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Image databases/repositories | Bioimaging

Human Protein…
Dataset

Human Protein Atlas

A knowledge-based portal with gene-centric expression profiles based on the…

A knowledge-based portal with gene-centric expression profiles based on the annotation of several antibodies towards the same protein target. Because all the data on the Human Protein Atlas are…

EMAP
Dataset

EMAP e-Mouse Atlas Project

Gathers digital models of mouse development. EMAP allows users to visualize…

Gathers digital models of mouse development. EMAP allows users to visualize embryo anatomy and gene expression of mice in 3D.

SCMD
Dataset

SCMD Saccharomyces Cerevisiae Morphological Database

Facilitates the analysis of abnormal cells. SCMD provides micrographs and…

Facilitates the analysis of abnormal cells. SCMD provides micrographs and quantitative data using the image-processing software for shapes of the daughter and mother cells, the localization of the…

BrainAligner
Desktop

BrainAligner

A program that automatically finds the corresponding landmarks in a subject…

A program that automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. BrainAligner registers 3D images of…

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EMAGE
Dataset

EMAGE

A freely available database of in situ gene expression patterns that allows…

A freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression.

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Allen Brain…
Dataset

Allen Brain Atlas

A growing collection of online public resources integrating extensive gene…

A growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools.

OpenFMRI
Dataset

OpenFMRI

Serves as a repository for the open sharing and dissemination of task-based…

Serves as a repository for the open sharing and dissemination of task-based functional magnetic resonance imaging (fMRI) data. OpenFMRI allows user to share uncurated datasets (clearly labeled as…

SSBD
Dataset

SSBD Systems Science of Biological Dynamics

Stores and shares quantitative biological dynamics data. SSBD currently…

Stores and shares quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei, and whole organisms in a wide variety of model organisms…

PhIS
Dataset

PhIS PhenoImageShare

Allows semantic discovery, phenotypic browsing and annotation of federated…

Allows semantic discovery, phenotypic browsing and annotation of federated phenotypic images. PhIS contains about 117,900 images federated from four different data resources with 53,000 regions of…

DMDD
Dataset

DMDD Deciphering the Mechanisms of Developmental Disorders

Contains image and phenotype data for embryonic lethal knockout mice. DMDD is…

Contains image and phenotype data for embryonic lethal knockout mice. DMDD is database allowing to search by gene, phenotype or tissue type. The data sheds new light on genes that are critical for…

CIL-CCDB
Dataset

CIL-CCDB

Compiles images, videos and animations of cells from multiple organisms, cell…

Compiles images, videos and animations of cells from multiple organisms, cell types, and processes, normal and pathological. CIL-CCDB is an open-source database including about 9250 images from 358…

OpenTein
Dataset

OpenTein Open Teratoma Investigation

Archives and freely distributes high-resolution whole-slide images and relevant…

Archives and freely distributes high-resolution whole-slide images and relevant records. OpenTein has been designed as a searchable, zoomable and annotatable web-based repository system. We have…

BRAINS Imagebank
Dataset

BRAINS Imagebank Brain Images of Normal Subjects Imagebank

A collection of anonymised images and associated clinical data. BRAINS…

A collection of anonymised images and associated clinical data. BRAINS Imagebank includes ‘normal’ individuals at all ages (from prenatal to old age). The data were collected from individuals…

CoralNet
Dataset

CoralNet

Allows users to browse images and annotations as well as for viewing and…

Allows users to browse images and annotations as well as for viewing and exporting estimated cover statistics. CoralNet is a repository and online annotation tool for benthic survey images. It allows…

WDDD
Dataset

WDDD Worm Developmental Dynamics Database

Stores a collection of quantitative information about cell division dynamics in…

Stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference.

