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on page 1 showing 20 out of 130 results

Cite this (3D MRI Atlas of Mouse Development, RRID:SCR_008090)

URL: http://mouseatlas.caltech.edu/

Resource Type: Resource, atlas, data or information resource

A 3D digital atlas of normal mouse development constructed from magnetic resonance image data. The download is a zipped file containing the six atlases Theiler Stages (ts) 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo. To view the atlases, download and install MBAT from: http://mbat.loni.ucla.edu Specimens were prepared in aqueous, isotonic solutions to avoid tissue shrinkage. Limited specimen handling minimized physical perturbation of the embryos to ensure accurate geometric representations of developing mouse anatomy. Currently, the atlas contains orthogonal sections through MRI volumes, three stages of embryos that have annotated anatomy, photographs of several stages of development, lineage trees for annotated embryos and a gallery of images and movies derived from the annotations. Anatomical annotations can be viewed by selecting a transverse section and selecting a pixel on the displayed slice.

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Cite this (3D Slicer, RRID:SCR_005619)

URL: http://slicer.org/

Resource Type: Resource, data visualization software, software application, data processing software, image analysis software, software resource

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

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    ADAPT

Cite this (ADAPT, RRID:SCR_006769)

URL: http://bmsr.usc.edu/software/adapt/

Resource Type: Resource, software resource, software application, simulation software, data processing software, data analysis software

Computational modeling platform developed for pharmacokinetic and pharmacodynamic applications. It is intended for basic and clinical research scientists and is designed to facilitate the discovery, exploration and application of the underlying pharmacokinetic and pharmacodynamic properties of drugs. Features in ADAPT 5
*Individual Analysis ** Estimation module (ID) includes weighted least squares, maximum likelihood (ML), generalized least squares (GLS), maximum a posterior Bayesian estimation (MAP) ** Simulation module (SIM) includes capabilities for single and multisubject simulations ** Sample schedule design module (SAMPLE) provides the ability to calculate D- and C-optimal designs * Population Analysis ** Parametric population PK/PD modeling using maximum likelihood estimation via the EM algorithm with sampling (MLEM), as introduced by Schumitzky (1995) and by Walker (1996), with extensions and enhancements by Bauer & Guzy (2004). ** Iterated two-stage (ITS) analysis as proposed by Prevost (1977) and Steimer, Mallet and colleagues (1984). ** Convenient standard two-stage (STS) and naive pooled data (NPD) modeling, each with WLS, ML, and MAP estimators. System Requirements * Operating System: Windows XP/Vista/7 * Other Software REQUIRED: Intel Visual Fortran 10.x XE2013

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Cite this (Adult Wistar Rat Atlas, RRID:SCR_006288)

URL: http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Resource Type: Resource, atlas, data or information resource

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

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    Annotare

Cite this (Annotare, RRID:SCR_000319)

URL: http://code.google.com/p/annotare/

Resource Type: Resource, software resource, software application, standalone software

A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

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Cite this (ANTS - Advanced Normalization ToolS, RRID:SCR_004757)

URL: http://www.picsl.upenn.edu/ANTS/

Resource Type: Resource, segmentation software, image analysis software, data processing software, software application, software resource, registration software

Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.

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    Atlas3D

Cite this (Atlas3D, RRID:SCR_001808)

URL: http://www.nesys.uio.no/Atlas3D/

Resource Type: Resource, data processing software, software application, data visualization software, software resource, atlas, data or information resource

A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

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Cite this (BAMS Cells, RRID:SCR_003531)

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

Resource Type: Resource, data or information resource, database

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.

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    BECA

Cite this (BECA, RRID:SCR_015846)

URL: http://www.iu.edu/~beca/

Resource Type: Resource, software resource, image analysis software, data visualization software, data processing software, software application

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

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Cite this (Berkeley Advanced Reconstruction Toolbox, RRID:SCR_016168)

URL: https://doi.org/10.5281/zenodo.592960

Resource Type: Resource, software resource, image reconstruction software, software application, data processing software, image analysis software

Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.

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Cite this (BioImage Suite: Image Analysis Software Package, RRID:SCR_002986)

URL: http://bioimagesuite.yale.edu/index.aspx

Resource Type: Resource, software resource, image analysis software, image processing software, data processing software, software application

A general purpose registration / segmentation / visualization suite. It also has facilities for DTI and fMRI processing. BioImage Suite has extensive capabilities for both neuro/cardiac and abdominal image analysis and state of the art visualization. Many packages are available that are highly extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. It can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM. This site provides information, downloads, documentation, and other resources for users of the software.

