Tag: imaging

The Alzheimer’s Disease Neuroimaging Initiative (ADNI) unites researchers with study data as they work to define the progression of Alzheimer’s disease (AD). ADNI researchers collect, validate and utilize data, including MRI and PET images, genetics, ...

The Cancer Imaging Archive (TCIA) is a service which de-identifies and hosts medical images of cancer for public download. The data are organized as “collections”; typically patients’ imaging related by a common disease (e.g. lung cancer), image moda ...

Autism Brain Imaging Data Exchange (ABIDE) initiative has aggregated functional and structural brain imaging data collected from laboratories around the world to accelerate our understanding of the neural bases of autism (ASD Autism Spectrum Disorder ...

OME-TIFF is a standardized file format for multidimensional image data. OME-TIFF was created to maximize the respective strengths of OME-XML and TIFF. It takes advantage of the metadata defined in OME-XML while retaining the pixels in multi-page TIFF ...

OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community. The purp ...

The OpenNeuro project (formerly known as the OpenfMRI project) was established in 2010 to provide a resource for researchers interested in making their neuroimaging data openly available to the research community. It is managed by Russ Poldrack and C ...

GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e. ...

This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular ...

PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells. PhenoM allows users to rapidly search and retrieve raw images ...

The Structural Biology Data Grid (SBGrid-DG) community-driven repository to preserve primary experimental datasets that support scientific publications. The SBGrid Data Bank is an open source research data management system enabling Structural Biolog ...

The e-Mouse Atlas of Gene Expression (EMAGE) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descripti ...

Gene expression and neuroanatomical data.

FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. The FlyCircuit Database currently contains about 30,000 high resolution 3D br ...

The Coherent X-ray Imaging Data Bank (CXIDB) offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. It arose from the need to share the terabytes of data generated from X-ray free- ...

The InterLex terminology is a lexicon of biomedical terms built on the foundation of NeuroLex and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies and BIRNLex (Biomedical Informatics R ...

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure. The purpose of EMPIAR is to provide easy access to s ...

The purpose of imzML is to facilitate the exchange and processing of mass spectrometry imaging data. This website is intended to provide all information neccesary to implement imzML. imzML was developed in the framework of the EU funded project COMPU ...

FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...

This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans. CogPO is a framework for the formal representation of the cognitive paradigms used in behavioral experiments, driven by cognit ...

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB ...

The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes.

PPMI is an observational clinical study to verify progression markers in Parkinson’s disease. The study is designed to establish a comprehensive set of clinical, imaging and biosample data that will be used to define biomarkers of PD progression. Onc ...

DICOM — Digital Imaging and Communications in Medicine — is the international standard for medical images and related information (ISO 12052). It defines the formats for medical images that can be exchanged with the data and quality necessary for cli ...

Community-editable fluorescent protein database, cataloging an expanded range of proteins and parameters, including a new spectra viewer.

The UCSC Cancer Genomics Browser is a web-based tool to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of experimental measurements for multiple samples, alongside their associated clinical ...

RNAiDB provides access to results from RNAi interference studies in C. elegans , including images, movies, phenotypes, and graphical maps.

The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system is an extensible, scalable informatics platform for TBI relevant imaging, assessment, genomics, and other data types. It was developed to share data across the entire ...

The PAIN Repository is a brain imaging archive for structural and functional magnetic resonance scans (MRI, fMRI and DTI) hosted at UCLA and open to all pain investigators.

Initiated in 2013, DMDD has the ambitious goal of identifying all embryonic lethal knockout lines made at the Wellcome Trust Sanger institute, through their work as a major centre for creation of individual mouse gene knockouts. DMDD uses a combinati ...

Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis ...

The Dynamic Proteomics database is a compendium of endogenously YFP-tagged human proteins and their time-lapse microscopy movies. These movies show the protein dynamics in space and in time in individual living human cancer cells in response to an an ...

The Neuroimaging Data Model (NIDM) is a collection of specification documents and examples that outline a domain specific extension to the W3C Provenance Data Model (PROV-DM) for the exchange and sharing of human brain imaging data. The goal of the d ...

LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.

The core of the system is tailored PACS (Picture Archiving and Communication System). It forms the basis for educational and research applications such as the development of databases of case studies describing the treatment of real patients. Images ...

ClinEpiDB is an open-access online resource for clinical and epidemiologic studies. The website allows users to visualize and subset data directly in the ClinEpiDB browser and explore potential associations. Supporting study documentation aids contex ...

GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel images of proteomes from organisms with known genome information (available at http://gelbank.anl.gov). GELBANK serves as a database for those proteomics labs t ...

Conformational features of DNA

BioImage Informatics Index (BIII) is a bioimaging resource that describes software tools, training materials and imaging datasets with the aim of helping researchers find, identify and propagate image analysis tools or workflows. BIII aims to help bi ...

