Tools   Select Another Resource Report Type

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://openslide.org/

Software C library that provides a simple interface to read whole-slide images (also known as virtual slides).

Proper citation: OpenSlide (RRID:SCR_028483) Copy   

•   Source: SciCrunch Registry

http://www.usc.edu/dept/biomed/UTRC/

Biomedical technology research center focusing on the development of very high frequency (above 20 MHz) ultrasonic transducers/arrays for applications in medicine and biology that include ophthalmology, dermatology, vascular surgery, and small animal imaging. The research is pursued simultaneously in three directions: novel piezoelectric materials, very high frequency single element transducers and linear arrays, and finite element modeling and material property measurements. The Center also serves the community through collaborative efforts with investigators having a research interest in high-frequency ultrasound imaging. In addition, it performs the function of training and information dissemination by offering conferences, seminars and specialized courses at the University of Southern California. The Center has set forth a number of goals which define its mission: * Conduct novel research and development of very high frequency (>20MHz) ultrasonic transducers, arrays and imaging applications * Collaborate with other academic institutions, non-profit organizations, and small businesses supported by the NIH to further the development of these high-frequency applications and provide the expertise in transducers necessary for project success * Serve as an educational center for training scientists and engineers interested in ultrasonic transducer technology One of the primary goals of the Center is to provide service to outside investigators and small business. Often an investigator or company has a specific application in mind but is without the expertise to develop the necessary ultrasonic device. Investigators at academic institutions, research institutes, or small businesses supported by NIH grants who have a need for medical ultrasound transducers and are interested in a collaborative effort should contact Dr. Hyung Ham Kim or Dr. K. Kirk Shung. Ultrasound transducers and components can be fabricated either completely by center personnel or in a joint effort with other investigators. In addition, collaborators are encouraged to visit the facility for additional training in fabrication and assembly.

Proper citation: Resource Center for Medical Ultrasonic Transducer Technology (RRID:SCR_001404) Copy   

•   Source: SciCrunch Registry

https://omics.pnl.gov/software/ms-gf

Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Proper citation: MS-GF+ (RRID:SCR_015646) Copy   

•   Source: SciCrunch Registry

https://maria.stanford.edu/index.php

Web multimodal recurrent neural network tool designed to predict HLA-II (Human Leukocyte Antigen class II) peptide ligand presentation. It uses cell HLA alleles, peptide sequences, and source genes to evaluate antigen presentation. Used for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles.

Proper citation: MARIA (RRID:SCR_028673) Copy   

•   Source: SciCrunch Registry

http://mus.well.ox.ac.uk/mouse/INBREDS/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.

Proper citation: Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) Copy   

•   Source: SciCrunch Registry

http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

•   Source: SciCrunch Registry

http://mouseatlas.caltech.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on October, 01, 2019.
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.

Proper citation: 3D MRI Atlas of Mouse Development (RRID:SCR_008090) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/validate29/

Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels.

Proper citation: VALiDATe29 Squirrel Monkey Brain Atlas (RRID:SCR_015542) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) Copy   

•   Source: SciCrunch Registry

http://www.zfatlas.psu.edu/

Atlas containing 2- and 3-dimensional, anatomical reference slides of the lifespan of the zebrafish to support research and education worldwide. Hematoxylin and eosin histological slides, at various points in the lifespan of the zebrafish, have been scanned at 40x resolution and are available through a virtual slide viewer. 3D models of the organs are reconstructed from plastic tissue sections of embryo and larvae. The size of the zebrafish, which allows sections to fall conveniently within the dimensions of the common 1 x 3 glass slide, makes it possible for this anatomical atlas to become as high resolution as for any vertebrate. That resolution, together with the integration of histology and organ anatomy, will create unique opportunities for comparisons with both smaller and larger model systems that each have their own strengths in research and educational value. The atlas team is working to allow the site to function as a scaffold for collaborative research and educational activity across disciplines and model organisms. The Zebrafish Atlas was created to answer a community call for a comprehensive, web-based, anatomical and pathological atlas of the zebrafish, which has become one of the most widely used vertebrate animal models globally. The experimental strengths of zebrafish as a model system have made it useful for a wide range of investigations addressing the missions of the NIH and NSF. The Zebrafish Atlas provides reference slides for virtual microscopic viewing of the zebrafish using an Internet browser. Virtual slide technology allows the user to choose their own field of view and magnification, and to consult labeled histological sections of zebrafish. We are planning to include a complete set of embryos, larvae, juveniles, and adults from approximately 25 different ages. Future work will also include a variety of comparisons (e.g. normal vs. mutant, normal vs. diseased, multiple stages of development, zebrafish with other organisms, and different types of cancer)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Zebrafish Atlas (RRID:SCR_006722) Copy   

•   Source: SciCrunch Registry

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases

Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.

Proper citation: Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) Copy   

•   Source: SciCrunch Registry

http://mind.loni.usc.edu

The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework.

Proper citation: LONI MiND (RRID:SCR_004820) Copy   

•   Source: SciCrunch Registry

http://www.pharmabase.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research.

Proper citation: Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) Copy   

•   Source: SciCrunch Registry

http://superfly.ucsd.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.

Proper citation: Homophila (RRID:SCR_007717) Copy   

•   Source: SciCrunch Registry

http://biositemaps.ncbcs.org/rds/search.html

Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members

Proper citation: Resource Discovery System (RRID:SCR_005554) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/home/recombinase

Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.

Proper citation: Recombinase (cre) Activity (RRID:SCR_006585) Copy   

•   Source: SciCrunch Registry