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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PrimerBank Resource Report Resource Website 1000+ mentions |
PrimerBank (RRID:SCR_006898) | PrimerBank | storage service resource, data repository, service resource, database, data or information resource | Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd. | electrophoresis, gene expression, quantitative pcr, gel, gene, agarose, algorithm, amplification, human, molecular probe, primer database, mouse, pcr, primer, primer pair, protein, quantification, reaction, secondary structure, polymerase chain reaction, real-time pcr, pcr primer, detection, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U01 HL66678 | PMID:22086960 PMID:19906719 PMID:19108745 PMID:14654707 |
Public, Acknowledgement requested, The community can contribute to this resource | nif-0000-21333, OMICS_02323, biotools:primerbank | https://bio.tools/primerbank | SCR_006898 | PrimerBank: PCR Primers for Gene Expression Detection and Quantification | 2026-08-04 09:41:44 | 1577 | ||||
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Whole Brain Catalog Resource Report Resource Website 1+ mentions |
Whole Brain Catalog (RRID:SCR_007011) | WBC | simulation software, image repository, storage service resource, software resource, software application, data repository, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research. | crowd sourcing, mouse, brain, cell, neuron, simulation, microscopy, neuroscience, electron microscopy, light microscopy, bioinformatics, neuroinformatics, computational biology, biology, visualization, animation, molecular structure, neuronal reconstruction, subcellular, annotation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: NeuroLex is related to: Cell Centered Database is related to: Neuroscience Information Framework is related to: INCF Software Center has parent organization: University of California at San Diego; California; USA is parent organization of: Whole Brain Catalog Blog is parent organization of: WholeBrainCatalog's Channel - YouTube |
Waitt Family Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23345 | http://www.nitrc.org/projects/incf_whole-brai | SCR_007011 | 2026-08-04 09:41:45 | 5 | ||||||
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VBASE2 Resource Report Resource Website 50+ mentions |
VBASE2 (RRID:SCR_007082) | VBASE2 | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed. | v gene sequence, v gene, gene, dna, sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: European Nucleotide Archive (ENA) is related to: Ensembl |
BMBF 031U110A/031U210A | PMID:15608286 | Acknowledgement requested | nlx_25238, biotools:germ-line_v_genes | https://bio.tools/germ-line_v_genes | SCR_007082 | VBASE2: the integrative germ-line V gene database | 2026-08-04 09:41:46 | 72 | ||||
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HUPO Brain Proteome Project Resource Report Resource Website 1+ mentions |
HUPO Brain Proteome Project (RRID:SCR_007302) | HBPP | topical portal, portal, data or information resource | An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI). | molecular neuroanatomy resource, brain, proteome, gene expression, expression profiling, proteomics, standard | has parent organization: HUPO - Human Proteome Organisation | Healthy, Neurodiseased, Aged, Alzheimer's disease, Parkinson's disease, Aging | BMBF | nif-0000-00173 | SCR_007302 | Human Brain Proteom Project, HUPO BPP | 2026-08-04 09:41:48 | 1 | ||||||
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Neurogenetics Online Resource Report Resource Website 1+ mentions |
Neurogenetics Online (RRID:SCR_007280) | topical portal, portal, data or information resource | Portal to neurogenetic resources: the mouse brain library, digital atlases of the mouse brain, extensive brain microarray data in WebQTL, and internet access to microscopes and stereology tools.Mouse Brain Library. Mouse Brain Library is an expanding collection of high-resolution histological images, atlases, MRIs, and databases on brain structure of more than 120 different lines of mice. Nervenet also includes several useful genetics and gene mapping databases to download (SNP databases, Map Manager databases, and the Portable Dictionary of the Mouse Genome). The publications section includes revised, expanded, and annotated papers, tutorials, and reviews on neurogenetics, gene mapping, complex trait analysis, stereology, and the control of neuron number. | training tools, atlas, qtl, neurogenetics | nif-0000-00035 | SCR_007280 | Nervenet | 2026-08-04 09:41:48 | 3 | ||||||||||
