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https://github.com/ccipd/MRQy

Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data.

Proper citation: MRQy (RRID:SCR_025779) Copy   

•   Source: SciCrunch Registry

https://github.com/Washington-University/HCPpipelines

Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space.

Proper citation: HCP Pipelines (RRID:SCR_026575) Copy   

•   Source: SciCrunch Registry

https://github.com/pyranges/ncls

Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups.

Proper citation: Nested containment list (RRID:SCR_027849) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/

Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Proper citation: UCSF Chimera (RRID:SCR_004097) Copy   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/projects/singlecell/

Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.

Proper citation: Velvet-SC (RRID:SCR_004377) Copy   

•   Source: SciCrunch Registry

http://martinos.org/mne/

Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.

Proper citation: MNE software (RRID:SCR_005972) Copy   

•   Source: SciCrunch Registry

https://www.researchmatch.org/

Free and secure registry to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It has been developed by major academic institutions across the country who want to involve you in the mission of helping today''''s studies make a real difference for everyone''''s health in the future. Anyone can join ResearchMatch. Many studies are looking for healthy people of all ages, while some are looking for people with specific health conditions. ResearchMatch can help ''''match'''' you with any type of research study, ranging from surveys to clinical trials, always giving you the choice to decide what studies may interest you.

Proper citation: ResearchMatch (RRID:SCR_006387) Copy   

•   Source: SciCrunch Registry

http://www.ctsaip.org/

Database that aggregates and markets technologies from CTSA institutions as well as those of the National Institutes of Health, with the goal of enhancing research activity and private partnerships across the CTSA consortium. Regular, automatic updating with a standardized template facilitates broad participation by CTSA consortium members. Currently, there are over a dozen CTSAs contributing information on their technologies to the site. CTSA-IP Mission * Intellectual Property information exchange * Links publicly available licensing opportunities from CTSI Institutions in an easily searchable format that connects providers & users. * Aim of creating a consortium view of IP, licensing & sponsored research opportunities. * Stimulus to collaboration and partnering with and between CTSA member institutions.

Proper citation: CTSA-IP (RRID:SCR_006380) Copy   

•   Source: SciCrunch Registry

http://ctdbase.org/

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

Proper citation: Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/eagle-i/

Ontology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee.

Proper citation: eagle-i research resource ontology (RRID:SCR_008784) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rician_Noise_Removal

Two Slicer3 modules removing rician noise in diffusion tensor MRI

Proper citation: Slicer3 Module Rician noise filter (RRID:SCR_009614) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/BrainParser

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/map3d.html

A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.

Proper citation: map3d (RRID:SCR_009628) Copy   

•   Source: SciCrunch Registry

http://mmcd.nmrfam.wisc.edu/

A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.

Proper citation: Madison Metabolomics Consortium Database (RRID:SCR_007803) Copy   

•   Source: SciCrunch Registry

http://mousemutant.jax.org/index.html

Producer and supplier of a collection of mice bearing spontaneous mutations. These mice contribute to a better understanding of the genetic bases of neurological, neuromuscular, sensory, metabolic, skeletal/craniofacial and developmental disorders and conditions such as diabetes, obesity and heart disease.

Proper citation: Mouse Mutant Resource (RRID:SCR_008367) Copy   

•   Source: SciCrunch Registry

http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.asp#alamo

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It houses chimpanzees that have been used in biomedical research, but no active, invasive research is conducted on the site. The APF provides for the long-term care and husbandry of chimpanzees that have been used in biomedical research. Charles River Laboratories Inc. operates the facility under contract with the National Institutes of Health. To be used in continuing virological research, the animals must be transferred to active chimpanzee research settings. All chimpanzees at the APF have been exposed to various microorganisms, such as hepatitis C virus and HIV. For this reason, they may be candidates for studies related to these diseases. The National Center for Research Resources (NCRR) may remove infected animals from the APF to other accredited chimpanzee facilities for research purposes. Investigators interested in the chimpanzees at the APF should contact Dr. Harold Watson in NCRR''s Division of Comparative Medicine to discuss research requirements.

Proper citation: Alamogordo Primate Facility (RRID:SCR_008376) Copy   

•   Source: SciCrunch Registry

http://loni.usc.edu/Software/CFMBIS

A computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data. Each interactive visualization element corresponding to the embedded function enables the end user to easily manipulate the image data. The visual environment of this tool provides an easy-to-use means of inspection and interpretation of image data using the LONI jViewbox library. CFMBIS uses the Java Image I/O plug-in architecture to read a wide variety of common medical image file formats.

Proper citation: Charged Fluid Model for Brain Image Segmentation (RRID:SCR_008281) Copy   

•   Source: SciCrunch Registry

http://nirc.louisiana.edu/index.html

NIRC maintains and provides available research facilities accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International; a ready source of chimpanzees of mixed ages and sex for use in biomedical and behavioral sciences, and also provides professional staff necessary to support investigators with their research needs. Current Research: Vaccine development and testing; pharmacokinetic, pharmacodynamic, preclinical safety, and efficacy studies. Services Provided: The University of Louisiana at Lafayette-New Iberia Research Center (UL Lafayette-NIRC) is an AAALAC-International-accredited nonhuman primate research facility dedicated to the support of basic and applied biomedical and behavioral research. All proposed programs must be approved by the presenting institution and the UL Lafayette-NIRC animal care and use committees. State-of-the-art biomedical support facilities are available that include access to ultrasound, radiography with automatic processor and computer imagery for diagnostic enhancement, and endoscopy and laparoscopy with video monitors, camera and color photo imagery. Diagnostic Laboratory: A 12,000-square-foot laboratory is available for investigators'' research support requirements. Capabilities within the laboratory include but are not limited to hematology, chemistry, microbiology, urinalysis, parasitology, and histology. Among the investigator support procedures are Ficoll gradient isolation of peripheral blood mononuclear cells, platelet aggregation profiles, nonhuman primate lymphocyte proliferation assay, and flow cytometry (lymphocyte enumeration). Emergency generator power is accessible in each laboratory unit and for all major instrumentation and critical freezers. Animals: The center cares for approximately 360 chimpanzees and 5,500 New and Old World species of nonhuman primates. In addition to chimpanzees, the following species of nonhuman primates are being bred at the center: Vervet monkey (Chlorocebus aethiops), cynomolgus macaque (Macaca fascicularis), pigtailed macaque (M. nemestrina), rhesus macaque (M. mulatta).

Proper citation: New Iberia Research Center (RRID:SCR_008279) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/MultiPhase-SEG

A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed.

Proper citation: MultiPhase-SEG (RRID:SCR_008275) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/DSM

The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats.

Proper citation: DualSurfaceMin (RRID:SCR_008278) Copy   

•   Source: SciCrunch Registry