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Imaging Biological Samples with Optical Microscopy

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Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...

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Updated: Jul 24, 2025

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

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Published on: April 10, 2016

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

Josh Moore¹, Daniela Basurto-Lozada², Sébastien Besson³

¹German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany. josh@openmicroscopy.org.

Histochemistry and Cell Biology

|July 10, 2023

Summary

This summary is machine-generated.

A new bioimaging file format, OME-Zarr, is being developed to address data challenges. This cloud-optimized format and associated tools aim to improve data accessibility and streamline scientific analysis.

Keywords:

Bioimaging Cloud Community Data FAIR Format

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Area of Science:

Bioimaging
Data Science
Scientific Computing

Background:

Bioimaging data faces scalability and heterogeneity challenges.
Existing file formats hinder efficient data management and analysis.
A community-driven effort is needed to develop a next-generation solution.

Purpose of the Study:

Introduce the OME-Zarr format, a cloud-optimized next-generation file format (NGFF) for bioimaging.
Describe tools and data resources that enhance FAIR data access.
Promote the unification of bioimaging file formats for improved data management and analysis.

Main Methods:

Community-driven design process for the OME-NGFF specification.
Development of the OME-Zarr format based on Zarr.
Integration of tools and resources for FAIR data principles.

Main Results:

OME-Zarr offers a scalable and heterogeneous solution for bioimaging data.
Available tools and resources facilitate FAIR data access.
The OME-NGFF specification provides a unified approach.

Conclusions:

OME-Zarr represents a significant advancement in bioimaging data handling.
The format and associated ecosystem lower barriers in the scientific process.
This initiative has the potential to standardize bioimaging file formats globally.