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Brain Explorer Atlas and Teaching Tool Resource Report Resource Website 10+ mentions |
Brain Explorer Atlas and Teaching Tool (RRID:SCR_013022) | software resource, atlas, data or information resource, training resource | Atlas of the brain and the disorders affecting it, aimed at general practitioners and specialists in training. It consists of three main parts: a description of the different parts of the normal brain and their functions, a description of the process of neurological control, and a description of 14 different brain disorders in psychiatry and neurology - as well as their cause, symptoms, and treatment. | neuroanatomy, glossary, human, mouse, brain atlas, neural anatomy | is related to: Allen Brain Atlas API | PMID:23493964 | Free, Available for download, Runs on Windows, Runs on Mac OS | nif-0000-00362 | http://brainexplorer.org/ | SCR_013022 | Brain Explorer | 2026-08-04 09:43:07 | 15 | ||||||
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Mouse Anatomical Dictionary Browser Resource Report Resource Website 1+ mentions |
Mouse Anatomical Dictionary Browser (RRID:SCR_012778) | Mouse Anatomical Dictionary | ontology, data set, data or information resource, controlled vocabulary | For each developmental stage (using the staging system defined by Theiler), the Mouse Anatomical Dictionary organizes the terms hierarchically from body region or system to tissue to tissue substructure. Modeling the anatomy hierarchically makes it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner. The Mouse Anatomical Dictionary Browser lets you navigate the extensive dictionary hierarchies for the different developmental stages, locate specific anatomical structures within those hierarchies, and see the expression results associated with those structures. Stages 1 through 26 (embryonic development) are being developed at the Department of Biomedical Sciences, University of Edinburgh, Scotland and the MRC Human Genetics Unit, Edinburgh, as part of The Mouse Atlas and 3D Graphical Gene Expression Database Project. Stage 28 (postnatal mouse) is being developed by the Gene Expression Database Project at The Jackson Laboratory. | development, anatomy, developmental stage, embryonic mouse, postnatal mouse, gene expression | has parent organization: Gene Expression Database | MRC ; BBSRC ; European Science Foundation |
nlx_47115 | SCR_012778 | 2026-08-04 09:43:05 | 3 | ||||||||
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HomeCageScan Resource Report Resource Website 10+ mentions |
HomeCageScan (RRID:SCR_014253) | data processing software, data analysis software, time-series analysis software, software resource, software application, data acquisition software | Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging. | automatic high throughput analysis, unconstrained rodent behavior, home cage, longitudinal study | is listed by: SoftCite | Available for purchase | SCR_014253 | 2026-08-04 09:43:22 | 29 | ||||||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-08-04 09:44:00 | 22 | ||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | portal, catalog, project portal, database, data or information resource | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-08-04 09:44:01 | 9 | ||||||||
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miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | data processing software, data analysis software, software resource, software application, data analytics software | Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications. | annotation, quantification, miRNA, smRNA-seq, data, functionally, distinct, isoform, isomiR, quality, sequencing, genome, mapping, statistic, tDR, yDR | PMID:28187421 | Free, Available for download, Freely available | SCR_017261 | miRquant 2.0 | 2026-08-04 09:44:09 | 1 | |||||||||
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NYU Langone’s Advanced Rodent Transgenics Laboratory ART-Lab Core Facility Resource Report Resource Website 1+ mentions |
