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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | software application, workflow software, software resource, data processing software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-02-12 09:43:06 | 11 | |||
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Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | data or information resource, portal, software resource, topical portal | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-02-12 09:43:06 | 83 | |||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | software resource, software application, data analysis software, data processing software | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-02-12 09:43:14 | 9 | ||||
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National Center for Research Resources - Primate Resources Resource Report Resource Website 1+ mentions |
National Center for Research Resources - Primate Resources (RRID:SCR_006863) | NCRR Primate Resources | organism supplier, material resource, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 16, 2013. NCRR has been absorbed into other parts of the National Institutes of Health. This organizational structure is no longer available. Provides laboratory scientists and clinical researchers with the resources and tools they need to understand, detect, treat and prevent a wide range of diseases. Animal models, such as nonhuman primates, are a critical component of biomedical research, having profound implications for public health. Scientists depend on laboratory animals and other nonhuman models for investigating biological processes, studying the causes of diseases and testing promising new therapies. Nonhuman primates, in particular, are important for translational research because of their close physiological similarities to humans. They enable discoveries that have direct application to human studies, bridging the gap between basic science and human medicine. Discoveries in animal models are helping scientists test treatments for human conditions such as drug addiction, obesity, malaria, HIV/AIDS and neurodegenerative diseases, accelerating the pace at which these research advances can be translated into treatments for patients. Through its Division of Comparative Medicine, NCRR offers a wide variety of primate resources for NIH-funded scientists across the nation. Additionally, funding opportunities are available to National Primate Research Centers. Eight National Primate Research Centers (NPRCs) located throughout the country provide animals, facilities and expertise in all aspects of nonhuman primate biology and husbandry. These facilities and resources enable collaborative research among NPRC staff scientists, investigators from the NPRC host institution and other NIH-funded researchers. Major areas of research benefiting from the primate centers include AIDS, avian flu, Alzheimer''s disease, Parkinson''s disease, diabetes, asthma and endo-metriosis. The centers????????????????? specialized resources are intended to support investigators who receive their primary research project funding from NIH, but they also may be used by investigators who are funded by other federal, state and local agencies, as well as by research foundations and the private sector. Together the primate centers have more than 28,000 nonhuman primates of 20 different species. This portal covers the following topics: * National Primate Research Centers * Monkey Research Resources * Chimpanzee Research Resources * Chimpanzee Management Program * Specific-Pathogen-Free Macaque Resources * Nonhuman Primate Research Reagents | grant, animal model, non-human primate, monkey, chimpanzee, reagent |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: Yerkes National Primate Research Center is parent organization of: Washington National Primate Research Center |
NCRR ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00495 | http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.aspcenters, http://www.ncrr.nih.gov/primates | SCR_006863 | Nonhuman Primate Research Resources | 2026-02-12 09:44:19 | 1 | |||||
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MRM NeAt (Neurological Atlas) Mouse Brain Database Resource Report Resource Website 1+ mentions |
MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) | MRM NeAt | reference atlas, database, atlas, data or information resource, image collection | Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data. | phenotype, mouse, brain, computational biology, in vivo, mouse brain atlas, magnetic resonance microscopy, mouse brain morphometry, image registration, in vitro, 3d brain atlas, adult mouse, male, c57bl/6j, autosegmentation, probabilistic atlas, t2 weighted protocol |
is related to: Mouse Brain Image Visualizer (MBIV) is related to: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery has parent organization: University of Florida; Florida; USA is parent organization of: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery |
National High Magnetic Field Laboratory ; NIBIB R01 EB 0023304; NCRR P41 RR16105; NIMH P50 MH58911 |
PMID:16165303 PMID:18958199 |
Registration required | nlx_59497 | http://brainatlas.mbi.ufl.edu | SCR_007053 | Magnetic Resonance Microimaging Neurological Atlas Mouse Brain Database, MRM Neurological Atlas Mouse Brain Database, C57BL/6J Mouse Atlas, Atlas of Adult C57BL/6J Mouse Brain, MRM NeAt Mouse Brain Database | 2026-02-12 09:44:27 | 8 | ||||
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Manual Align RTS2000 Resource Report Resource Website |
Manual Align RTS2000 (RRID:SCR_007107) | software application, image processing software, software resource, data processing software | Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place. | alignment, process, image, adjust, correct, misalignment |
is affiliated with: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Center for Microscopy and Imaging Research |