The Clinical…
Mobile

The Clinical Atlas of Intravascular Optical Coherence Tomography

Offers an interactive guidance to a systematic and scientifically critical…

Offers an interactive guidance to a systematic and scientifically critical interpretation of optical coherence tomography (OCT) images. The Clinical Atlas of Intravascular OCT consists of eight…

Huntington's…
Dataset

Huntington's Disease Animal Models

An MRI database for animal models of Huntington disease. The Cambridge MRI…

An MRI database for animal models of Huntington disease. The Cambridge MRI repository comprising 400 datasets to date from mouse models of Huntington disease. The data include raw images as well as…

UMCD
Dataset

UMCD USC Multimodal Connectivity Database

An interactive web-based platform for brain connectivity matrix sharing and…

An interactive web-based platform for brain connectivity matrix sharing and analysis. UMCD enables users to download connectivity matrices shared by other users, upload matrices from their own…

FABA
Dataset

FABA Four-dimensional Ascidian Body Atlas

Represents an image resource for ascidian development. FABA allows users to…

Represents an image resource for ascidian development. FABA allows users to understand the embryonic organization at the single cell level. It defines the stages of early embryonic development from…

BossDB
Dataset

BossDB Block & Object Storage System DataBase

Contains petascale, multi-dimensional image data and associated co-registered…

Contains petascale, multi-dimensional image data and associated co-registered voxel annotations. BossDB allows indexation of massive multi-dimensional image and annotation datasets. It enables…

SOCR
Web

SOCR Statistics Online Computational Resource

Aims to design, validate and disseminate knowledge. SOCR is a technique that…

Aims to design, validate and disseminate knowledge. SOCR is a technique that enables investigation of biological mechanisms related to morphological changes in cell nucleus through quantitative…

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SCPortalen
Dataset

SCPortalen

Provides a single-cell centric dataset to provide a gateway to utilize the…

Provides a single-cell centric dataset to provide a gateway to utilize the untapped potential of single-cell dataset. SCPortalen contains metadata about the biological samples, used protocols and…

eHistology
Dataset

eHistology

Contains annotated coronal sections captured and annotated for the "Atlas…

Contains annotated coronal sections captured and annotated for the "Atlas of Mouse Development Supplement with new Coronal Sections". eHistology is an image index that includes annotations…

DIADEM
Dataset

DIADEM DIgital reconstruction of Axonal and DEndritic Morphology

A selection of six data set collections from different animal species, brain…

A selection of six data set collections from different animal species, brain regions, neuron types, and visualization methods. The DIADEM data sets were compiled during the DIADEM Challenge, a…

CPD
Dataset

CPD Cellular Phenotype Database

A repository for data derived from high-throughput systems microscopy studies.…

A repository for data derived from high-throughput systems microscopy studies. The aims of this resource are: (i) to provide easy access to cellular phenotype and molecular localization data for the…

YRC PIR
Dataset

YRC PIR The Yeast Resource Center Public Image Repository

Provides a large number of images and their associated metadata for many…

Provides a large number of images and their associated metadata for many proteins across multiple organisms. YRC PIR is a database of fluorescence microscopy images. It allows researchers to find,…

Maize Cell…
Dataset

Maize Cell Genomics Database

A public database, developed to organize a large data set of confocal images…

A public database, developed to organize a large data set of confocal images generated from the maize marker lines, for studying native gene expression in specific cell types and subcellular…

FlyMove
Dataset

FlyMove

A database combining movies, animated schemata, interactive "modules"…

A database combining movies, animated schemata, interactive "modules" and pictures that will greatly facilitate the understanding of Drosophila development. FlyMove aims to use multimedia…

The cell
Dataset

The cell

A freely accessible, easy-to-search, public repository of reviewed and…

A freely accessible, easy-to-search, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular…

LOCATE
Dataset

LOCATE

A curated database that houses data describing the membrane organization and…

A curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

BreakHis
Dataset

BreakHis Breast Cancer Histopathological Database

A dataset of 7909 breast cancer (BC) histopathology images acquired on 82…

A dataset of 7909 breast cancer (BC) histopathology images acquired on 82 patients. BreakHis includes both benign and malignant images. The task associated to this dataset is the automated…

