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https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry

https://usa.brainreader.net

Software application as image segmentation tool. Brain volumetry assessment software. Processes MRI scans and provides self explanatory patient report with total brain volume, hippocampal volume and volumetric data on key segments of brain measured against healthy database.

Proper citation: Neuroreader (RRID:SCR_017309) Copy   

•   Source: SciCrunch Registry

https://github.com/bheAI/MonkeyCBP_CLI

Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.

Proper citation: MonkeyCBP (RRID:SCR_017640) Copy   

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http://www.nitrc.org/projects/kwyk/

Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation.

Proper citation: Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pubmed/28653482

Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room.

Proper citation: StimVision (RRID:SCR_017457) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/brainmaker

Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context.

Proper citation: BrainMaker (RRID:SCR_017666) Copy   

•   Source: SciCrunch Registry

https://github.com/AllenInstitute/AllenSDK

Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.

Proper citation: Allen Software Development Kit (RRID:SCR_018183) Copy   

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http://netbio.bgu.ac.il/tissuenet/

Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues.

Proper citation: TissueNet - The Database of Human Tissue Protein-Protein Interactions (RRID:SCR_002052) Copy   

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http://www.cabiatl.com/mricro/anatomy/home.html

Annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. This neuroanatomy atlas shows regions on normalized MRI scans. Normalization is the process of warping a brain to match a standard size, orientation and shape of other brains. You can normalize MRI scans using programs like AIR, FLIRT or SPM. Once normalized, the overall shape of your MRI scan will approximately match those in this atlas. However, normalization preserves the unique sulcal features of each brain, so there will be some variation between your image and the images shown in this atlas. There is a great deal of individual variability even after normalization, so any atlas is only a rough guide to the shape and location of structures in an individuals brain. As I have noted before, secondary and tertiary sulci are not found in all individuals (Ono et al. 1990, Atlas of Cerebral Sulci). Another benefit of normalizing brains is it makes it easy to complete an accurate "scalp stripping" with brain extracting software (my MRIcro software implements Steve Smith's BET for this task). You can then create a useful volume rendering of the cortical surface. Typically, it is much easier to identify cortical sulci and gyri by looking at a rendered image of the brain's surface. This atlas shows you how to recognize these landmarks on a rendered MRI scan.

Proper citation: Neuroanatomy Atlas (RRID:SCR_002402) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) Copy   

•   Source: SciCrunch Registry

https://bams1.org/cells/list.php, https://bams1.org/cells/search_bams_ref.php, https://bams1.org/cells/search_by_brain_region.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.

Proper citation: BAMS Cells (RRID:SCR_003531) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org

Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

Proper citation: eMouseAtlas (RRID:SCR_002981) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/DRG

Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

Proper citation: Drug Related Gene Database (RRID:SCR_003330) Copy   

•   Source: SciCrunch Registry

http://hendrix.imm.dtu.dk/services/jerne/brede/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.

