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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | topical portal, data or information resource, 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 | 2026-02-15 09:19:44 | 2 | |||||
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BIRN Coordinating Center Resource Report Resource Website |
BIRN Coordinating Center (RRID:SCR_007290) | BIRN-CC | organization portal, systems interoperability software, software application, portal, software resource, data or information resource | 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 | 2026-02-15 09:19:32 | 0 | |||||||
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Stimulate Resource Report Resource Website 10+ mentions |
Stimulate (RRID:SCR_007375) | software application, data visualization software, data processing software, software resource, data analysis 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 | 2026-02-15 09:19:45 | 10 | ||||||||
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Mouse Mutant Resource Resource Report Resource Website 1+ mentions |
Mouse Mutant Resource (RRID:SCR_008367) | MMR | organism supplier, material resource, cell repository, biomaterial supply 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 | 2026-02-15 09:19:30 | 2 | |||||
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Alamogordo Primate Facility Resource Report Resource Website |
Alamogordo Primate Facility (RRID:SCR_008376) | APF | organism supplier, material resource, biomaterial supply 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 | 2026-02-15 09:19:50 | 0 | |||||||
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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, data processing software, software resource, 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 | 2026-02-15 09:19:46 | 0 | |||||||
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New Iberia Research Center Resource Report Resource Website 10+ mentions |
New Iberia Research Center (RRID:SCR_008279) | organism supplier, material resource, biomaterial supply 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 | 2026-02-15 09:19:29 | 41 | ||||||||
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MultiPhase-SEG Resource Report Resource Website |
MultiPhase-SEG (RRID:SCR_008275) | software application, data processing software, software resource, 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 | 2026-02-15 09:19:45 | 0 | |||||||
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DualSurfaceMin Resource Report Resource Website |
DualSurfaceMin (RRID:SCR_008278) | DSM | software application, image processing software, data processing software, software resource | The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats. | software, image processing, optimization, deformable surface, surface extraction |
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-0000-23322 | SCR_008278 | 2026-02-15 09:19:49 | 0 | |||||||
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Sub-Volume Thresholding Analysis Resource Report Resource Website |
Sub-Volume Thresholding Analysis (RRID:SCR_008272) | SVT | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:19:46 | 0 | |||||||
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New England Primate Research School Resource Report Resource Website |
New England Primate Research School (RRID:SCR_008290) | portal, research forum portal, data or information resource, topical portal, disease-related 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 | 2026-02-15 09:19:49 | 0 | |||||||
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Kojak Resource Report Resource Website 1+ mentions |
Kojak (RRID:SCR_021028) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:31 | 3 | ||||||||
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LYSIS Resource Report Resource Website 50+ mentions |
LYSIS (RRID:SCR_001385) | LYSIS | software application, source code, data processing software, software resource, simulation software, software toolkit, data analysis 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 | 2026-02-15 09:18:05 | 55 | |||||||
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Harvard - Oxford Cortical Structural Atlas Resource Report Resource Website 100+ mentions |
Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) | Atlases | atlas, data or information resource, 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 | 2026-02-15 09:18:06 | 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 | software application, image analysis software, data processing software, software resource | 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 | 2026-02-15 09:18:16 | 0 | |||||
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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 | organization portal, data or information resource, 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 | 2026-02-15 09:17:54 | 0 | |||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software application, data processing software, software resource | 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 | 2026-02-15 09:19:00 | 120 | |||||
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Zebrafish Atlas Resource Report Resource Website 1+ mentions |
Zebrafish Atlas (RRID:SCR_006722) | Zebrafish Atlas | atlas, data or information resource, 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 | 2026-02-15 09:19:33 | 3 | |||||
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Autopack Resource Report Resource Website 1+ mentions |
Autopack (RRID:SCR_006830) | autoPack | software application, data processing software, software resource | 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 | 2026-02-15 09:19:22 | 3 | ||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | software application, data visualization software, data processing software, software resource, simulation software, software toolkit | 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 | 2026-02-15 09:18:19 | 21 |
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