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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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University of Alabama Neurobiology Resource Report Resource Website |
University of Alabama Neurobiology (RRID:SCR_007493) | data or information resource, department portal, organization portal, portal | The Department of Neurobiology offers students interested in the nervous system a program of study that leads to the Ph.D. in Neurobiology or a combined M.D./Ph.D. through The University of Alabama School of Medicine located at UAB. The graduate program has numerous faculty members with active research programs from a broad range of areas in contemporary neuroscience with a major focus on topics of biomedical importance. Molecular, cellular and biophysical approaches are emphasized to address fundamental problems of brain function, development and disease. All students take a series of graduate courses in biochemistry and molecular biology, cell biology, ion channel biophysics, synaptic function, developmental neurobiology and medical neurobiology. Evidence of the faculty's national and international impact in fundamental Neuroscience research includes: their substantial number of publications in high impact journals; appointments to editorial boards and editorships of leading neuroscience journals; appointments to NIH and NSF study sections and review boards; awards of over 28 million dollars in annual research grant funds; and numerous invitations to speak at national and international research symposia. Faculty members also have received numerous national and international awards recognizing excellence in research and training. | nif-0000-02130 | http://www.neurobiology.uab.edu/ | SCR_007493 | SciCrunch Registry | UAB Department of Neurobiology | 2026-10-24 12:45:59 | 0 | ||||||||||
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DFBIdb Resource Report Resource Website |
DFBIdb (RRID:SCR_009456) | DFBIdb | data management software, software application, software resource | A suite of tools for efficient management of neuroimaging project data. Specifically, DFBIdb was designed to allow users to quickly perform routine management tasks of sorting, archiving, exploring, exporting and organising raw data. DFBIdb was implemented as a collection of Python scripts that maintain a project-based, centralised database that is based on the XCEDE 2 data model. Project data is imported from a filesystem hierarchy of raw files, which is an often-used convention of imaging devices, using a single script that catalogues meta-data into a modified XCEDE 2 data model. During the import process data are reversibly anonymised, archived and compressed. The import script was designed to support multiple file formats and features an extensible framework that can be adapted to novel file formats. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export, convert and organise customisable subsets of project data according to user-specified criteria. | magnetic resonance, neuroimaging, python, data management software, project management | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20838938 | GNU General Public License | nlx_155602 | SCR_009456 | SciCrunch Registry | 2026-10-24 12:46:13 | 0 | |||||||
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DIAMOND Resource Report Resource Website 1000+ mentions |
DIAMOND (RRID:SCR_009457) | DIAMOND | software resource | Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans. | reusable library, analyze, database application, dicom, format conversion, image display, image reconstruction, magnetic resonance, nifti, python, software, visualization, workflow, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Davis; California; USA |
nlx_155603 | SCR_009457 | SciCrunch Registry | UC Davis IDeA Lab Applications for Management Of Neuroimaging Data | 2026-10-24 12:46:13 | 4156 | ||||||||
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GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | data analysis software, data processing software, software application, software resource, time-series analysis software | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
NIBIB EB022911 | PMID:31070732 | Free, Available for download, Freely available | nlx_154361, biotools:GMA | https://github.com/chaoning/GMA, https://bio.tools/GMA | http://www.montana.edu/kalinowski/GMA/GMA_Home.htm | SCR_009212 | SciCrunch Registry | Granger Mediation Analysis | 2026-10-24 12:46:16 | 0 | |||
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CBS High-Res Brain Processing Tools Resource Report Resource Website 10+ mentions |
CBS High-Res Brain Processing Tools (RRID:SCR_009452) | CBS High-Res Brain Processing Tools | software resource | A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit is related to: MIPAV: Medical Image Processing and Visualization |
Free | nlx_155596 | SCR_009452 | SciCrunch Registry | 2026-10-24 12:46:13 | 20 | ||||||||
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CCSeg - Corpus Callosum Segmentation Resource Report Resource Website 1+ mentions |
CCSeg - Corpus Callosum Segmentation (RRID:SCR_009453) | CCSeg | data processing software, image analysis software, segmentation software, software application, software resource | An open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation. | c++, magnetic resonance, segmentation, shape analysis, corpus callosum |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:9873919 | BSD License | nlx_155597 | SCR_009453 | SciCrunch Registry | Corpus Callosum Segmentation Tool | 2026-10-24 12:46:13 | 1 | ||||||