Longitudinal…
Dataset
IDR
Dataset

IDR Image Data Resource

Links experimental perturbations to public genetic or chemical databases, and…

Links experimental perturbations to public genetic or chemical databases, and cell and tissue phenotypes to controlled vocabularies expressed as ontologies. IDR collects and integrates imaging data…

JCB DataViewer
Dataset

JCB DataViewer

A web-based, multi-dimensional image data-viewing application. JCB DataViewer…

A web-based, multi-dimensional image data-viewing application. JCB DataViewer is a tool for visualization and simple analysis of original image data files associated with JCB articles. Image data are…

DICCCOL
Dataset

DICCCOL Dense Individualized and Common Connectivity-based Cortical Landmarks

Consists of a dense and consistent map of 358 cortical landmarks. Each DICCCOL…

Consists of a dense and consistent map of 358 cortical landmarks. Each DICCCOL is defined by group-wise consistent white-matter fiber connection patterns derived from diffusion tensor imaging (DTI)…

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IN Situ Gene…
Dataset

IN Situ Gene Expression Image Database

Gathers information for 14 pigment cell-expressed genes of the developing…

Gathers information for 14 pigment cell-expressed genes of the developing melanocyte and Ribulose-phosphate 3-epimerase (RPE) lineages. IN Situ Gene Expression Image Database consists in an online…

The…
Dataset

The Multi-Dimensional Human Embryo

Improves the distribution of human embryological image data. The…

Improves the distribution of human embryological image data. The Multi-Dimensional Human Embryo intends to collect 3D magnetic resonance data of normal human embryos from Carnegie stages 10–23. It…

Mindboggle
Desktop

Mindboggle

A fully automated feature-matching approach to assign anatomical labels to…

A fully automated feature-matching approach to assign anatomical labels to cortical structures and activity in human brain magnetic resonance images (MRI) data. Mindboggle employs each atlas in a…

ImageNet
Dataset

ImageNet

Provides a global image library. Imagenet contains over 14 197 000 annotated…

Provides a global image library. Imagenet contains over 14 197 000 annotated images, classified according to the WordNet hierarchy. The database aims to furnish over 500 images per synset. It allows…

TOBIKOBACHI
Dataset

TOBIKOBACHI

Gathers information about Japanese Encyrtid wasps. TOBIKOBACHI is a photograph…

Gathers information about Japanese Encyrtid wasps. TOBIKOBACHI is a photograph library based on a personal collection published to help entomologists and biologists as well as taxonomists in getting…

HANABACHI
Dataset

HANABACHI

Provides a repository for detailed information about Japanese bees. HANABACHI…

Provides a repository for detailed information about Japanese bees. HANABACHI inventories The Kyushu University Museum collection and provides detailed record about each species. Each entry is…

Radiogenomics
Dataset

Radiogenomics

A comprehensive radiogenomic study to explore the association between…

A comprehensive radiogenomic study to explore the association between multi-platform genomic profiles and MRI-based tumor phenotypes for breast invasive carcinoma. Radiogenomics integrates data from…

WormAtlas
Dataset

WormAtlas

Provides information about the structural anatomy of Caenorhabditis elegans.…

Provides information about the structural anatomy of Caenorhabditis elegans. WormAtlas offers a simple interface allowing the user to easily navigate through every anatomical structure of the worm.…

NeuroMorpho.Org
Dataset

NeuroMorpho.Org

A centrally curated inventory of digitally reconstructed neurons associated…

A centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. NeuroMorpho.Org contains contributions from over 100 laboratories worldwide and is…

FlyView
Dataset

FlyView

An image database for Drosophila development and genetics, particularly for…

An image database for Drosophila development and genetics, particularly for gene-expression patterns. The concept of FlyView includes compatibility to FlyBase, the main Drosophila database.

