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http://www.strokecenter.org/radiology/

The Internet Stroke Center at Washington University is pleased to offer this module for viewing CT, MR, and angiogram images of cerebrovascular and neurological diseases. While this project is still being perfected -- and many more cases have yet to be added -- we hope that you will find this collection useful in your education and practice. The images presented here are for educational use only. This information may not be used for diagnosis or treatment. All images are protected property of the Internet Stroke Center at Washington University and may not be reproduced without permission. Permission may be granted to students and professionals to borrow images from this site for educational purposes and/or presentations; we just ask that an email be sent detailing both the desired material and the intended use. Please direct all comments, questions, and requests to the Site Editor of the Internet Stroke Center.

Proper citation: Neurology Image Library from The Internet Stroke Center (RRID:SCR_013633) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

http://findlab.stanford.edu/functional_ROIs.html

Atlas of functional ROI's, including individual networks (auditory network, sensorimotor network, etc.). Atlases of individual networks and combined networks are available for download directly from the website.

Proper citation: 90 fROI atlas (RRID:SCR_014757) Copy   

•   Source: SciCrunch Registry

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

Project that is a translation of the BraVa arterial vasculature database into the NIFTI MRI file format that can be applied to stroke studies, fMRI resting state imaging studies and other clinical neuroscience studies. Group artery region labels and arterial density maps are provided as well. Human Brain Major Artery Atlas 10.7490/f1000research.1114378.1

Proper citation: Bravissima (RRID:SCR_016229) Copy   

•   Source: SciCrunch Registry

http://www.cdtdb.neuroinf.jp/CDT/Top.jsp

A platform that allow users to visualize and analyze transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Users can search for cerebellar development genes by name, ID, keyword, expression, and tissue specificity. Search results include general information, links, temporal, spatial, and tissue information, and gene category.

Proper citation: Brain Transcriptome Database (RRID:SCR_014457) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resources/Tools/record/nlx_144509-1/6b508d2a-fd5f-56f2-93cf-462fcd52548e/search?q=*&l=&facet%5B%5D=Parent%20Organization:University%20of%20Michigan;%20Michigan;%20USA&sort=added

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 12, 2017.

Dataset in Bilingual exposure optimizes left-hemisphere dominance for selective attention processes in the developing brain by Arredondo, Su, Satterfield, & Kovelman (XX) Does early bilingual exposure alter the representations of cognitive processes in the developing brain? Theories of bilingual development have suggested that bilingual language switching might improve children''s executive function and foster the maturation of prefrontal brain regions that support higher cognition. To test this hypothesis, we used functional Near Infrared Spectroscopy to measure brain activity in Spanish-English bilingual and English-monolingual children during a visuo-spatial executive function task of attentional control (N=27, ages 7-13). Prior findings suggest that while young children start with bilateral activation for the task, it becomes right-lateralized with age (Konrad et al., 2005). Indeed monolinguals showed bilateral frontal activation, however young bilinguals showed greater activation in left language areas relative to right hemisphere and relative to monolinguals. The findings suggest that bilingual experience optimizes attention mechanisms in the language hemisphere, and highlight the importance of early experiences for neurodevelopmental plasticity of higher cognition. These data are made available from Ioulia Kovelman''s Language and Literacy Lab at University of Michigan and may be exported through the NIF Data Federation. To cite these data please use this text Data were published by Arredondo et al. (XX) and made available via the NIF at XX

Proper citation: Arredondo ANT fNIRS dataset1 (RRID:SCR_002653) Copy   

•   Source: SciCrunch Registry

http://www.internationalbrainbee.com

A world-wide neuroscience competition for high school students that aims to motivate them to learn about the brain and to pursue neuroscience careers. Brain Bee tests knowledge of the human brain, including topics like intelligence, emotions, memory, sleep, vision, hearing, sensations, Alzheimer's disease, Parkinson's disease, stroke, schizophrenia, epilepsy, depression, addictions and brain research.

Proper citation: Brain Bee (RRID:SCR_002248) Copy   

•   Source: SciCrunch Registry

http://ranchobiosciences.com/gse4271/

Curated data set from a study that investigated 77 primary high-grade astrocytomas and 23 matched recurrences so that changes in gene expression related to both survival and disease progression can be identified. Samples in the study include WHO grade III and IV astrocytomas with a wide range of survival times.

Proper citation: GSE4271 (RRID:SCR_003643) Copy   

•   Source: SciCrunch Registry

http://nif.nimh.nih.gov/

Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates.

