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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Pharmabase - an open content cheminformatics resource linking physiology with pharmacology Resource Report Resource Website |
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) | Pharmabase | image collection, data or information resource, database | 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. | function, cell, compound, graphic, illustration, membrane, molecular, pharmacological, pharmacology, protein, transport, metabolism, intracellular messenger, cell signaling, disease, tissue, cell type, pathway, pharmacology, channel, pump, carriers, protein transporter, membrane transport | has parent organization: BioCurrents Research Center | NCRR P41 RR001395 | PMID:18428760 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21324 | SCR_002462 | 2026-07-28 09:40:26 | 0 | ||||||
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UMMC Center for Psychiatric Neuroscience Labs and Facilities Resource Report Resource Website |
UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) | UMMC CPN Labs & Facilities, UMMC CPN Labs and Facilities | brain bank, tissue bank, biomaterial supply resource, material resource | Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core. | postmortem, brain, tissue, imaging, molecular biology, genomics |
is listed by: One Mind Biospecimen Bank Listing is listed by: ScienceExchange is related to: University of Mississippi Medical Center Labs and Facilities is related to: University of Mississippi Medical Center Animal Behavior Core Facility has parent organization: University of Mississippi Medical Center; Mississippi; USA |
Depression, Normal, Mental disease | NCRR | Free | SciEx_8930 | SCR_002688 | CPN Research Resource Cores, University of Mississippi Medical Center Center for Psychiatric Neuroscience, UMMC Center for Psychiatric Neuroscience Research Resource Cores, UMMC Center for Psychiatric Neuroscience Labs & Facilities, UMMC CPN Research Resource Cores | 2026-07-28 09:40:29 | 0 | |||||
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LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | data visualization software, software resource, software application, data processing software | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-07-28 09:40:04 | 0 | ||
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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, topical portal, portal, software resource | 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 | 2026-07-28 09:40:08 | 83 | |||||
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Kojak Resource Report Resource Website 1+ mentions |
Kojak (RRID:SCR_021028) | software application, software resource, data analysis software, data processing software | Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets. | Mass spectra, cross-linked peptides identification, protein complexes analysis, novel data analysis, existing data analysis |
is used by: Protein Cross-Linking Database has parent organization: University of Washington; Seattle; USA |
National Science Foundation MRI grant 0923536; NIGMS P50 GM076547; NIGMS P50 GM08722150; NCRR S10 RR027584; NIGMS P41 GM103533 |
PMID:25812159 | Free, Available for download, Freely available | SCR_021028 | 2026-07-28 09:45:01 | 3 | ||||||||
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Charged Fluid Model for Brain Image Segmentation Resource Report Resource Website |
Charged Fluid Model for Brain Image Segmentation (RRID:SCR_008281) | CFMBIS | software application, software resource, data processing software, segmentation software, image analysis software | 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. | plugin, software, 2D image, brain image segmentation, brain MR image, image analysis, segementation |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
Available for educational and research purposes only | nif-0000-23325 | SCR_008281 | 2026-07-28 09:42:06 | 0 | |||||||
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New Iberia Research Center Resource Report Resource Website 10+ mentions |
New Iberia Research Center (RRID:SCR_008279) | organism supplier, biomaterial supply resource, material resource | 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). | endoscopy, animal, assay, behavioral, biomedical, blood, cell, chemistry, chimpanzee, chlorocebus aethiops, cynomolgus, cytometry, development, hematology, histology, imagery, laboratory, laparoscopy, lymphocyte, macaca fascicularis, macaca mulatta, macaca nemestrina, macaque, microbiology, monkey, mononuclear, nonhuman, parasitology, peripheral, pharmacodynamic, pharmacokinetic, photo, pigtailed, platelet, primate, radiography, research, rhesus, science, testing, ultrasound, urinalysis, vaccine, vervet | has parent organization: University of Louisiana; Louisiana; USA | NIH Office of the Director R24 OD010947; NCRR U42 RR01 5087 |
nif-0000-24364 | SCR_008279 | NIRC | 2026-07-28 09:42:18 | 41 | ||||||||
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MultiPhase-SEG Resource Report Resource Website |
MultiPhase-SEG (RRID:SCR_008275) | software application, software resource, data processing software, segmentation software, image analysis software | 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. | segementation, visualization, 3D, software |
is related to: Laboratory of Neuro Imaging is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23319 | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16 | SCR_008275 | 2026-07-28 09:42:06 | 0 | |||||||
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Sub-Volume Thresholding Analysis Resource Report Resource Website |
Sub-Volume Thresholding Analysis (RRID:SCR_008272) | SVT | software application, software resource, data analysis software, data processing software | Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software. | data processing, data analysis, functional magnetic resonance imaging, fMRI, software, brain, brain functional studies |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23314 | SCR_008272 | 2026-07-28 09:42:18 | 0 | |||||||
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New England Primate Research School Resource Report Resource Website |