Proper citation: Brede Database (RRID:SCR_003327) Copy   

•   Source: SciCrunch Registry

http://www.mknt.hu/sites/default/files/NEPSYBANK_0.doc

The Hungarian Society of Clinical Neurgenetics established a nationwide collaboration for prospective collection of human biological materials and databases from patient with neurological and psychiatric diseases. The basic triangle of the NEPSYBANK is the sample, the information and the study management. The present participants of the NEPSYBANK are the Department of Neurology and Psychiatry of the four Medical Universities (in Budapest, Debrecen, Pecs, Szeged) and the National Institute of Psychiatry and Neurology in Budapest. The NEPSYBANK is a disease based biobank collecting both phenotypical and environmental data and biological materials such as DNA/RNA, whole blood, plasma, cerebral spinal fluid, muscle / nerve / skin biopsy, brain, and fibroblast. The target of the diseases is presently (Phase I): stroke syndromes, dementias, movement disorders, motoneuron diseases, epilepsy, multiple sclerosis, schizophrenia, alcohol addiction. In the near future (Phase II.) it is planned to enlarge the scale with headaches, disorders of the peripheral nerves, disorders of neuromuscular transmission, disorders of skeletal muscle, depression, anxiety. DNA/RNA is usually extracted from whole blood, but occasionally different tissues such as muscle, brain etc. can be used as well. The extracting procedures differ among the institutes, but in all cases the concentration and the quality of the DNA/RNA must be registered in the database. Participating institutional biobanks have committed themselves to follow common quality standards, which provide access to samples after prioritization on scientific grounds only. In every case the following data are registered. 1. General data: main bank categories, age, sex, ethnicity, body height, body weight, economic stats, education, type of place of living, marital status, birth complications, alcohol, drugs, smoking. 2. Sample properties (sample ID, type of sample, date of extraction, concentration, and level of purity). General patient data as blood pressure, heart rate, internal medical status, ECG, additional diseases. Disease specific question e.g. in schizophrenia the diagnosis after DSMIV and ICD 10, detailed diagnostic questions after both classification, detailed psychiatric and neurological status, laboratory findings, rating scales, data of neuroimaging, genetic tests, applied medication (with generic name, dose, duration), adverse drug effects and other treatments. The Biobank Information Management System (BIMS) is responsible for linkage of databases containing information on the individual sample donors. If you want to have samples from the NEPSYBANK an application must be submitted containing the following information: short research plan including aims and study design, ethic application with a positive decision, specific demands regarding the right of disposition, agreements with grant organizations which regulate immaterial property, information about financing (academic grants, support from industry). All participants have the right to withdraw their samples through a simple order.

Proper citation: Hungarian Neurological-Psychiatric Biobank (RRID:SCR_003715) Copy   

•   Source: SciCrunch Registry

http://www.brainbankforautism.org.uk/

Encourages and facilitates brain tissue donation for use in the best scientific studies to better understand the biological basis of autism down to the cellular and molecular levels and through that understanding bring about the development of effective interventions for those affected by autism spectrum disorders. To ensure the best co-ordinated use of brain tissue, the UK Brain Bank for Autism works in collaboration with the Autism Tissue Program in the US and shares the same Tissue Advisory board. The Brain Bank for Autism & Related Developmental Research was established in 2009. It is an initiative to develop a similar program in the UK to the Autism Tissue Program, which has been developed in the US since 1998. Our Brain Bank is the first extension outside the US of the Autism Tissue Program and is integrated with it. The Brain Bank is based at Oxford University, where it forms part of the Thomas Willis Oxford Brain Collection. It operates in accordance with all UK legal and ethical requirements. The donation of post-mortem brain tissue for this research program is of fundamental importance to our understanding of the causes of autism and to help us develop more effective diagnostic measures and interventions. A separate brain bank for autism is necessary because we need to understand how, in autism, the brain develops over time and how the brain functions as a whole. However, our Brain Bank will promote close cooperation across all relevant brain banks in order to take the research forward. Our research focuses on: * people within the autism spectrum or their family members * people not affected by autism but who are affected by epilepsy * individuals without autism or epilepsy.

Proper citation: Brain Bank for Autism (RRID:SCR_004664) Copy   

•   Source: SciCrunch Registry

http://www.morf-brain.com/

Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide.

Proper citation: Mononucleotide Repeat Frameshift Portal (RRID:SCR_021125) Copy   

•   Source: SciCrunch Registry

http://brancusi.usc.edu/bkms/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7th, 2019. BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships.

Proper citation: BAMS Nested Regions (RRID:SCR_000238) Copy   

•   Source: SciCrunch Registry

http://brainevolutionnews.blogspot.com/

Brain Evolution in the News pulls in blogs from a variety of resources on topic.

Proper citation: Brain Evolution in the News (RRID:SCR_000592) Copy   

•   Source: SciCrunch Registry

http://www.eideneurolearningblog.blogspot.com/

Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more.

Proper citation: Eide Neurolearning Blog (RRID:SCR_000680) Copy   

•   Source: SciCrunch Registry