A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling t ...

Brainbase is a data management, collaboration and sharing platform for the human neuroscience community. The platform provides private research collaboration workspaces, tools to flexibly organize and track subjects and sessions within studies, valid ...

CycloBranch is an open and platform-free software that provide the de novo generation of molecular formulas of unknown compounds in both liquid chromatography/mass spectrometry and mass spectrometry imaging datafiles.

Database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to most structures present in the electron ...

A web based virtual gallery of biological specimens using X-ray microtomography. Micro-computed tomography or microCT is a method of non-destructive 3D x-ray microscopy, which allows the users to create 3D models of objects from a series of x-ray pro ...

A myocardial infarction risk knowledge base. Myocardial Infarction Risk Knowledge Base. MIRKB (the Myocardial Infarction Risk Knowledge Base) is a database that collected single factors, combined factors, and risk models which are article-supported ...

A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.

MorphoSource is a digital repository where researchers, museum curators, and the general public can find, download, and upload 3D media representing physical objects, most commonly biological specimens. If you are a researcher, you can use MorphoSour ...

The Semantic Sensor Network (SSN) ontology is an ontology for describing sensors and their observations, the involved procedures, the studied features of interest, the samples used to do so, and the observed properties, as well as actuators. SSN foll ...

The National COVID-19 Chest Imaging Database is a joint collaboration between NHSX, BSTI and Royal Surrey NHS Foundation Trust to create a centralised UK database of X-Ray, CT and MRI images from hospital patients to inform the COVID-19 response. The ...

CPRD GOLD linked Hospital Episode Statistics Diagnostic Imaging Dataset (HES DID) data contain information about NHS diagnostic imaging tests, such as x-rays and MRI scans, in England (but not the images themselves).

CPRD Aurum linked Hospital Episode Statistics Diagnostic Imaging Dataset (HES DID) data contain information about NHS diagnostic imaging tests, such as x-rays and MRI scans, in England (but not the images themselves).

Contains pseudo-anonymised and linkable clinical imaging data from the National Picture Archiving and Communication System (NPACS).

Imaging and bio-sample data sets related to patients with active and inactive Inflammatory Bowel Disease

Longitudinal routine data for 128,000 admissions to hospital as an emergency from a care home; including treatments, interventions, ITU admissions and outcomes. Deeply phenotyped longitudinal data including serial physiology, blood biomarkers.

GOSH is the custodian of the latest study dataset - IMPORT. All of the trial/study datasets include: full patient and tumour demographics, associated congenital abnormalities, tumour stage, treatment received and follow up for relapse and death. GOSH ...

A granular dataset of over 65,000 emergency admissions, with detailed patient flow through hospital detailing day-to-day variation in case mix. Severity, demographics, multi-morbidity, completion of review, interventions, treatments and outcomes.

The CXI file format was created as common format for all the data in the Coherent X-ray Imaging Data Bank (CXIDB). Naturally its scope is all experimental data collected during Coherent X-ray Imaging experiments as well as all data generated during th ...

A repository for DNA and RNA nanostructures.

An automated approach to spectral unmixing of fluorescent biological images.

ColTapp is an automated image analysis application for efficient microbial colony growth dynamics quantification.

A large eldercare-oriented BEnchmark database of SSVEP-BCI for The Aging population (eldBETA)

CpGmotifs is a tool to discover DNA motifs associated to CpG methylation events.

The Face Image Meta-Database (fIMDb) provides researchers with the tools to find the face imagesbest suited to their research, with filters to locate databases with people of a varied racial and ethnic backgrounds and ages.

STL files describe only the surface geometry of a three-dimensional object without any representation of color, texture or other common CAD model attributes. The STL format specifies both ASCII and binary representations.

Ebolabase is a comprehensive source for ebola-human interactions has been developed. Ebolabase contains experimentally verified entries of ebola-human interactions. The interactions are visualized as network images. This study provides the informatio ...

CNGB (China National GeneBank) Nucleotide Sequence Archive (CNSA) is a service that provides online data submitting of data and metadata of projects, samples, experiments and sequencing. The CNSA is a system for archiving global omics data, dedicated ...

B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5544 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets.

DODO is a graph database to facilitate access and interaction with disease and phenotype ontologies. The aim of DODO is to allow an easier way to interact and explore disease ontologies and their identifiers. The database is build on Neo4j and incorp ...

PAI-WSIT (Pathologists Annotated and AI-empowered Whole-Slide Image Database for Tumors) is a comprehensive curated resource for cancerous pathology with deep learning. PAI-WSIT allows you to store your Digital Pathology images into the cloud platfor ...

The proposed Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines described here aims to deliver a set of rules representing the minimal information required to report and support interpretation and assessment of data ...