New England Primate Research School (RRID:SCR_008290) | research forum portal, disease-related portal, data or information resource, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A center that focuses on performing bio-medical research on nonhuman primates to aid in human health research. The center also focuses on training young scientists for professional careers in bio-medical research and primate biology. One of the New England Primate Research School's main accomplishments was the creation of an animal model for AIDS that first demonstrated that vaccine protection could be possible. Recent research has led to the development of novel agents for brain imaging that will aid in the diagnosis and treatment of Parkinson's disease. | aids, biology, biomedical, disease, parkinson's, primate, protection, research, scientific, smoking, training, treatment, vaccine | has parent organization: Harvard University; Cambridge; United States | NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24357 | SCR_008290 | NEPRC | 2026-07-28 09:42:07 | 0 | |||||||
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Mouse Mutant Resource Resource Report Resource Website 1+ mentions |
Mouse Mutant Resource (RRID:SCR_008367) | MMR | cell repository, organism supplier, biomaterial supply resource, material resource | 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. | live, cryopreserved, frozen, spontaneous mutation, dna, mutant, gene, disease model, mouse model, embryo, germplasm, mutation, phenotype |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Jackson Laboratory |
Spontaneous mutation | Jackson Laboratory ; NCRR ; NIH Blueprint for Neuroscience Research ; NIH Office of the Director P40OD010972; NIH Office of the Director OD01116302; NCRR RR001183; NCRR RR032339 |
Public | nif-0000-25583 | SCR_008367 | JAX Mouse Mutant Resource, Mouse Mutant Gene Resource, The Mouse Mutant Resource | 2026-07-28 09:42:19 | 2 | |||||
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Alamogordo Primate Facility Resource Report Resource Website |
Alamogordo Primate Facility (RRID:SCR_008376) | APF | organism supplier, biomaterial supply resource, material resource | 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. | animal, biomedical, chimpanzee, comparative medicine, disease, hepatitis c, hiv, husbandry, infection, microorganism, primate, research, virological, virus | NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25894 | SCR_008376 | Alamogordo Primate Facility | 2026-07-28 09:42:19 | 0 | |||||||
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eagle-i research resource ontology Resource Report Resource Website 1+ mentions |
eagle-i research resource ontology (RRID:SCR_008784) | ERO | software application, service resource, data or information resource, data repository, database, source code, software resource, ontology, controlled vocabulary, storage service resource | 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. | research, resource, biomedical, owl |
is listed by: BioPortal is related to: Ontobee is related to: CTSA ShareCenter has parent organization: Eagle I has parent organization: Google Code |
ARRA ; NCRR U24RR029825 |
New BSD License | nlx_144312 | SCR_008784 | 2026-07-28 09:42:13 | 1 | |||||||
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LONI Brain Parser Resource Report Resource Website 1+ mentions |
LONI Brain Parser (RRID:SCR_009572) | Brain Parser | software application, software resource, data processing software, segmentation software, image analysis software | 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. | analyze, anatomic, application, 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 |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
GNU General Public License, LONI Software License | nlx_155783 | http://www.nitrc.org/projects/brainparser | SCR_009572 | BrainParser | 2026-07-28 09:42:27 | 3 | |||||
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map3d Resource Report Resource Website 1+ mentions |
map3d (RRID:SCR_009628) | map3d | data visualization software, software resource, software application, data processing software | 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. | c++, eeg, meg, electrocorticography, forward - inverse, linux, macos, microsoft, modeling, posix/unix-like, visualization, win32 (ms windows), windows, windows 95/98/2000 |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Map3d License | nlx_155857 | http://www.nitrc.org/projects/map3d | SCR_009628 | 2026-07-28 09:42:20 | 3 | ||||||
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Berkeley Advanced Reconstruction Toolbox Resource Report Resource Website 1+ mentions |
Berkeley Advanced Reconstruction Toolbox (RRID:SCR_016168) | BART | software application, image reconstruction software, software resource, data processing software, image analysis software | Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. | mri, reconstruction, magnetic, resonance, neuroimaging, array, transform, algorithm | is listed by: Debian | NCRR R41 RR09784; American Heart Association 12BGIA9660006; NIBIB R01 EB009690; UC Discovery 193037; Sloan Research Fellowship ; GE Healthcare |
Open source, Free | https://mrirecon.github.io/bart/, https://sources.debian.org/src/bart/ | SCR_016168 | 2026-07-28 09:44:07 | 7 | |||||||
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Fitness Browser Resource Report Resource Website 1+ mentions |
Fitness Browser (RRID:SCR_018981) | data or information resource, software resource, data access protocol, web service | Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function. | Genome browser, bacteria, mutant phenotype, bacterial genes, unknown function, data | has parent organization: University of California at Berkeley; Berkeley; USA | NCRR S10 RR029668; NCRR S10 RR027303; NIH Office of the Director OD018174; Office of Science of the US Department of Energy |
PMID:29769716 | Free, Freely available | SCR_018981 | 2026-07-28 09:45:02 | 8 | ||||||||
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Laplace Beltrami Filter on QuadEdge Meshes Resource Report Resource Website |
Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) | software application, software resource, data processing software, data acquisition software | A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface. | data acquisition software, filter, laplace beltrami, surface harmonic |
is used by: Insight Segmentation and Registration Toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIBIB R01-EB008171-01A1; NCRR P41-RR015241 |
Available to the research community | SCR_014133 | Laplace-Beltrami Filter on QuadEdge Meshes | 2026-07-28 09:43:24 | 0 | ||||||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | software application, software resource, data analysis software, data processing software | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-07-28 09:43:23 | 2805 | ||||||||
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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 | 2026-07-28 09:41:41 | 3 |
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