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

Atlas for studies of older adult brain. Includes T1-weighted template of older adult brain and tissue probability maps. Exhibits high image sharpness, provides higher inter-subject spatial normalization accuracy compared to other standardized templates and similar normalization accuracy to well-constructed study-specific templates.

Proper citation: MIITRA atlas (RRID:SCR_017566) Copy   

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http://www.braindonors.org

An Australian brain bank which aims to collect, store, characterize and provide tissue to national and international researchers studying disorders of the brain such as alcohol-related brain damage and mental illness, like schizophrenia. The program encourages those who are medically healthy to donate.

Proper citation: Using our Brains Tissue Donor Program (RRID:SCR_000705) Copy   

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https://neuropsychological-assessment-tests.com/sanzen-tower-london-test

CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.

Proper citation: Colorado Assessment Tests - Tower of London (RRID:SCR_003507) Copy   

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http://www.bcgsc.ca/project/pleiades-promoter-project

Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy.

Proper citation: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders (RRID:SCR_003282) Copy   

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http://www.linkrbrain.eu

An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file.

Proper citation: linkRbrain (RRID:SCR_014562) Copy   

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

Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data.

Proper citation: MultiXplore (RRID:SCR_014814) Copy   

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https://www.nitrc.org/projects/atpp

Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). "

Proper citation: Automatic Tractography-based Parcellation Pipeline (RRID:SCR_014815) Copy   

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https://github.com/BlueBrain/BluePyOpt

An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.

Proper citation: BluePyOpt (RRID:SCR_014753) Copy   

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http://brainmap.org/software.html#GingerALE

Software available from brainmap.org to perform meta-analyses via the activation likelihood estimation (ALE) method. It also includes the transforms for icbm2tal conversions.

Proper citation: GingerALE (RRID:SCR_014921) Copy   

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http://www.guardian.co.uk/science/neurophilosophy

Blog about molecules, minds and everything in between, written by Mo, a molecular and developmental neurobiologist turned science writer. He aims to produce well-written and easily accessible articles about all aspects of neuroscience, so that he might help to improve public understanding of it. This blog has been featured for two consecutive years in the Open Lab annual anthologies of the best science blogging. AFTER four years at ScienceBlogs.com, Neurophilosophy has moved to a new home. It is now hosted by The Guardian.

Proper citation: Neurophilosophy (RRID:SCR_006514) Copy   

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https://github.com/openconnectome/Rambo3D

A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels.

Proper citation: Rambo3D (RRID:SCR_006357) Copy   

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http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

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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   

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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   

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http://www.tmf-ev.de/BiobankenRegisterEN/Registry.aspx?udt_2021_param_detail=84

A brain bank which collects brain tissue from patients who died from various neurological and psychiatric diseases. These tissues are available for biochemical, molecular biological, and other work groups with the aim of supporting research on the pathogenesis, diagnosis, and therapy of these diseases. Collected brains are clinically and neuropathologically well-characterized. The collection and distribution of brain tissue samples is an ongoing process. NeuroBiobank Munich offers help with the organization and implementation of autopsies as well as with the neuropathologic diagnostics. The thematic emphasis of the NeuroBiobank Munich is Parkinson's disease and demential degenerative disorders such as Alzheimer's disease or Creutzfeldt-Jakob disease. NeuroBiobank Munich coordinates the German national brain tissue bank (BrainNet) and the European brain tissue bank (BrainNet Europe).

Proper citation: NeuroBiobank Munich (RRID:SCR_005014) Copy   

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http://udn.nichd.nih.gov/brainatlas_home.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.

Proper citation: Brain atlas of the common marmoset (RRID:SCR_005135) Copy   

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http://www.alzheimersinfo.org/research.html

A brain bank which has obtained brains from individuals who suffered from some form of dementia. Clinical records and a family history are obtained for each donor in order to better understand each dementing illness and to work towards the improvement of diagnosing, treating, and preventing these diseases.

Proper citation: Dementia Brain Bank Research Program (RRID:SCR_005129) Copy   

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https://www.stanleygenomics.org/

The Stanley Online Genomics Database uses samples from the Stanley Medical Research Institute (SMRI) Brain Bank. These samples were processed and run on gene expression arrays by a variety of researchers in collaboration with the SMRI. These researchers have performed analyses on their respective studies using a range of analytic approaches. All of the genomic data have been aggregated in this online database, and a consistent set of analyses have been applied to each study. Additionally, a comprehensive set of cross-study analyses have been performed. A thorough collection of gene expression summaries are provided, inclusive of patient demographics, disease subclasses, regulated biological pathways, and functional classifications. Raw data is also available to download. The database is derived from two sets of brain samples, the Stanley Array collection and the Stanley Consortium collection. The Stanley Array collection contains 105 patients, and the Stanley Consortium collection contains 60 patients. Multiple genomic studies have been conducted using these brain samples. From these studies, twelve were selected for inclusion in the database on the basis of number of patients studied, genomic platform used, and data quality. The Consortium collection studies have fewer patients but more diversity in brain regions and array platforms, while the Array collection studies are more homogenous. There are tradeoffs, the Consortium results will be more variable, but findings may be more broadly representative. The collections contain brain samples from subjects in four main groups: Bipolar Schizophrenia, Depression, and Controls Brain regions used in the studies include: Broadman Area 6, Broadman Area 8/9, Broadman Area 10, Broadman Area 46, Cerebellum The 12 studies encompass a range of microarray platforms: Affymetrix HG-U95Av2, Affymetrix HG-U133A, Affymetrix HG-U133 2.0+, Codelink Human 20K, Agilent Human I, Custom cDNA Publications based on any of the clinical or genomic data should credit the Stanley Medical Research Institute, as well as any individual SMRI collaborators whose data is being used. Publications which make use of analytic results/methods in the database should additionally cite Dr. Michael Elashoff. Registration is required to access the data.

Proper citation: Stanley Medical Research Institute Online Genomics Database (RRID:SCR_004859) Copy   

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http://www.psychologytoday.com/blog/the-compass-pleasure

A blog written by David J. Linden, Ph.D., professor of Neuroscience at the Johns Hopkins University School of Medicine, focusing on the brain''s pleasure circuits. Topics covered include exercise, pleasure and the brain; and understanding the biology of runners high. The Compass of Pleasure: How Our Brains Make Fatty Foods, Orgasm, Exercise, Marijuana, Generosity, Vodka, Learning, and Gambling Feel So Good is also a book and available for purchase. David J. Linden, Ph.D., is a professor in the Department of Neuroscience at the Johns Hopkins University School of Medicine. His laboratory has worked for many years on the cellular substrates of memory storage in the brain and a few other topics. He has a longstanding interest in scientific communication and serves as the Chief Editor of the Journal of Neurophysiology. He has written two books for a general audience about the biological basis of mental function: The Compass of Pleasure (Viking Press, 2011) and The Accidental Mind (Harvard/Belknap, 2007).

Proper citation: Compass of Pleasure (RRID:SCR_004756) Copy   

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http://mindblog.dericbownds.net/

Deric Bownds'' Mindblog reports new ideas and work on mind, brain, and behavior - as well as random curious stuff. Deric Bownds, retired Univ. Wisc. Professor, studies brain and mind. My laboratory research of ~35 years contributed to our understanding of how vision works. This work was gradually phased out in the 1990''s as I devoted increasing time to studying the evolution, development, and function of humans brains.

Proper citation: Deric Bownds Mindblog (RRID:SCR_005492) Copy   

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