Sample databases

Public sample image databases across various imaging modalities.

For more OME-Zarr datasets, check out the OME-NGFF Data Resources page, which lists publicly available OME-Zarr datasets for testing and exploration.

If you come across image databases that are missing from the list below, create an issue or submit a pull request on napari/docs to help us expand it.

Database	Description
Allen Brain Atlases	Human and mouse brain atlas containing gene expression, anatomic, and genomic data
Allen Cell Explorer	Database of cell data, segmentations, and analyses with multiple experimental parameters.
Berkeley Drosophila Genome Project (BDGP) in situ database	Patterns of gene expression in Drosophila embryogenesis.
The Cell Image Library	Public resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes.
FlyLight Imagery	3D fly’s central nervous system captured by confocal laser scanning microscope.
OpenCell	A proteome-scale collection of protein localization and interaction measurements in human cells. Contains fluorescence microscopy and IP-MS data.
Whole Slide Imaging Repository	Collections of whole slide imaging repositories.
BioImage Archive	Description and data of biological studies; links to databases at EMBL-EBI (European Molecular Biology Laboratory–European Bioinformatics Institute).
Image Data Resource (IDR)	Public data repository for storing and integrating image data sets from published scientific studies.
Systems Science of Biological Dynamics (SSBD)	Set of quantitative data and microscopy images from a variety of species, sources, and methods.
Cancer Imaging Archive	Collections of cancer medical images.
Brain Image Library	A public resource to deposit, analyze, mine, share, and interact with large brain image datasets.
EMPIAR	The Electron Microscopy Public Image Archive (EMPIAR) is a public resource for raw images underpinning 3D cryo-EM maps and tomograms.
OME-NGFF files on IDR	Catalog of IDR images formatted as OME-NGFF.
Cell Tracking Challenge	Repository of annotated videos from the Cell Tracking Challenge; contains contrast-enhancing (PhC, DIC) or fluorescence (widefield, confocal, multiphoton, and light sheet microsocopy) data.
Bio-Formats supported formats	Example files for Bio-Formats supported formats.
BioImage Informatics Index (BIII) datasets	Mix of datasets and links to other data repositories.
SCIFIO	Example images with CC0 licenses.
EPFL Super-resolution microscopy datasets	Super-resolution microscopy datasets.
Brain Observatory Storage Service & Database	BossDB is a volumetric database for 3D and 4D neuroscience data, with API access.
Mouse Brain Atlas	Spatiotranscriptomics data of mouse brain.
Broad Bioimage Benchmark Collection	Benchmark images with ground truth segmentation.
DANDI Archive	The BRAIN Initiative archive for publishing and sharing neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments.
Human BioMolecular Atlas Program (HuBMAP)	An open platform to discover, visualize and download standardized healthy single-cell and spatial tissue data.
OpenOrganelle	A data portal for volume electron microscopy datasets and accompanying segmentations available for exploration.
Wellcome Sanger Institute OME-Zarr	A collection of datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format (NGFF) specifications for storing and serving bioimaging data.
WEBKNOSSOS OME-Zarr Gallery	A gallery of OME-Zarr datasets from WEBKNOSSOS.
Human Organ Atlas	The Human Organ Atlas bridges cellular and whole organ scales with images of whole intact organs at 8-20 μm resolution and region of interest zooms at 1 μm.