NCRR P41 RR04050 | Free, no longer available | nif-0000-10514 | SCR_007107 | 2026-02-12 09:44:30 | 0 | ||||||||
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Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | data or information resource, portal, topical portal | The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. | fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network is parent organization of: BXH/XCEDE Tools is parent organization of: FBIRN Image Processing Scripts |
NIGMS ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
nif-0000-00070 | http://www.nitrc.org/projects/fbirn | http://nbirn.net/tools/browse_tools.shtm | SCR_007291 | Functional Imaging BIRN | 2026-02-12 09:44:30 | 2 | |||||
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BIRN Coordinating Center Resource Report Resource Website |
BIRN Coordinating Center (RRID:SCR_007290) | BIRN-CC | organization portal, software resource, software application, data or information resource, portal, systems interoperability software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. It was established to develop, implement and support the information infrastructure necessary to achieve large-scale data sharing among the test bed participants (function, morphometry and mouse birn). The BIRN-CC consists of a unique and well-established partnership between computer scientists, neuroscientists and engineers. This partnership addresses a large array of technical, policy, and architectural issues to fundamentally enable a new suite of information technology supported database and analysis tools that allow scientists to analyze and interpret significantly larger sets of data than is possible in the traditional single-institution study paradigm. | fmri, 3d models, anatomy, atlas, data management, data storage, dohhs architecture, imaging, map, model, mri, neuroinformatics, ontology, portal, software, talairach, warping |
has parent organization: University of Southern California; Los Angeles; USA has parent organization: University of Chicago; Illinois; USA has parent organization: University of California at Irvine; California; USA has parent organization: University of California at Los Angeles; California; USA |
NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00068 | SCR_007290 | 2026-02-12 09:44:40 | 0 | |||||||
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Stimulate Resource Report Resource Website 10+ mentions |
Stimulate (RRID:SCR_007375) | software resource, software application, data analysis software, data processing software, data visualization software | An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays. | fmri, workflow, data visualization software, data analysis software | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | NCRR RR08079 | Free for use by non-profit research institutions, Not to be sold or used for profit. | nif-0000-00344 | SCR_007375 | 2026-02-12 09:44:27 | 10 | ||||||||
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Madison Metabolomics Consortium Database Resource Report Resource Website 50+ mentions |
Madison Metabolomics Consortium Database (RRID:SCR_007803) | MMCD | data or information resource, database, resource | 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. | database, metabolomics, metabolite, consortium, nmr, mas spectroscopy, FASEB list |
is listed by: 3DVC has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NIDDK R21 DK070297; NCRR P41 RR02301 |
PMID:18259166 | Public | nif-0000-03148 | SCR_007803 | Madison Metabolomics Consortium Database (MMCD) | 2026-02-12 09:44:34 | 60 | |||||
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Center for Computational Biology at UCLA Resource Report Resource Website |
Center for Computational Biology at UCLA (RRID:SCR_000334) | CCB, UCLA CCB, USC CCB | data or information resource, portal, organization portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging. | functional, genetic, biological system, brain, clinical, computational, computational mathematic, disease, health, image processing, physiological, population, structural, neuroimaging, computational neuroscience, imaging genomics, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NCRR U54 RR021813 | PMID:22081221 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10492 | http://ccb.loni.ucla.edu/ | http://www.nitrc.org/projects/ccb, http://cms.loni.ucla.edu/CCB/ | SCR_000334 | CCB at UCLA, Center for Computational Biology | 2026-02-12 09:42:57 | 0 | |||
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Harvard - Oxford Cortical Structural Atlas Resource Report Resource Website 100+ mentions |
Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) | Atlases | data or information resource, atlas, reference atlas | 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. | male, female, t1-weighted image, cortical, subcortical, neuroanatomy, cortex |
has parent organization: Harvard University; Cambridge; United States is a plug in for: FSL |
Healthy | NCRR R01 RR16594-01A1; NIMH K01 MH01798; NINDS R01 NS052585-01; NIMH K08 MH01573 |
Free, Freely available | nlx_152707 | SCR_001476 | , Harvard Oxford Cortical Structural Atlas, Harvard-Oxford cortical and subcortical structural atlases, Harvard Oxford Atlas | 2026-02-12 09:43:10 | 144 | |||||
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Functional Regression Analysis of DTI Tract Statistics Resource Report Resource Website |
Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) | FRATS | image analysis software, software application, software resource, data processing software | Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. | computational neuroscience, imaging genomics, magnetic resonance, regression analysis, dti, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NSF BCS-08-26844; NCRR UL1-RR025747-01; NIMH MH086633; NIA AG033387; NIMH MH064065; NICHD HD053000; NIMH MH070890; NINDS R01NS055754; NIBIB U54 EB005149-01 |
