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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   

•   Source: SciCrunch Registry

http://alzheimer.ucdavis.edu/research/resources.php#tissue

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Support research in Alzheimer's disease (AD) offering pilot grants, recruitment of research subjects, access to database, tissue samples, and statistical and research study design consultation for investigators. The scientific effort of the program seeks to: promote research directed at understanding factors that influence the expression and progression of Alzheimer's disease; develop and maintain cohorts of carefully diagnosed and well characterized research subjects available for research studies on Alzheimer's disease and dementia; provide support to investigators in subject recruitment, clinical research, experimental design, and statistical analysis of data; and maintain a variety of samples (brain, DNA, serum) and an extensive electronic database suitable for developing new research and supporting existing programs.

Proper citation: UC Davis Alzheimers Disease Center - Resources (RRID:SCR_010699) Copy   

•   Source: SciCrunch Registry

http://www.hedtags.org/

Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.

Proper citation: HED Tags (RRID:SCR_014074) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/software/fluorender.html

Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation.

Proper citation: FluoRender (RRID:SCR_014303) Copy   

•   Source: SciCrunch Registry

http://knowledge-space.org/

A community encyclopaedia that links brain research concepts with data, models and literature from around the world. It is an open project where users can participate and contribute to the global research community.

Proper citation: KnowledgeSpace (RRID:SCR_014539) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.neuroanatomy.wisc.edu/

Training materials including Web edition modules of the neuroanatomy coursebooks used by first-year medical students at the University of Wisconsin Medical School (UWMS), videos, and images. Topics include spinal cord, brain stem, Cerebellum, Thalamus, Cranial Nerves and National Board Review practice questions.

Proper citation: UW-Madison Neuroscience Resources (RRID:SCR_001649) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/bric/ideagroup/free-softwares/abeat-a-toolbox-for-consistent-analysis-of-longitudinal-adult-brain-mri

A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

Proper citation: aBEAT (RRID:SCR_002238) Copy   

•   Source: SciCrunch Registry

http://chronux.org

Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ''''c'''' for continuous, ''''pb'''' for binned point processes, and ''''pt'''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data.

Proper citation: Chronux (RRID:SCR_005547) Copy   

•   Source: SciCrunch Registry

http://www.research.va.gov/programs/tissue_banking/als/

A human tissue bank that collects, processes, stores and gives out research specimens for future scientific studies. Presently, the VABBB is obtaining neurologic tissue specimens from Veterans who suffer from amyotrophic lateral sclerosis (ALS) and other illnesses that affect Veterans, along with relevant clinical data, essential for research. Currently, neither the cause nor prevention of ALS is known. Medical researchers are currently examining environmental, toxic, genetic, traumatic, medical, and occupational influences as possible contributors to the development and progression of ALS. Veterans have a higher risk of developing ALS compared with non-Veterans; however, the reasons for this higher risk are currently unknown. Any Veteran with ALS in the U.S. may enroll in the VABBB.

Proper citation: VA Biorepository Brain Bank (RRID:SCR_006546) Copy   

•   Source: SciCrunch Registry

http://www.utdallas.edu/bbs/

Mission of the School of Behavioral and Brain Sciences is to understand the intersection of mind, brain and behavior; enhance the health, education, and quality of life of children and families; and create and implement technologies and therapies that repair and strengthen human abilities. The School is housed in Green Hall on the main UT Dallas campus in Richardson. It also has satellite research centers and facilities in downtown Dallas.

Proper citation: University of Texas at Dallas School of Behavioral and Brain Sciences (RRID:SCR_004645) Copy   

•   Source: SciCrunch Registry

http://crcns.org

Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

Proper citation: CRCNS (RRID:SCR_005608) Copy   

•   Source: SciCrunch Registry

https://www.bminds.brain.riken.jp/

Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus), prepared from histological sections of the marmoset brain using various staining techniques.

Proper citation: Digital Brain Atlas of the Common Marmoset (RRID:SCR_005069) Copy   

•   Source: SciCrunch Registry

http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html

V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.

Proper citation: V3D (RRID:SCR_008646) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/labs-at-nimh/research-areas/research-support-services/hbcc/index.shtml

A collection of brain tissue from individuals suffering from schizophrenia, bipolar disorder, depression, anxiety disorders, and substance abuse, as well as healthy individuals. The research mission of the NIMH Brain Bank is to better understand the underlying biological mechanisms and pathways that contribute to schizophrenia and other neuropsychiatric disorders, as well as to study normal human brain development.

Proper citation: NIMH Brain Tissue Collection (RRID:SCR_008726) Copy   

•   Source: SciCrunch Registry

http://www.utsouthwestern.edu/education/medical-school/departments/neurology/programs/alzheimers-disease-center/brain-tissue-donation-program.html

Brain tissue donation program at the UT Southwestern Memory Clinic that aims to utilize these contributions for research on Alzheimer's. Diagnosis of Alzheimer's disease or other dementias are made through autopsy, the results of which are available to family members.

Proper citation: UT Southwestern ADC Brain Tissue Donation Program (RRID:SCR_008837) Copy   

•   Source: SciCrunch Registry

https://brainiak.org

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/dublinbrainbank/home

A biomaterial supply resource that collects and distributes human brain tissue samples. The Dublin Brain Bank is a collaboration between the Neuropathology Department of Beaumont Hospital and the Royal College of Surgeons in Ireland. Investigators interested in applying for tissue samples need to complete tissue requisition forms and provide a record of the research groups'' ethical approval.

Proper citation: Dublin Brain Bank (RRID:SCR_010597) Copy   

•   Source: SciCrunch Registry

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://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