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Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
https://github.com/cwatson/braingraph/
Software R package for performing graph theory analyses of brain MRI data.
Proper citation: brainGraph (RRID:SCR_017260) Copy
http://www.brainimagelibrary.org
Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data.
Proper citation: Brain Image Library (RRID:SCR_017272) Copy
https://www.mbfbioscience.com/neuroinfo
Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies.
Proper citation: NeuroInfo (RRID:SCR_017346) Copy
https://github.com/zuoxinian/CCS
Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.
Proper citation: Connectome Computation System (RRID:SCR_017342) Copy
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) Copy
https://www.ibis-network.org/index.html
Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers
Proper citation: IBIS Network (RRID:SCR_017399) Copy
Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.
Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy
Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
Proper citation: NeMO Analytics (RRID:SCR_018164) Copy
http://bioinformatics.istge.it/cldb/indexes.html
Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.
Proper citation: Hyper Cell Line Database (RRID:SCR_007730) Copy
Popular science magazine which includes news and blogs on topics including Health & Medicine, Mind & Brain, Technology, Space, Human origins, Living World, Environment, and Physics & Math. NIF Indexes include: The Brain: DISCOVER blogger, columnist, and contributing editor Carl Zimmer''s monthly column will make your brain happy. Discover Interview: The magazine''s signature in-depth discussion with the leading lights of the world of science Vital Signs: A medical mystery, as written by the doctor involved.
Proper citation: Discover Magazine (RRID:SCR_008787) Copy
http://www.functionalneurogenesis.com/blog/
A blog focusing on the function of adult neurogenesis in the dentate gyrus of the hippocampus, including discussion of scientific research papers, methods and protocols, and other trends or observations about the field.
Proper citation: Functional Neurogenesis (RRID:SCR_008830) Copy
http://www.msbrainbank.org.au/
Biomaterial supply resource which provides high quality and well-chracaterized brain tissue samples for MS research. Registered MS brain donors and their families are kept up to date on the latest progress in MS research.
Proper citation: Multiple Sclerosis Research Australia Brain Bank (RRID:SCR_010747) Copy
http://titan.biotec.uiuc.edu/bee/honeybee_project.htm
A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.
Proper citation: Honey Bee Brain EST Project (RRID:SCR_002389) Copy
http://www.fmri.wfubmc.edu/cms/software
Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.
Proper citation: Advanced Neuroscience Imaging Research Laboratory Software Packages (RRID:SCR_002926) Copy
http://www.brain-connectivity-toolbox.net
A large selection of complex network measures in Matlab that are increasingly used to characterize structural and functional brain connectivity datasets. Several people have contributed to the toolbox, and if you wish to contribute with a new function or set of functions, please contact Olaf Sporns. All efforts have been made to avoid errors, but users are strongly urged to independently verify the accuracy and suitability of toolbox functions for the chosen application. Please report bugs or substantial improvements.
Proper citation: Brain Connectivity Toolbox (RRID:SCR_004841) Copy
http://ki.se/ki/jsp/polopoly.jsp?d=29350&a=36311&l=en
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study to investigate symptoms of Attention Deficit Hyperactivity Disorder (ADHD) according to DSM-IV in adults with special focus on attention deficit. Information is used from the Swedish Twin study of Adults: genes and Environment (STAGE) from the Swedish Twin Registry. ADHD-discordant and concordant samples of pairs of twins for ADHD are selected from STAGE for studies of brain structure and function with Functional Magnetic Resonance Imaging (fMRI).
Proper citation: KI Biobank STAGE-ADHD (RRID:SCR_005921) Copy
http://ki.se/imm/cefalo-studien
Saliva taken from participants in a study investigating the association between environmental exposures and brain tumors in children aged 7-19 years and the interaction between these risk factors and genetic polymorphisms, which may confer susceptibility to effects of exogenous agents. Sample types: * Saliva Number of sample donors: 886 (sample collection completed)
Proper citation: KI Biobank - CEFALO (RRID:SCR_006034) Copy
A topical portal and providers of brain injury rehabilitation services. Resources * Pharmacology Guide * Glossary of Brain Injury Terms * Brain Injury Research Articles * Common Brain Injury Assessment Tools / Rating Scale * Certified Continuing Education Courses * Links to Resource Sites
Proper citation: Centre for Neuro Skills (RRID:SCR_006106) Copy
http://www.alz.washington.edu/
A clinical research, neuropathological research and collaborative research database that uses data collected from 29 NIA-funded Alzheimer's Disease Centers (ADCs). The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Any researcher, whether affiliated with an ADC or not, may request a data file for analysis or aggregate data tables. Requested aggregate data tables are produced and returned as soon as the queue allows (usually within 1-3 days depending on the complexity).
Proper citation: National Alzheimer's Coordinating Center (RRID:SCR_007327) Copy
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