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BrainSolution Resource Report Resource Website |
BrainSolution (RRID:SCR_009447) | BrainSolution | data processing software, image analysis software, segmentation software, software application, software resource | A collection of tools for MRI T1 brain image segmentation in the Windows environment. It helps construct a complete pipeline with necessary preprocessing and postprocessing procedures besides brainparser, the core program of our fast brain segmentation. The execution of the whole pipeline can be completed in 2 hours with good segmentation results. Execution requires: FSL | analyze, c++, console (text based), labeling, linux, microsoft, magnetic resonance, posix/unix-like, region of interest, segmentation, sh/bash, unix shell, windows, windows nt/2000, windows vista, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155591 | SCR_009447 | SciCrunch Registry | 2026-10-24 12:46:16 | 0 | ||||||||
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National Mouse Metabolic Phenotyping Centers Resource Report Resource Website 500+ mentions |
National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997) | MMPC, NIDDKMMPC | data or information resource, database, service resource | Center mission is to advance medical and biological research by providing the scientific community with standardized, high quality metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders. | phenotype, phenotyping, metabolism, cardiovascular, gastrointestinal, endocrine, energy, analytic, blood composition, in vivo, hormone, energy balance, eating, exercise, organ function, morphology, physiology, histology, experimental protocol, assay, strain, measurement, animal husbandry, FASEB list |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is used by: Hypothesis Center is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: dkCOIN has parent organization: Augusta University; Georgia; USA has parent organization: Case Western Reserve University; Ohio; USA has parent organization: University of Cincinnati; Ohio; USA has parent organization: Vanderbilt University School of Medicine; Tennessee; USA has parent organization: University of California at Davis; California; USA has parent organization: University of Massachusetts Medical School; Massachusetts; USA has parent organization: Yale School of Medicine; Connecticut; USA is parent organization of: MMPC-Vanderbilt University School of Medicine Animal Health and Welfare Core is parent organization of: MMPC-Vanderbilt University School of Medicine Analytical Resources Core is parent organization of: MMPC-University of Michigan Medical School Microbiome Core is parent organization of: MMPC-Vanderbilt University School of Medicine Metabolic Regulation Core is parent organization of: MMPC-University of Michigan Medical School Microvascular Complications Core is parent organization of: MMPC-University of Massachusetts Medical School Cardiovascular Core is parent organization of: MMPC-Vanderbilt University School of Medicine is parent organization of: MMPC-University of Michigan Medical School is parent organization of: MMPC-University of Massachusetts Medical School Humanized Mouse Cell Transplantation and Assessment Core is parent organization of: MMPC-University of Cincinnati Medical Center Energy Metabolism Food Intake and Body Weight Regulation Core is parent organization of: MMPC-University of Massachusetts Medical School Islet Core is parent organization of: MMPC-University of Massachusetts Medical School Metabolism Core is parent organization of: MMPC-University of Massachusetts Medical School Animal Care Core is parent organization of: MMPC-University of Cincinnati Medical Center is parent organization of: University of Massachusetts Medical School Metabolic Disease Research Center Core Facility is parent organization of: MMPC-University of Massachusetts Medical School Analytical Core is parent organization of: MMPC-University of California Davis Energy Balance Exercise and Behavior Core is parent organization of: MMPC-University of Cincinnati Medical Center Lipid Lipoprotein and Glucose Metabolism Core is parent organization of: MMPC-University of California Davis Administrative Core is parent organization of: MMPC-University of California Davis Microbiome and Host Response Core is parent organization of: MMPC-University of Cincinnati Medical Center Cardiovascular and Renal Function Core is parent organization of: MMPC-University of California Davis Endocrinology and Metabolism Core is parent organization of: MMPC-University of California Davis is parent organization of: MMPC-University of California Davis Animal Care Surgery and Pathology Core is parent organization of: MMPC-University of Michigan Medical School Metabolism Bariatric Surgery and Behavior Core is parent organization of: MMPC-Vanderbilt University School of Medicine Cardiovascular Pathophysiology Core is parent organization of: MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core has organization facet: MMPC-University of California Davis has organization facet: MMPC-University of Cincinnati Medical Center has organization facet: University of Massachusetts Medical School Metabolic Disease Research Center Core Facility has organization facet: MMPC-University of Michigan Medical School has organization facet: MMPC-Vanderbilt University School of Medicine |