Human…
Dataset

Human Evolution Microtomographic Archive

A web based archive that contains tomographic scans (as well as various types…

A web based archive that contains tomographic scans (as well as various types of associated digital data) of fossils from the site of Kromdraai B, South Africa that are curated at the Ditsong…

CCDB
Dataset

CCDB Cell Centered Database

A web accessible database for high resolution 2D, 3D and 4D data from light and…

A web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging. Techniques range from wide field mosaics taken with multiphoton…

TCIA
Dataset

TCIA The Cancer Imaging Archive

The image data is organized into purpose-built collections of subjects. The…

The image data is organized into purpose-built collections of subjects. The subjects typically have a cancer type and/or anatomical site (lung, brain, etc.) in common. Each link in the table below…

Lumbar…
Dataset

Lumbar vertebra segmentation CT image database

Provides a vertebra database. Lumbar vertebra segmentation CT image database is…

Provides a vertebra database. Lumbar vertebra segmentation CT image database is a downloadable resource that contains computerized tomography (CT) images of the lumbar spine for different subjects…

Japanese Ant…
Dataset

Japanese Ant Image Database

Gathers photographs of Japanese ant species.

Gathers photographs of Japanese ant species.

MCPA
Dataset

MCPA Mammalian Crania Photographic Archive

Provides access to more than 10,000 photographs of mammalian crania. MCPA is a…

Provides access to more than 10,000 photographs of mammalian crania. MCPA is a database allowing to search photographs for more than 1800 cranial specimens using a phylogenetic tree or by scientific,…

Gastrointestina…
Dataset

Gastrointestinal Medical Image Database

Provides a medical database with gastrointestinal image. Gastrointestinal…

Provides a medical database with gastrointestinal image. Gastrointestinal Medical Image Database is an online resource compiled with the cooperation of the National Cancer Center, regional cancer…

Kyoto Human…
Dataset

Kyoto Human Embryo Visualization Project

Contains almost 1300 images of human embryos. Kyoto Human Embryo Visualization…

Contains almost 1300 images of human embryos. Kyoto Human Embryo Visualization Project is an online platform allowing user to analyze complex morphogenetic events thanks to a lot of 3D images of…

Taxonomy Icon
Dataset

Taxonomy Icon

Provides a repository of illustrations available for Fungi, Animals, Protists,…

Provides a repository of illustrations available for Fungi, Animals, Protists, Plants and Bacteria. Taxonomy Icon includes over 200 images free for use and distribution. The database provides four…

EPFDB
Dataset

EPFDB Entomopathogenic Fungi Database

Aims to furnish a repository for fungi’s characterization by collecting…

Aims to furnish a repository for fungi’s characterization by collecting images. EPFDB aims to heap micro photographs from volunteers to constitute a photograph library about entomopathogenic fungi…

J-EDI
Dataset

J-EDI JAMSTEC E-library of Deep-sea Images

Offers sea images and dive surveys. J-EDI permits users to build they own…

Offers sea images and dive surveys. J-EDI permits users to build they own library of deep-sea photos and movies.

Plastimatch
Desktop

Plastimatch

Serves for radiotherapy image processing. Plastimatch focuses on volumetric…

Serves for radiotherapy image processing. Plastimatch focuses on volumetric registration medical images like: positron emission tomography (PET), magnetic resonance imaging (MRI), and X-ray computed…

MorphoSource
Dataset

MorphoSource

Provides 3D morphological data sets and allows storage, organization, sharing…

Provides 3D morphological data sets and allows storage, organization, sharing and distribution of user’s 3D data. MorphoSource is a public repository and a virtual museum and archive aiming to…

NCI Visuals…
Dataset

NCI Visuals Online

Provides an image bank of photographs and illustrations that can be used in a…

Provides an image bank of photographs and illustrations that can be used in a communicational goal. NCI Visuals Online concerns biomedical, science, and patient-care related illustrations and images…

FlyTED
Dataset

FlyTED

Provides a web access to gene expression images and their metadata. FlyTED is a…

Provides a web access to gene expression images and their metadata. FlyTED is a biological database for images of gene expression in the testis of Drosophila melanogaster. This resource includes the…

PSLID
Dataset

PSLID Protein Subcellular Location Image Database

It is both a web service providing access to collections of images showing…

It is both a web service providing access to collections of images showing subcellular location patterns and an open-source image database software system. There are two main collections: the…

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