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Cite this (Biomedical Simulations Resource, RRID:SCR_001952)

URL: http://bmsr.usc.edu/

Resource Type: Resource, biomedical technology resource center, training resource

Biomedical technology resource center dedicated to the advancement of the state-of-the-art in biomedical modeling and simulation through Core and Collaborative Research projects, as well as the dissemination of this knowledge and related software through Service, Training and Dissemination activities aimed at the biomedical community at large. The BMSR includes four core research projects: * Pharmacokinetic/Pharmacodynamic Systems Analysis * Nonlinear Modeling of Complex Biomedical Systems * Modeling of Autonomic, Metabolic and Vascular Control Interactions * Nonlinear Modeling of the Hippocampus Fifteen Collaborative Research Projects serve as challenging test grounds for the Resource's methodologies and expertise.

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Cite this (BioMEMS Resource Center, RRID:SCR_001417)

URL: http://www.biomemsrc.org/

Resource Type: Resource, biomedical technology research center, material resource, training resource

Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments.

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Cite this (Brain Architecture Management System, RRID:SCR_007251)

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

Resource Type: Resource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resource

Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. BAMS is also an online knowledge management system designed to handle neurobiological information at different levels of organization of the vertebrate nervous system (NS).

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Cite this (BrainInfo, RRID:SCR_003142)

URL: http://braininfo.rprc.washington.edu

Resource Type: Resource, topical portal, database, standard specification, narrative resource, portal, atlas, data or information resource

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

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Cite this (Brainstorm, RRID:SCR_001761)

URL: http://neuroimage.usc.edu/brainstorm/

Resource Type: Resource, image analysis software, data processing software, software application, data visualization software, software resource, image processing software

Open-source application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) data analysis (visualization, processing and advanced source modeling). Its rich and intuitive graphic interface does not require any programming knowledge or experience with Matlab. Although Brainstorm is developed with Matlab (and Java), it does not require users to own a Matlab license: an executable, platform-independent (Windows, MacOS, Linux) version is made available in the downloadable package. What you can do with Brainstorm * MEG/EEG recordings: ** Read data from the most popular file formats ** Interactive access to data files in native formats ** Import data in Matlab ** Import and order data in a well-organized database (by studies, subjects, conditions) ** Review, edit, import, export event markers in continuous, ongoing recordings ** Automatic detection of well-defined artifacts (eye blinks, heartbeats...) ** Artifact correction using Signal Space Projections (SSP) * Pre-processing: Epoching; Detection of bad trials / bad channels; Baseline correction; Frequency filtering; Resampling; Multiple options for epoch averaging; Estimation of noise statistics for improved source modeling * Powerful and versatile visualization: ** Various time series displays (epoched, continuous raw, butterfly, columns, etc.) ** Data mapping on 2D or 3D surfaces (disks, true geometry of sensor array, scalp surface, etc.) ** Generate slides and animations (export as contact sheets, movies, jpegs, ...) ** Channel selection and sensor clustering (save and organize your favorites, share with your collaborators, etc.) * MRI visualization and coregistration: ** Use individual or template anatomy (MNI / Colin27 brain) ** Template anatomy can be warped to individual head surface ** Import MRI volumes and tessellated surface envelopes from most of the existing file formats ** Automatic or interactive co-registration with the MEG/EEG coordinate system ** Volume rendering (multiple display modes) * Database: Keep your data organized ** Ordering of data, source models, time-frequency maps, statistical maps, etc. by protocol, subject and condition/event ** Quick access to all the data in a study for efficient, batch processing ** Quick access to comparisons between subjects or conditions ** Graphical batching tools (apply the same process to many files e.g., your entire study, in a few clicks) * Head modeling: ** MEG: Single sphere, overlapping spheres ** EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG) ** Interactive interface to define the best-fitting sphere * Source modeling: L2 Minimum-norm current estimates; dSPM; sLORETA; All models can be cortically-constrained or not, and with/without constrained orientations * Source display and analysis: ** Multiple options for surface and volume rendering of the source maps ** Re-projection of the sources in the MRI volume (from surface points to voxels) ** Definition of regions of interest (scouts) ** Re-projection of estimated sources on a surface with higher or lower resolution, on a group template ** Surface or volume spatial smoothing (group analysis) ** Share your results: screen captures, make movies and contact sheets! ** Import and display of Xfit (MEG Elekta software) dipole models * Time-frequency decompositions: Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transfor, and Hilbert transform; Define time and frequency scales of interest; Multiple display modes available * Group analysis: Registration of individual brains to a brain template (MNI/Colin27); Statistical analysis (t-tests) * Documentation and support: Easy and automatic updates of the software; Detailed step-by-step tutorials for most common features; Active user forum

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Cite this (BrainSuite, RRID:SCR_006623)

URL: http://users.loni.ucla.edu/~shattuck/brainsuite/

Resource Type: Resource, software resource, image analysis software, data visualization software, data processing software, software application

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

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    BraVa

Cite this (BraVa, RRID:SCR_001407)

URL: http://cng.gmu.edu/brava

Resource Type: Resource, data or information resource, database

A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).

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Cite this (Cambridge Brain Activation, RRID:SCR_007109)

URL: http://www.bmu.psychiatry.cam.ac.uk/software/

Resource Type: Resource, image analysis software, workflow software, data processing software, software application, software resource, software toolkit

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

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