Diabetes, Obesity, Diabetic complication, Metabolic disease, Cardiovascular disease, Nephropathy, Neuropathy, Retinopathy | NIDDK U24 DK076174; NIDDK U24 DK092993; NIDDK U24 DK059630; NIDDK U24 DK093000; NIDDK U24 DK059637; NIDDK U24 DK059635 |
Freely available, | SCR_015358, nlx_152633 | SCR_008997 | SciCrunch Registry | Mouse Metabolic Phenotyping Centers | 2026-10-24 12:46:12 | 725 | |||||
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Biomatik Resource Report Resource Website 500+ mentions |
Biomatik (RRID:SCR_008944) | Biomatik | commercial organization | An Antibody supplier, Core facility | is listed by: ScienceExchange | nlx_152303, SciEx_8952 | SCR_008944 | SciCrunch Registry | 2026-10-24 12:46:12 | 871 | ||||||||||
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Beckman Coulter Resource Report Resource Website 100+ mentions |
Beckman Coulter (RRID:SCR_008940) | commercial organization | An Organization portal, Material service resource, Antibody supplier, Instrument supplier | biotechnology, diagnostic, life science, biomedical, testing, analyzer, immunochemistry, dna analysis, flow cytometer |
is related to: ONE Study is parent organization of: Diagnostic Systems Laboratories |
nlx_152293 | SCR_008940 | SciCrunch Registry | Beckman Coulter Inc. | 2026-10-24 12:46:12 | 160 | |||||||||
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Fluid Registration and Atlas Toolkit Resource Report Resource Website |
Fluid Registration and Atlas Toolkit (RRID:SCR_009478) | FRAT | data processing software, image analysis software, registration software, software application, software library, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 05, 2013. It has been superseeded by the CALATK, available here http://www.calatk.org c++ libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping (LDDM) registration method and implements discretized fluid registration. This registration method is then applied to time series analysis, cross-sectional atlas building, and longitudinal atlas building. The individual tool components are: * LDDM: Fluid registration between two images. * TimeSeries: Time series analysis of longitudinal data for a single subject. * AtlasBuilder: Cross-sectional atlas building for a population of images. * LongitudinalAtlasBuilder: Longitudinal atlas building for a population of subjects, each with a longitudinal data set. * FRATUtils: A collection of utility functions for working with volumes and time series files | atlas application, c++, console (text based), image-to-image, linux, magnetic resonance, nonlinear warp, nrrd, posix/unix-like, registration, spatial transformation, warping |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CalaTK |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155625 | SCR_009478 | SciCrunch Registry | 2026-10-24 12:46:16 | 0 | ||||||||
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HAP-SAMPLE Resource Report Resource Website 1+ mentions |
HAP-SAMPLE (RRID:SCR_009234) | HAP-SAMPLE | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | nlx_154392 | SCR_009234 | SciCrunch Registry | 2026-10-24 12:46:13 | 4 | |||||||||
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FBIRN Image Processing Scripts Resource Report Resource Website 1+ mentions |
FBIRN Image Processing Scripts (RRID:SCR_009471) | FIPS | data management software, software application, software resource | A FSL package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control. | analyze, csh/tcsh, database application, dicom, linux, macos, magnetic resonance, posix/unix-like, statistical operation, unix shell, web environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Function BIRN |
BIRN License, BSD License | nlx_155618 | SCR_009471 | SciCrunch Registry | FBIRN Image Processing Scripts (FIPS) | 2026-10-24 12:46:14 | 5 | |||||||
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A sample size calculation method Resource Report Resource Website |
A sample size calculation method (RRID:SCR_009469) | A sample size calculation method | software resource | Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author. | is listed by: OMICtools | PMID:24314022 | OMICS_01228 | SCR_009469 | SciCrunch Registry | 2026-10-24 12:46:14 | 0 | |||||||||
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Coursera Resource Report Resource Website 50+ mentions |