Proper citation: Neurophysiology Imaging Facility (RRID:SCR_004080) Copy   

•   Source: SciCrunch Registry

http://www.chibi.ubc.ca/WhiteText/

Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.

Proper citation: Automated recognition of brain region mentions in neuroscience literature. (RRID:SCR_002731) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-8/search?q=*

A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.

Proper citation: Integrated Nervous System Connectivity (RRID:SCR_006391) Copy   

•   Source: SciCrunch Registry

http://casestudies.brain-map.org/celltax

Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.

Proper citation: CellTax vignette (RRID:SCR_017000) Copy   

•   Source: SciCrunch Registry

http://neuralsci.org/neuracell

Core facility provides neural stem cells (NSC) and everything you need to grow them, custom lentiviral shRNA and over-expression vectors, consult based characterization service where we can assess how your products or reagents affect stem cell performance and behavior. Services include:Cell Supply,Adult SVZ Neural Stem Cells,Any Age Embryonic stem cells from any region of the brain,Human Retinal Pigmented Epithelial cells,RPE iPSCs,iPSCs,Neural Progenitor Cells (NPCs),Custom Orders,Media/ Dissociation Reagents,High-performance Media formulated according to optimal cell growth conditions,Complete Defined Media for Neural Stem Cell Culture,Complete Defined Media for Human Retinal Pigmented Epithelial Culture,Cell characterization. Performs assays to verify how stem cell populations behave in response to certain environments, plastics, reagents, etc., using trade secret assays via FACS and cell culture techniques. This can be used for neural stem cells as well as embryonic stem cells.Cell banking solutions shall ensure that their integrity is maintained, and that sufficient supply is readily available. We will also expand cells, harvest cells, generation the freezing medium and thaw cells to test performance. Provides Generation of custom lentiviral shRNA constructs,Generation of custom lentiviral over-expression constructs,Supply of NSC lines already expressing these shRNA or over-expression constructs.

Proper citation: Neural Stem Cell Institute NeuraCell Core Facility (RRID:SCR_017821) Copy   

•   Source: SciCrunch Registry

https://www.utsouthwestern.edu/education/medical-school/departments/neurology/research/microscopy-facility/

Core suited to advance study of traumatic brain injury, as well as other neurological and psychiatric disorders.Utilizes microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. Provides access to microscopes including TissueCyte 1000 multi-photon microscopes,Hamamatsu NanoZoomer 2.0-HT,Zeiss Axioscan.Z1. Offers access to fluorescence stereomicroscope and upright microscope, both with digital cameras, as well as sectioning equipment (cryostat, microtome, and vibrotome). Provide computer available for use running MicroBrightField Stereo Investigator and Neurolucida software packages for offline stereological analysis, neuron tracing, and 3D rendering of large, whole-brain datasets.

Proper citation: Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility (RRID:SCR_017949) Copy   

•   Source: SciCrunch Registry

https://www.bidmc.org/research/research-by-department/radiology/mri-research/mri-facilities/translational-mri-research-core

Core provides MRI capabilities for imaging human subjects and potentially large animals as part of research studies. Facility operates GE Discovery MR750 3T whole-body scanner and can provide access to 1.5T system. Scanner is FDA cleared for clinical use. It has proprietary software including pulse programming environments and reconstruction programs and customizable software and protocols for applications including functional and structural brain imaging, abdominal perfusion and diffusion, muscle functional imaging and spectroscopy are available to users.Support for fMRI acquisition and visual and auditory stimulus presentation, diffusion tensor imaging, spectroscopy, and high quality anatomic imaging is available. The system has specialized receiver coils for sensitive imaging of particular anatomy. Additional customized coils can be manufactured in our RF lab. The system also has full broadband capability for multinuclear MRI and MRS, including (F-19, C-13, P-31, and Na-23).Our facility can also provide Image Post-processing and computerized image transfer, assistance to ensure MRI equipment safety, and can facilitate Clinical Readings.

Proper citation: Beth Israel Deaconess Medical Center Translational MRI Research Core Facility (RRID:SCR_017950) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/whs-sd-atlas/

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy   

•   Source: SciCrunch Registry

http://catlas.org/mousebrain/#!/

Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans.

Proper citation: CATlas (RRID:SCR_018690) Copy   

•   Source: SciCrunch Registry

http://mouse.brain-map.org/

Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.

Proper citation: ABA Mouse Brain: Atlas (RRID:SCR_017479) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.pymvpa.org

A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages.

Proper citation: PyMVPA (RRID:SCR_006099) Copy   

•   Source: SciCrunch Registry