Tools   Select Another Resource Report Type

http://www.rrcancer.ca/en/publique/accueil

An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate students.

Proper citation: Cancer Research Network of the FRSQ (RRID:SCR_004225) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/biobank/physicalbloom

The UCL/UCLH Biobank for Studying Health and Disease has been primarily established to support the Research Programme and scientific needs, of the Pathology Department UCLH & the UCL Cancer Institute. The establishment of the core programme enables a centralised approach to the management and integration of all research groups working within these institutions, providing appropriate structure and support. The biobank has policies and guidelines to guarantee compliance with HTA legislation and to ensure quality standards will be maintained. The biobank stores normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids, as well as human tissue used in xenograft experiments. Stored tissues include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues include resection specimens obtained surgically or by needle core biopsy. Bodily fluids include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (eg. pleura and peritoneum) are also collected. Where appropriate the biobank also stores separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples are stored in the diagnostic archive.

Proper citation: UCL/UCLH Biobank for Studying Health and Disease (RRID:SCR_004610) Copy   

•   Source: SciCrunch Registry

http://www.zfatlas.psu.edu/

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.

Proper citation: Zebrafish Atlas (RRID:SCR_006722) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/Cyno

A reference atlas of cynomolgus macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual cynomolgus monkeys and studies. We have used MRI volumes from a group of 18 normal adult cynomulgus monkeys (Macaca fascicularis) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous cynomolgus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the cynomolgus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas (RRID:SCR_008793) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dti_rat_atlas/

3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file.

Proper citation: 3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood (RRID:SCR_009437) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vervet_atlas/

Vervet (Chlorocebus aethiops sabaeus) probabilistic atlas that defines an anatomical space (template) with associated tissue and regional prior probability maps. The atlas was produced from whole head MRI of 10 normal adult animal subjects. The package consists of two atlases. The Biased directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The Unbiased directory contains the atlas constructed using unbiased estimation. The atlas is suitable for use in any segmentation tool using a probabilistic atlas, for example those in Slicer.

Proper citation: Vervet Probabilistic Atlas (RRID:SCR_000426) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MCCL

A comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.

Proper citation: Cell Line Ontology by Mahadevan (RRID:SCR_010281) Copy   

•   Source: SciCrunch Registry

http://irc.cchmc.org/software/pedbrain.php

Brain imaging data collected from a large population of normal, healthy children that have been used to construct pediatric brain templates, which can be used within statistical parametric mapping for spatial normalization, tissue segmentation and visualization of imaging study results. The data has been processed and compiled in various ways to accommodate a wide range of possible research approaches. The templates are made available free of charge to all interested parties for research purposes only. When processing imaging data from children, it is important to take into account the fact that the pediatric brain differs significantly from the adult brain. Therefore, optimized processing requires appropriate reference data be used because adult reference data will introduce a systematic bias into the results. We have shown that, in the in the case of spatial normalization, the amount of non-linear deformation is dramatically less when a pediatric template is used (left, see also HBM 2002; 17:48-60). We could also show that tissue composition is substantially different between adults and children, and more so the younger the children are (right, see also MRM 2003; 50:749-757). We thus believe that the use of pediatric reference data might be more appropriate.

Proper citation: CCHMC Pediatric Brain Templates (RRID:SCR_003276) Copy   

•   Source: SciCrunch Registry

http://www.humanconnectomeproject.org/

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy   

•   Source: SciCrunch Registry

http://www.pediatricmri.nih.gov/

Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2.

Proper citation: NIH MRI Study of Normal Brain Development (RRID:SCR_003394) Copy   

•   Source: SciCrunch Registry

http://brain-development.org/ixi-dataset/

Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information eXtraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available. The data has been collected at three different hospitals in London: * Hammersmith Hospital using a Philips 3T system * Guy''s Hospital using a Philips 1.5T system * Institute of Psychiatry using a GE 1.5T system

Proper citation: IXI dataset (RRID:SCR_005839) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/art

ART ''''acpcdetect'''' program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans. ART ''''brainwash'''' program for automatic multi-atlas skull-stripping of 3D structural MRI scans. ART ''''3dwarper'''' program of non-linear inter-subject registration of 3D structural MRI scans. Software (art2) for linear rigid-body intra-subject inter-modality (MRI-PET) image registration. Data resource: The ART projects makes available corpus callosum segmentations of 316 normal subjects from the OASIS cross-sectional database. ART ''''yuki'''' program for fast, robust, and fully automatic segmentation of the corpus callosum on 3D structural MRI scans.

Proper citation: Automatic Registration Toolbox (RRID:SCR_005993) Copy   

•   Source: SciCrunch Registry

https://www.braintest.org/brain_test/BrainTest

A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.

Proper citation: Brain Test (RRID:SCR_006212) Copy   

•   Source: SciCrunch Registry

http://embryoimaging.org/

Collection of high resolution images and movies of mouse and human embryos produced using high resolution episcopic microscopy (HREM). Each data set is a series of block-face images generated during sectioning through an entire embryo, typically cut at 2-3 micrometers. Datasets are organized by approximate developmental stage and each embryo has been assigned a specimen ID (SID) for identification. This is an ongoing project funded by the Wellcome Trust to provide comprehensive imaging of normal and mutant mouse embryos that will complement the standard anatomical texts and form the basis for systematic phenotyping. * Movies: A 3D reconstruction shows each embryo, and lower resolution movies created through each orthogonal plane enable you to quickly review the data set. * Image Stacks: In the stack viewer, you can step through the images in sequence, zoom in to see fine details and adjust the image contrast. * NEW: Embryo Comparison: Two image stacks can now be compared in the stack viewer.

Proper citation: Embryo Imaging (RRID:SCR_006329) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~brdsmith/Research.html

Data set of image collections and movies including Magnetic Resonance Imaging of Embryos, Human Embryo Imaging, MRI of Cardiovascular Development, and Live Embryo Imaging. Individual MRI slice images, three-dimensional images, animations, stereo-pair animations, animations of organ systems, and photo-micrographs are included.

Proper citation: Brad Smith Magnetic Resonance Imaging of Embryos (RRID:SCR_006300) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/cv-gmodels

Repository of geometric models collected from on-going and past research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford University. The geometric models are mostly built from imaging data of healthy and diseased individuals. For each of the models, a short description is given with a reference. The geometric models are in VTK PolyData XML .vtp format. * Audience: Biomechanical and computational researchers interested in complex models of cardiovascular applications * Long Term Goals and Related Uses: Allow users to download geometric models for cardiovascular applications. These geometric models can be used for research purposes, such as meshing and scientific visualization. Users are welcome to contact the project administrator, join the project and contribute additional models.

Proper citation: Cardiovascular Model Repository (RRID:SCR_002679) Copy   

•   Source: SciCrunch Registry

http://www.umc.edu/Administration/Centers_and_Institutes/Center_for_Psychiatric_Neuroscience/Core_Research_Resources.aspx

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.

Proper citation: UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) Copy   

•   Source: SciCrunch Registry

http://www.diabetesgenome.org

Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself.

Proper citation: DGAP (RRID:SCR_003036) Copy   

•   Source: SciCrunch Registry

https://www.pathology.umn.edu/research/liver-tissue-cell-distribution-system

Tissue bank that provides human liver tissue from regional centers for distribution to scientific investigators throughout the United States. These USA regional centers have active liver transplant programs with human subjects approval to provide portions of the resected pathologic liver for which the transplant is performed.

Proper citation: Minnesota Liver Tissue Cell Distribution System (RRID:SCR_004840) Copy   

•   Source: SciCrunch Registry