Tools   Select Another Resource Report Type

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

http://caprica.genetics.kcl.ac.uk/BRAINEAC/

Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders.

Proper citation: Braineac (RRID:SCR_015888) Copy   

•   Source: SciCrunch Registry

http://www.uimcimes.es/contenidos/golink?p=1

Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.

Proper citation: QModeling (RRID:SCR_016358) Copy   

•   Source: SciCrunch Registry

http://brainarchitecture.org/allen-atlas-brain-toolbox

Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.

Proper citation: Brain Gene Expression Analysis toolbox (RRID:SCR_017438) Copy   

•   Source: SciCrunch Registry

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

Software package that performs several multivariate and mass univariate lesion symptom mapping analyses. Uses patient imaging lesion masks of brain insults and correlates them in multiple ways with patient behavioral and covariate data. Several permutation based SPMs are computed along with power, variance explained, and lesion coverage maps.

Proper citation: CLIMB Lesion Symptom Mapping Software (RRID:SCR_018298) Copy   

•   Source: SciCrunch Registry

http://spot.colorado.edu/~dubin/talks/agnosia.html

Compilation terms with definitions that describe altered states that are associated with brain injury (e.g., trauma, stroke, tumor) or with developmental deficits. Although the list deals with primarily CNS-associated disorders, in some cases the term does not distinguish between a CNS cause or a peripheral or neuromuscular cause. Terms that are primarily psychiatric diagnoses (e.g., schizophrenia) are not included. AGNOSIA is a general term for a loss of ability to recognize objects, people, sounds, shapes, or smells; that is, the inability to attach appropriate meaning to objective sense-data. It usually is used when the primary sense organ involved is not impaired. APHASIA is a general term relating to a loss of language ability. APRAXIA is a general term for disorders of practice. These conditions are usually caused by brain injury due to trauma, stroke and/or tumor. Many of these terms have two synonymous forms that differ in whether the word starts with a- or with dys- such as alexia and dyslexia. Here the a- form is usually defined and the other is noted as syn:, except when the dys- form is the more common usage. (If you cannot find a term in one of these forms, look for it in the other. All other synonyms are defined in both forms.) Sources: These definitions are paraphrased from definitions in a large number or print and online dictionaries. Thus this list is not meant to be considered my own, but rather is a compilation. Note: When a word appears in italics, that indicates it is defined elsewhere in this list.

Proper citation: AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders (RRID:SCR_005336) Copy   

•   Source: SciCrunch Registry

http://www.rad.upenn.edu/sbia/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher.

Proper citation: SBIA (RRID:SCR_013628) 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   

•   Source: SciCrunch Registry

http://www.chimpanzeebrain.org/

Collection and distribution of chimpanzee neuroimaging data and postmortem brain tissue. Portal to access chimpanzee brain atlas tools, data repository, bibliography of publications, educational information, and links to other chimpanzee brain resources and datasets on the Internet. Serves as repository for in vivo structural MRI scans of chimpanzee brains, in vivo and postmortem diffusion tensor images (DTI), as well as postmortem fixed and frozen brain specimens.

Proper citation: National Chimpanzee Brain Resource (RRID:SCR_019183) 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

https://github.com/markmikkelsen/Gannet

Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.

Proper citation: Gannet (RRID:SCR_016049) Copy   

•   Source: SciCrunch Registry

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

Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12.

Proper citation: MRTool (RRID:SCR_015956) Copy   

•   Source: SciCrunch Registry

http://marmosetbrain.org/

Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex.

Proper citation: Marmoset Brain Connectivity Atlas (RRID:SCR_015964) Copy   

•   Source: SciCrunch Registry

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

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

•   Source: SciCrunch Registry

https://kinarm.com/solutions/kinarm-end-point-lab/

Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force.

Proper citation: Kinarm: End-Point Lab (RRID:SCR_017060) Copy   

•   Source: SciCrunch Registry