PMID:20335089 | Academic Free License | nlx_155629 | SCR_002293 | Functional Regression Analysis of DTI | 2026-02-12 09:43:20 | 0 | |||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software application, software resource, data processing software | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-02-12 09:44:08 | 120 | |||||
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Zebrafish Atlas Resource Report Resource Website 1+ mentions |
Zebrafish Atlas (RRID:SCR_006722) | Zebrafish Atlas | data or information resource, atlas, reference atlas | 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. | embryo, eosin, expression, genetic, adult, anatomical, anatomy, cancer, development, hematoxylin, histological, histology, juvenile, larvae, lifespan, model, slide, sagittal, coronal, transverse, stage, embryonic zebrafish, juvenile zebrafish, immature zebrafish, larval zebrafish, young zebrafish, adult zebrafish | has parent organization: Pennsylvania State University | Normal, Mutant, Cancer | NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24352 | SCR_006722 | Penn State Zebrafish Atlas, Zebrafish Atlas - A Lifespan Atlas of the Zebrafish, PSU Zebrafish Atlas | 2026-02-12 09:44:24 | 3 | |||||
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Autopack Resource Report Resource Website 1+ mentions |
Autopack (RRID:SCR_006830) | autoPack | software application, software resource, data processing software | An open-source general packing algorithm that packs 3D objects onto surfaces, into volumes, and around volumes. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPack can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the loose packing problem which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.) Most popular 3D software programs now contain robust physics engines based on Bullet that can separate small collections of overlapping objects or allow volumes to be filled by pouring shapes from generators, but these approaches fails for large complex systems and result in either overlapping geometry, crashed software, or non-random gradients. Most packing algorithms are designed to position objects as efficiently as possible, but autoPack allows the user to select from random loose packing to highly organized packing methods����??even to choose both methods at the same time. autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures. * zero to minimal overlaps depending on the method used * accuracy vs speed parameters selected by the user * zero edge effects * complete control, from fully random to fully ordered distributions * agent-based interaction, weighting, and collision control | 3d visualization software, modeling software, 3d packing software, packing, 3d object, surface, volume, algorithm |
is related to: Cellpack has parent organization: Google Code has parent organization: Scripps Research Institute is parent organization of: Cellpack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151791 | https://sites.google.com/site/autofill21/ http://code.google.com/p/autofill/ |
SCR_006830 | 2026-02-12 09:44:35 | 3 | ||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | software toolkit, software resource, simulation software, software application, data processing software, data visualization software | A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6. | modeling, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BioMesh3D is related to: BioMesh3D is related to: BioPSE is related to: BioPSE has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Free, Available for download, Freely available | nlx_155949 | http://www.nitrc.org/projects/scirun | SCR_002541 | 2026-02-12 09:43:23 | 21 | ||||||
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BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase https://doi.org/10.17616/R3G61K |
http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-02-12 09:43:16 | 82 | ||||
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LONI ShapeTools Resource Report Resource Website 1+ mentions |
LONI ShapeTools (RRID:SCR_002697) | ShapeTools | software toolkit, software resource, software application, software development tool, software library | Software library that is a collection of Java classes that enable Java programmers to model, manipulate and visualize geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines. * File format readers that implement ShapeIO interface (modeled after Java ImageIO) are automatically used when appropriate. * Storage of additional metadata of arbitrary type (other than shape vertices and interconnections) is enabled by the use of data attributes. * Shapes may contain a set of child shapes allowing for the construction and manipulation of complex hierarchies of shapes. * The various components of a shape are specified as interfaces with specific implementations, making it easy to create specialized implementations of a shape component when different performance characteristics are required. | data visualization, java, shape analysis software, computed tomography, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: LONI ShapeViewer has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
Free, Freely available | nif-0000-23323 | SCR_002697 | 2026-02-12 09:43:26 | 1 | |||||||
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LYSIS Resource Report Resource Website 50+ mentions |
LYSIS (RRID:SCR_001385) | LYSIS | software toolkit, source code, software resource, simulation software, software application, data analysis software, data processing software | Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x | modeling, data analysis, system modeling, analysis, nonlinear, principal dynamic modes, nonlinear modeling, windows, matlab | has parent organization: Biomedical Simulations Resource | NIBIB P41-EB001978; NCRR P41-RR01861 |
Free, Freely Available | nlx_152571 | SCR_001385 | 2026-02-12 09:43:08 | 55 |
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