NYU Langone’s Advanced Rodent Transgenics Laboratory ART-Lab Core Facility (RRID:SCR_017692) | access service resource, core facility, service resource | Core offers services for researchers who want to apply advanced molecular genetic techniques in rodent models of physiology and disease. Provides expertise in generating novel mutant and transgenic mouse strains using genome engineering in mouse embryos and in embryonic stem cells (ESCs). Available technologies include:Generation of genome-edited mice by embryo pronuclear microinjection of DNA and genome editors (e.g., CRISPR/Cas9, site-specific recombinases) or traditional BAC transgenesis;Generation of genome-edited mice from mouse embryonic stem cells (mESCs) by chimeric blastocyst injection;Generation of genome-edited mice from mESCs by tetraploid blastocyst injection; Generation of mice from induced pluripotent stem cells;Assisted reproductive technologies; Sperm and embryo cryopreservation, storage and import/export;in vitro fertilization (IVF); Embryo rederivation technologies for animal import into barrier vivaria through quarantine. | Rodent, model, generation, mutant, mouse, strain, gene, targeting, embryonic, stem, cell, genetically, modified, CRISPR, Cas9, editing, in vivo, EZ-mouse model, in vitro, fertilization, cryopreservation, sperm, service, core, ABRF, USEDit |
is listed by: ABRF CoreMarketplace has parent organization: New York University School of Medicine; New York; USA |
Open | ABRF_822, ABRF_105, SCR_017925, SCR_017713 | https://coremarketplace.org/?FacilityID=822 | https://coremarketplace.org/?FacilityID=105, NYU School of Medicine Rodent Genetic Engineering Laboratory | SCR_017692 | NYU School of Medicine Rodent Genetic Engineering Laboratory Core Facility, Advanced Rodent Transgenics Laboratory (ART-Lab), NYU Langone Rodent Genetic Engineering Laboratory, New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory Core Facility, ART-Lab, RGEL, New York University Langone Medical Center Rodent Genetic Engineering Laboratory | 2026-08-04 09:44:11 | 4 | ||||||
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ABA Adult Mouse Brain Ontology Resource Report Resource Website |
ABA Adult Mouse Brain Ontology (RRID:SCR_010286) | ABA-AMB | ontology, data or information resource, controlled vocabulary | Allen Brain Atlas P56 Mouse Ontology | owl |
is listed by: BioPortal has parent organization: Allen Institute for Brain Science |
nlx_157311 | SCR_010286 | Allen Brain Atlas (ABA) Adult Mouse Brain Ontology, Allen Brain Atlas Adult Mouse Brain Ontology | 2026-08-04 09:42:38 | 0 | ||||||||
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miRDB Resource Report Resource Website 1000+ mentions |
miRDB (RRID:SCR_010848) | miRDB | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | An online database for miRNA target prediction and functional annotations. | mirna, target, pathway, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18426918 PMID:18048393 |
OMICS_00403, biotools:miRDb | https://bio.tools/miRDB | SCR_010848 | 2026-08-04 09:42:49 | 1862 | |||||||
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TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NIGMS GM067031; Howard Hughes Medical Institute ; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-08-04 09:42:48 | 10783 | |||||
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ADaCGH Resource Report Resource Website 1+ mentions |
ADaCGH (RRID:SCR_010916) | ADaCGH | data analysis service, analysis service resource, software resource, production service resource, service resource | A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/ | is listed by: OMICtools | PMID:17710137 | Acknowledgement requested, Free | OMICS_00700 | SCR_010916 | Analysis of data from aCGH, ADaCGH: analysis of data from aCGH | 2026-08-04 09:42:49 | 1 | |||||||
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CMHD - Centre for Modeling Human Disease Resource Report Resource Website 10+ mentions |
CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) | CMHD | material service resource, analysis service resource, biomaterial manufacture, production service resource, service resource, database, data or information resource | Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges | mutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human disease |
has parent organization: Toronto Centre for Phenogenomics is parent organization of: Centre for Modeling Human Disease Gene Trap Resource |
Human disease | CIHR ; Genome Canada |
Non-CMHD users are required to register and log in only if you wish to view images on our mouse models. | nlx_151636 | SCR_006101 | Centre for Modeling Human Disease | 2026-08-04 09:41:30 | 12 | |||||
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MMMDB - Mouse Multiple tissue Metabolome DataBase Resource Report Resource Website 1+ mentions |
MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) | MMMDB | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. | metabolite, metabolome, cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, plasma, metabolomic pathway, capillary electropherograms time-of-flight mass spectrometry, electropherogram, mass spectrometry, annotation, isotope, fragment, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:22139941 | Free | nlx_151467, biotools:mmmdb | https://bio.tools/mmmdb | SCR_006064 | Mouse Multiple tissue Metabolome DataBase | 2026-08-04 09:41:30 | 1 | |||||
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MICe - Mouse Imaging Centre Resource Report Resource Website 1+ mentions |
MICe - Mouse Imaging Centre (RRID:SCR_006145) | MICe | portal, topical portal, reference atlas, production service resource, service resource, atlas, data or information resource | A unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics. The goals of the Mouse Imaging Centre are: * To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT). * To screen large numbers of mice for models of human diseases. * To image an individual mouse over time to observe development, disease progression and responses to experimental treatment. * To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. * To work by collaboration with researchers throughout the world. When we look for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease. The Mouse Imaging Centre (MICe) has developed high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, MICe is screening randomly mutagenized mice to look for phenotypes that represent human diseases and is taking established human disease models in mice and using imaging to follow the progression of disease and response to treatment over time. It is clear that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse models. MICe is staffed by an exciting new team of about 30 investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. The Mouse Imaging Centre (MICe) is not a fee-for-service facility but works through collaborations. Services include: * Projects involving MicroCT are available as a fee for service. * We will eventually move to the same model above with MRI. * Ultrasound Biomicroscopy is used for cardiac, embryo and cancer studies and is available as fee for service at $100 per study or in some cases on a collaborative basis. * Optical Projection Tomography has only limited availability on a collaborative basis. Mouse Atlas As our images are inherently three-dimensional, we will be able to make quantitative measures of size and volume. With this in mind, we are developing a mouse atlas showing the normal deviation of organ sizes. This atlas is an important resource for biologists as it has the potential to eliminate the need to sacrifice as many controls when making comparisons with mutants. Mouse Atlas Examples: * Variational Mouse Brain Atlas * Cerebral Vascular Atlas of the CBA Mouse * Neuroanatomy Atlas of the C57Bl/6j Mouse * Vascular Atlas of the Developing Mouse Embryo * Micro-CT E15.5 Mouse Embryo Atlas | imaging, functional genomics, mutant mouse, mri, micro computed tomography, ultrasound biomicroscopy, optical projection tomography, phenotype, genetic variant, brain, image | has parent organization: Toronto Centre for Phenogenomics | Human disease | Burroughs Wellcome Fund ; Canada Foundation for Innovation ; Canada Research Chairs ; Canadian Institutes of Health Research ; National Cancer Institute of Canada ; NIH ; Ontario Innovation Trust ; Ontario Research and Development Challenge Fund ; commercial partners |
nlx_151635 | SCR_006145 | Mouse Imaging Centre, Mouse Imaging Center, Mouse Imaging Centre (MICe) | 2026-08-04 09:41:31 | 3 | ||||||
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neuroVIISAS Resource Report Resource Website 1+ mentions |
neuroVIISAS (RRID:SCR_006010) | neuroVIISAS | data processing software, d visualization software, software resource, software application, data analytics software, data visualization software, network graph visualization software | An open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS. | platform, simulation, mapping data, connectivity data, central nervous system, tracing, connectivity, java, image modality, pynest, nest, animation, brain, nervous system, brain mapping, neuroimaging, terminology, ontology, connectomics, atlas, population spike analysis, analytics, connectome, 3d visualization, visual analytics, ontology |
is listed by: 3DVC has parent organization: University of Rostock; Mecklenburg-Vorpommern; Germany |
PMID:22350719 | nlx_151398 | http://139.30.176.116/index-Dateien/Page455.htm | SCR_006010 | neuro Visualization Imagemapping Information System for Analysis and Simulation | 2026-08-04 09:41:29 | 8 |
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