Neuroscience data and tool sharing

Eckersley, Peter; Egan, Gary F.; Schutter, Erik De; Tang, Yi‐Yuan; Novák, Mirko; Šebesta, Václav; Matthiessen, Line; Jaaskelainen, Irio P.; Ruotsalainen, Ulla; Herz, Andreas V. M.; Hoffmann, Klaus‐Peter; Ritz, Raphael; Ravindranath, Viji; Beltrame, Francesco; Амари, Шун-ичи; Usui, Shiro; Lee, Sang Yup; Pelt, Jaap van; Bjaalie, Jan G.; Wróbel, Anna; Silva, Fernando Mira Da; González, Carmen; Grillner, Sten; Verschure, Paul F. M. J.; Dalkara, Turgay; Bennett, Rob; Willshaw, David; Koslow, Stephen H.; Miller, Perry L.; Subramaniam, Shankar; Toga, Arthur W.

doi:10.1007/s12021-003-0002-1

Cited by 56 publications

(16 citation statements)

References 19 publications

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“…The present release of Micro3D for the general user community is inspired by recent efforts in the field of neuroinformatics, and new initiatives for the sharing of tools and developments among neuroscience laboratories (Amari et al, 2002;Eckersley et al, 2003). These initiatives are important at several levels.…”

Section: Discussionmentioning

confidence: 99%

Micro3d: Computer Program for Three-Dimensional Reconstruction, Visualization, and Analysis of Neuronal Populations and Brain Regions

Bjaalie

Leergaard

Pettersen

2006

International Journal of Neuroscience

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This article presents a computer program, Micro3D, designed for 3-D reconstruction, visualization, and analysis of coordinate-data (points and lines) recorded from serial sections. The software has primarily been used for studying shapes and dimension of brain regions (contour line data) and distributions of cellular elements such as neuronal cell bodies or axonal terminal fields labeled with tract-tracing techniques (point data). The tissue elements recorded could equally well be labeled with use of other techniques, the only requirement being that the data collected are saved as x,y,z coordinates. Data are typically imported from image-combining computerized microscopy systems or image analysis systems, such as Neurolucida (MicroBrightField, Colchester, VT) or analySIS (Soft Imaging System, Gmbh, Münster, Germany). System requirements are a PC running LINUX. Reconstructions in Micro3D may be rotated and zoomed in real-time, and submitted to perspective viewing and stereo-imaging. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the reconstruction. Flattening of curved sheets of points layers (e.g., neurons in a layer) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps. Opportunities for translation of data from different reconstructions into common coordinate systems are also provided. This article demonstrates the use of Micro3D for visualization of complex neuronal distribution patterns in somatosensory and auditory systems. The software is available for download on conditions posted at the NeSys home pages (http://www.nesys.uio.no/) and at The Rodent Brain Workbench (http://www.rbwb.org/).

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Section: Discussionmentioning

confidence: 99%

Micro3d: Computer Program for Three-Dimensional Reconstruction, Visualization, and Analysis of Neuronal Populations and Brain Regions

Bjaalie

Leergaard

Pettersen

2006

International Journal of Neuroscience

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“…In parallel, data collection, storage, and sharing, have been improved at both technical and policy levels, have advanced (Eckersley et al, 2003), together with technologies used to consolidate, search and access the data (Van Horn and Toga, 2009; Wood et al, 2014). This allows massive amounts of data to be consolidated into databases and searched in efficient ways.…”

Section: Motivationmentioning

confidence: 99%

A Multi-facetted Visual Analytics Tool for Exploratory Analysis of Human Brain and Function Datasets

Angulo

Schneider

Oliver

et al. 2016

Front. Neuroinform.

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Brain research typically requires large amounts of data from different sources, and often of different nature. The use of different software tools adapted to the nature of each data source can make research work cumbersome and time consuming. It follows that data is not often used to its fullest potential thus limiting exploratory analysis. This paper presents an ancillary software tool called BRAVIZ that integrates interactive visualization with real-time statistical analyses, facilitating access to multi-facetted neuroscience data and automating many cumbersome and error-prone tasks required to explore such data. Rather than relying on abstract numerical indicators, BRAVIZ emphasizes brain images as the main object of the analysis process of individuals or groups. BRAVIZ facilitates exploration of trends or relationships to gain an integrated view of the phenomena studied, thus motivating discovery of new hypotheses. A case study is presented that incorporates brain structure and function outcomes together with different types of clinical data.

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“…The shift to full web-based solutions has occurred somewhat haphazardly since the early 2000s (Eckersley et al, 2003; Millan and Yunda, 2014; Sherif et al, 2014; Wood et al, 2014) and closely tracked the increasing rise and power of the web browser as a middleware platform and the expressiveness of the JavaScript programming language. Web-based solutions are especially appealing as they do not require the installation of any client-side software other than a standard web browser which enhances accessibility and usability.…”

Section: Introductionmentioning

confidence: 99%

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

Bernal-Rusiel

Rannou²,

Gollub

et al. 2017

Front. Neuroinform.

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In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

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Neuroscience data and tool sharing

Cited by 56 publications

References 19 publications

Micro3d: Computer Program for Three-Dimensional Reconstruction, Visualization, and Analysis of Neuronal Populations and Brain Regions

Micro3d: Computer Program for Three-Dimensional Reconstruction, Visualization, and Analysis of Neuronal Populations and Brain Regions

A Multi-facetted Visual Analytics Tool for Exploratory Analysis of Human Brain and Function Datasets

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

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