Sample databases#

Public sample image databases across various imaging modalities.

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.



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.


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.


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.


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.