Literature DB >> 29519589

Data integration through brain atlasing: Human Brain Project tools and strategies.

Ingvild E Bjerke1, Martin Øvsthus1, Eszter A Papp1, Sharon C Yates1, Ludovico Silvestri2, Julien Fiorilli3, Cyriel M A Pennartz3, Francesco S Pavone2, Maja A Puchades1, Trygve B Leergaard1, Jan G Bjaalie4.   

Abstract

The Human Brain Project (HBP), an EU Flagship Initiative, is currently building an infrastructure that will allow integration of large amounts of heterogeneous neuroscience data. The ultimate goal of the project is to develop a unified multi-level understanding of the brain and its diseases, and beyond this to emulate the computational capabilities of the brain. Reference atlases of the brain are one of the key components in this infrastructure. Based on a new generation of three-dimensional (3D) reference atlases, new solutions for analyzing and integrating brain data are being developed. HBP will build services for spatial query and analysis of brain data comparable to current online services for geospatial data. The services will provide interactive access to a wide range of data types that have information about anatomical location tied to them. The 3D volumetric nature of the brain, however, introduces a new level of complexity that requires a range of tools for making use of and interacting with the atlases. With such new tools, neuroscience research groups will be able to connect their data to atlas space, share their data through online data systems, and search and find other relevant data through the same systems. This new approach partly replaces earlier attempts to organize research data based only on a set of semantic terminologies describing the brain and its subdivisions.
Copyright © 2018 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Entities:  

Keywords:  Brain atlasing; Data integration; Neuroinformatics

Mesh:

Year:  2018        PMID: 29519589     DOI: 10.1016/j.eurpsy.2018.02.004

Source DB:  PubMed          Journal:  Eur Psychiatry        ISSN: 0924-9338            Impact factor:   5.361


  10 in total

1.  Brain signal predictions from multi-scale networks using a linearized framework.

Authors:  Espen Hagen; Steinn H Magnusson; Torbjørn V Ness; Geir Halnes; Pooja N Babu; Charl Linssen; Abigail Morrison; Gaute T Einevoll
Journal:  PLoS Comput Biol       Date:  2022-08-12       Impact factor: 4.779

2.  Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain.

Authors:  David M Young; Siavash Fazel Darbandi; Grace Schwartz; Zachary Bonzell; Deniz Yuruk; Mai Nojima; Laurent C Gole; John Lr Rubenstein; Weimiao Yu; Stephan J Sanders
Journal:  Elife       Date:  2021-02-11       Impact factor: 8.140

3.  Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool.

Authors:  Maja A Puchades; Gergely Csucs; Debora Ledergerber; Trygve B Leergaard; Jan G Bjaalie
Journal:  PLoS One       Date:  2019-05-29       Impact factor: 3.240

4.  The Human Brain Project-Synergy between neuroscience, computing, informatics, and brain-inspired technologies.

Authors:  Katrin Amunts; Alois C Knoll; Thomas Lippert; Cyriel M A Pennartz; Philippe Ryvlin; Alain Destexhe; Viktor K Jirsa; Egidio D'Angelo; Jan G Bjaalie
Journal:  PLoS Biol       Date:  2019-07-01       Impact factor: 8.029

5.  Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging.

Authors:  Anan Li; Yue Guan; Hui Gong; Qingming Luo
Journal:  Genomics Proteomics Bioinformatics       Date:  2019-12-02       Impact factor: 7.691

6.  QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain.

Authors:  Sharon C Yates; Nicolaas E Groeneboom; Christopher Coello; Stefan F Lichtenthaler; Peer-Hendrik Kuhn; Hans-Ulrich Demuth; Maike Hartlage-Rübsamen; Steffen Roßner; Trygve Leergaard; Anna Kreshuk; Maja A Puchades; Jan G Bjaalie
Journal:  Front Neuroinform       Date:  2019-12-03       Impact factor: 4.081

Review 7.  Evolution of Human Brain Atlases in Terms of Content, Applications, Functionality, and Availability.

Authors:  Wieslaw L Nowinski
Journal:  Neuroinformatics       Date:  2021-01

8.  3D Atlas of the Pituitary Gland of the Model Fish Medaka (Oryzias latipes).

Authors:  Muhammad Rahmad Royan; Khadeeja Siddique; Gergely Csucs; Maja A Puchades; Rasoul Nourizadeh-Lillabadi; Jan G Bjaalie; Christiaan V Henkel; Finn-Arne Weltzien; Romain Fontaine
Journal:  Front Endocrinol (Lausanne)       Date:  2021-08-23       Impact factor: 5.555

9.  Towards an Architecture of a Multi-purpose, User-Extendable Reference Human Brain Atlas.

Authors:  Wieslaw L Nowinski
Journal:  Neuroinformatics       Date:  2021-11-26

10.  Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies.

Authors:  Ingvild E Bjerke; Martin Øvsthus; Krister A Andersson; Camilla H Blixhavn; Heidi Kleven; Sharon C Yates; Maja A Puchades; Jan G Bjaalie; Trygve B Leergaard
Journal:  Front Neuroanat       Date:  2018-11-02       Impact factor: 3.856

  10 in total

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