Coursera (RRID:SCR_008931) | Coursera | data or information resource, online course, open course, training resource, video resource | An open course site where you can take the World''s Best Courses, Online, For Free. We are a social entrepreneurship company that partners with the top universities in the world to offer courses online for anyone to take, for free. We envision a future where the top universities are educating not only thousands of students, but millions. Our technology enables the best professors to teach tens or hundreds of thousands of students. Through this, we hope to give everyone access to the world-class education that has so far been available only to a select few. We want to empower people with education that will improve their lives, the lives of their families, and the communities they live in. Our Courses Classes offered on Coursera are designed to help you master the material. When you take one of our classes, you will watch lectures taught by world-class professors, learn at your own pace, test your knowledge, and reinforce concepts through interactive exercises. When you join one of our classes, you''ll also join a global community of thousands of students learning alongside you. We know that your life is busy, and that you have many commitments on your time. Thus, our courses are designed based on sound pedagogical foundations, to help you master new concepts quickly and effectively. Key ideas include mastery learning, to make sure that you have multiple attempts to demonstrate your new knowledge; using interactivity, to ensure student engagement and to assist long-term retention; and providing frequent feedback, so that you can monitor your own progress, and know when you''ve really mastered the material. We offer courses in a wide range of topics, spanning the Humanities, Medicine, Biology, Social Sciences, Mathematics, Business, Computer Science, and many others. Whether you''re looking to improve your resume, advance your career, or just learn more and expand your knowledge, we hope there will be multiple courses that you find interesting. | education, course, training, lecture, discussion, interactive | has parent organization: Stanford University; Stanford; California | Free | nlx_151772 | SCR_008931 | SciCrunch Registry | 2026-10-24 12:46:12 | 80 | ||||||||
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NGC Resource Report Resource Website |
NGC (RRID:SCR_009342) | NGC | software resource | A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files. | is listed by: OMICtools | PMID:23066097 | OMICS_00964 | SCR_009342 | SciCrunch Registry | 2026-10-24 12:46:13 | 0 | |||||||||
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DW-MRI registration in FSL Resource Report Resource Website 1+ mentions |
DW-MRI registration in FSL (RRID:SCR_009461) | DW-MRI registration in FSL | data processing software, image analysis software, registration software, software application, software resource | This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images (DW-MRIs) by extending FLIRT (linear registration of 3D scalar volumes) and FNIRT (non-linear registration of 3D scalar volumes) in the FMRIB Software Library (FSL) to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation (Tao, X., Miller, J. V., 2006. A method forregistering diffusion weighted magnetic resonance images. In: MICCAI. Vol. 9. pp. 594?602), which is implemented and extended to non-linear registration, based on the FLIRT and FNIRT models in FSL. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00041/abstract. The code does not overwrite FLIRT, FNIRT or any of the FSL C++ code. It is added as FLIRT4D, FNIRT4D and supporting cost functions. The makefiles will however be overwritten to compile the new code, without affecting any version of FSL. | magnetic resonance, diffusion weighted magnetic resonance image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL |
PMID:23596381 | FSL License | nlx_155607 | SCR_009461 | SciCrunch Registry | 2026-10-24 12:46:16 | 2 | |||||||
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DbGaP Cleaner Resource Report Resource Website 1+ mentions |
DbGaP Cleaner (RRID:SCR_009462) | data processing software, software application, software resource, workflow software | Tool to assist site staff with curation of data dictionary, data item, and subject item files for preparation to uploading and sharing data with DbGaP resource. | gpl-style open source, data, curation, dictionary, sharing, site, tool, workflow software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NCBI database of Genotypes and Phenotypes (dbGap) |
nlx_155609 | SCR_009462 | SciCrunch Registry | DbGaP_Cleaner | 2026-10-24 12:46:14 | 1 | |||||||||
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AMERICAN DIAGNOSTICA Resource Report Resource Website |
AMERICAN DIAGNOSTICA (RRID:SCR_008928) | commercial organization | An Antibody supplier. | nlx_152266 | http://american-diagnostica.de, https://sekisuidxcoag.com/ | SCR_008928 | SciCrunch Registry | Sekisu | 2026-10-24 12:46:15 | 0 | ||||||||||
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BeeBase Resource Report Resource Website 50+ mentions |
BeeBase (RRID:SCR_008966) | BeeBase | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service resource | Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page. | genome, gene set, sequence, bee, genomics, entomology, blast, annotation, pest, pathogen, honey, beehive, insect, bee pollen, bee product, bee culture, pollination, pollinator, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: University of Missouri; Missouri; USA |
Texas Agricultural Experiment Station ; Golden Heritage Foods and Sioux Honey Association ; NHGRI 5-P41-HG000739-13; USDA 2008-35302-18804 |
PMID:21071397 | Open unspecified license, Acknowledgement requested, Data Usage Policy | nlx_152034, biotools:hgd, r3d100010925 | https://bio.tools/hgd, https://doi.org/10.17616/R3Z629 | SCR_008966 | SciCrunch Registry | Hymenoptera Genome Database | 2026-10-24 12:46:12 | 56 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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