Collaboratories

No abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34569/1/1440360103_ftp.pd

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

NeuroTerrain – a client-server system for browsing 3D biomedical image data sets

BACKGROUND: Three dimensional biomedical image sets are becoming ubiquitous, along with the canonical atlases providing the necessary spatial context for analysis. To make full use of these 3D image sets, one must be able to present views for 2D display, either surface renderings or 2D cross-sections through the data. Typical display software is limited to presentations along one of the three orthogonal anatomical axes (coronal, horizontal, or sagittal). However, data sets precisely oriented along the major axes are rare. To make fullest use of these datasets, one must reasonably match the atlas' orientation; this involves resampling the atlas in planes matched to the data set. Traditionally, this requires the atlas and browser reside on the user's desktop; unfortunately, in addition to being monolithic programs, these tools often require substantial local resources. In this article, we describe a network-capable, client-server framework to slice and visualize 3D atlases at off-axis angles, along with an open client architecture and development kit to support integration into complex data analysis environments. RESULTS: Here we describe the basic architecture of a client-server 3D visualization system, consisting of a thin Java client built on a development kit, and a computationally robust, high-performance server written in ANSI C++. The Java client components (NetOStat) support arbitrary-angle viewing and run on readily available desktop computers running Mac OS X, Windows XP, or Linux as a downloadable Java Application. Using the NeuroTerrain Software Development Kit (NT-SDK), sophisticated atlas browsing can be added to any Java-compatible application requiring as little as 50 lines of Java glue code, thus making it eminently re-useable and much more accessible to programmers building more complex, biomedical data analysis tools. The NT-SDK separates the interactive GUI components from the server control and monitoring, so as to support development of non-interactive applications. The server implementation takes full advantage of data center's high-performance hardware, where it can be co-localized with centrally-located, 3D dataset repositories, extending access to the researcher community throughout the Internet. CONCLUSION: The combination of an optimized server and modular, platform-independent client provides an ideal environment for viewing complex 3D biomedical datasets, taking full advantage of high-performance servers to prepare images and subsets of associated meta-data for viewing, as well as the graphical capabilities in Java to actually display the data

Brain-Inspired Computing

This open access book constitutes revised selected papers from the 4th International Workshop on Brain-Inspired Computing, BrainComp 2019, held in Cetraro, Italy, in July 2019. The 11 papers presented in this volume were carefully reviewed and selected for inclusion in this book. They deal with research on brain atlasing, multi-scale models and simulation, HPC and data infra-structures for neuroscience as well as artificial and natural neural architectures

Modelo de referencia de laboratorios virtuales y aplicación a sistemas de teleeducación

El origen de esta tesis es encontrar respuestas a la siguiente pregunta: ¿De que forma se puede optimizar el uso de los equipos de laboratorio para que puedan ser utilizados por el máximo número de personas? La opción básica que se ha elegido es el control remoto de los instrumentos a través de internet. Con ello se consigue una accesibilidad total del laboratorio: a cualquier hora, en cualquier día, se pueden realizar medidas sencillamente con disponer de una conexión a internet. Partiendo de esta situación, se ha realizado un estudio de la evolución y situación actal de la instrumentación, de internet y de la teleeducación, los tres pilares en los que se apoya este trabajo. Se observa cómo la instrumentación está tendiendo a la conectividad global al comenzar a incorporar una conexión a red, y la posibilidad de transferir directamente resultados de medida o incluso el control directo del equipo a través de un navegador. Comienza una colaboración que se prevé estrecha entre internet y la instrumentación. La educación a distancia también está tomando un camino similar. El nuevo canal de comunicación que supone la red y la evolución de los ordenadores está permitiendo que se puedan conseguir entornos de trabajo para educación que incorporan desde el sencillo texto con hiperenlaces, herramienta básica del web, hasta transmisión en directo de clases, con vídeo, audio, transparencias e intercomunicación entre los usuarios. De esta forma, la distancia que separa al profesor de los estudiantes y a los estudiantes entre sí, queda minimizada por las capacidades de colaboración y diálogo existentes. A partir de aquí en la tesis se ha pasado al estudio de los instrumentos virtuales, las piezas básicas para el montaje de un laboratorio virtual. Se ha hecho una extensa investigación y clasificación de unos y otros lo cual ha permitido hacerse una idea de los elementos necesarios para la realización de un laboratorio virtual.Rodrigo Peñarrocha, VM. (2003). Modelo de referencia de laboratorios virtuales y aplicación a sistemas de teleeducación [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/7221Palanci

A Guide to Authentic e-Learning

Part of the groundbreaking Connecting with e-Learning series, A Guide to Authentic e-Learning provides effective, working examples to engage learners with authentic tasks in online settings. As technology continues to open up possibilities for innovative and effective teaching and learning opportunities, students and teachers are no longer content to accept familiar classroom or lecture-based pedagogies that rely on information delivery and little else. Situated and constructivist theories advocate that learning is best achieved in circumstances resembling the real-life application of knowledge. While there are multiple learning design models that share similar foundations, authentic e-learning tasks go beyond process to become complex, sustained activities that draw on realistic situations to produce realistic outcomes