain Imaging Data
Tomographic neuroimaging techniques allow visualization of functionally and structurally specific signals in the mouse and rat brain. The interpretation of the image data relies on accurate determination of anatomical location, which is frequently obstructed by the lack of structural information in the data sets. Positron emission tomography (PET) generally yields images with low spatial resolution and little structural contrast, and many experimental magnetic resonance imaging (MRI) paradigms give specific signal enhancements but often limited anatomical information. Side-by-side comparison of image data with conventional atlas diagram is hampered by the 2-D format of the atlases, and by the lack of an analytical environment for accumulation of data and integrative analyses. We here present a method for reconstructing 3-D atlases from digital 2-D atlas diagrams, and exemplify 3-D atlas-based analysis of PET and MRI data. The reconstruction procedure is based on two seminal mouse and brain atlases, but is applicable to any stereotaxic atlas. Currently, 30 mouse brain structures and 60 rat brain structures have been reconstructed. To exploit the 3-D atlas models, we have developed a multi-platform atlas tool (available via The Rodent Workbench, http://rbwb.org) which allows combined visualization of experimental image data within the 3-D atlas space together with 3-D viewing and user-defined slicing of selected atlas structures. The tool presented facilitates assignment of location and comparative analysis of signal location in tomographic images with low structural contrast
Recommendations for repositories and scientific gateways from a neuroscience perspective
Digital services such as repositories and science gateways have become key
resources for the neuroscience community, but users often have a hard time
orienting themselves in the service landscape to find the best fit for their
particular needs. INCF (International Neuroinformatics Coordinating Facility)
has developed a set of recommendations and associated criteria for choosing or
setting up and running a repository or scientific gateway, intended for the
neuroscience community, with a FAIR neuroscience perspective. These
recommendations have neurosciences as their primary use case but are often
general. Considering the perspectives of researchers and providers of
repositories as well as scientific gateways, the recommendations harmonize and
complement existing work on criteria for repositories and best practices. The
recommendations cover a range of important areas including accessibility,
licensing, community responsibility and technical and financial sustainability
of a service.Comment: 10 pages, submitted to Scientific Dat
QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain
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 a stereological approach or image-based feature extraction typically used. 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. First, 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). Second, 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
Linking brain structure, activity and cognitive function through computation
Understanding the human brain is a “Grand Challenge” for 21st century research. Computational approaches enable large and complex datasets to be addressed efficiently, supported by artificial neural networks, modeling and simulation. Dynamic generative multiscale models, which enable the investigation of causation across scales and are guided by principles and theories of brain function, are instrumental for linking brain structure and function. An example of a resource enabling such an integrated approach to neuroscientific discovery is the BigBrain, which spatially anchors tissue models and data across different scales and ensures that multiscale models are supported by the data, making the bridge to both basic neuroscience and medicine. Research at the intersection of neuroscience, computing and robotics has the potential to advance neuro-inspired technologies by taking advantage of a growing body of insights into perception, plasticity and learning. To render data, tools and methods, theories, basic principles and concepts interoperable, the Human Brain Project (HBP) has launched EBRAINS, a digital neuroscience research infrastructure, which brings together a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits
Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies
In experimental neuroscientific research, anatomical location is a key attribute of experimental observations and critical for interpretation of results, replication of findings, and comparison of data across studies. With steadily rising numbers of publications reporting basic experimental results, there is an increasing need for integration and synthesis of data. Since comparison of data relies on consistently defined anatomical locations, it is a major concern that practices and precision in the reporting of location of observations from different types of experimental studies seem to vary considerably. To elucidate and possibly meet this challenge, we have evaluated and compared current practices for interpreting and documenting the anatomical location of measurements acquired from murine brains with different experimental methods. Our observations show substantial differences in approach, interpretation and reproducibility of anatomical locations among reports of different categories of experimental research, and strongly indicate that ambiguous reports of anatomical location can be attributed to missing descriptions. Based on these findings, we suggest a set of minimum requirements for documentation of anatomical location in experimental murine brain research. We furthermore demonstrate how these requirements have been applied in the EU Human Brain Project to optimize workflows for integration of heterogeneous data in common reference atlases. We propose broad adoption of some straightforward steps for improving the precision of location metadata and thereby facilitating interpretation, reuse and integration of data
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