Open Microscopy Environment

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Open Microscopy Environment
AbbreviationOME
Formation2005;20 years ago (2005)
Founder Jason Swedlow, Ilya Goldberg, Peter K. Sorger
TypeResearch consortium
PurposeOpen tools and standards for managing and sharing microscopy image data
ProductsOMERO; Bio-Formats; OME-TIFF; OME-Zarr
Fields bioimage informatics; microscopy
Website www.openmicroscopy.org

The Open Microscopy Environment, or OME, is a consortium that develops open-source infrastructure for microscopy. OME is known for maintaining the OMERO server system for managing microscopy files, the Bio-Formats library for converting proprietary file formats to interoperable alternatives as well as the image standards OME-TIFF and OME-Zarr.

Contents

History

The project started around 2001 by Jason Swedlow, Ilya Goldberg and Peter Sorger, had its original vision published in Science in 2003, and launched officially in 2005. [1] [2] [3] [4]

The consortium published the OME-XML metadata model in 2005, which led to the file format OME-TIFF. [1] In 2010, the BioFormats library was released, enabling conversion of proprietary file formats (such as Zeiss' .czi and Leica's .lif) to an open, interoperable format. [5] [6]

The OMERO.server software, for managing and sharing images, was built in 2012, using BioFormats to provide wide compatibility. [7] It has been continuously improved, with extensions for multi-dimensional files and high-content screening. [8] [9] In 2017, OME launched The Image Data Repository, an open source database of bio-image files, built upon an OMERO server. [10] [11]

In 2021, the consortium published the efforts for new file formats compatible with cloud computing. The OME-NGFF (Next-Generation File Formats) community agreed upon using Zarr, subsequently starting a process to develop the OME-Zarr standard. [12] [13]

Jason Swedlow led the project with a team at the University of Dundee, jointly with the company Glencoe Software, until 2025, when he joined the Chan Zuckerberg Initiative. [14] The consortium migrated to a leadership team composed of Jean-Marie Burel (University of Dundee), Josh Moore (German BioImaging), Stefanie Weidtkamp-Peters (HHU), Matthew Hartley (EMBL-EBI), and Virginie Uhlmann (University of Zurich). [14]

OMERO

The OME consortium developed and maintains OMERO, a modular, open-source platform for managing microscopy data. It uses the BioFormats library to translate over 100 proprietary file formats used in microscopy (such as Zeiss' .czi and Leica's .lif) to an open, interoperable format, the OME Model, using OME-XML. [5] [6] [7]

The platform includes multiple components, including a Java back-end application (named OMERO.server) which orchestrates communication with databases hosting the metadata (e.g. in PostgreSQL) and the servers hosting the pixel data for images. [7]

Users are able to interact with the database via clients, which interact with OMERO.server via a common API. For example, the application named OMERO.web, is a Django-based web application that communicates with the OMERO database, enabling users to explore microscopy collections in a browser. [7] This provides an advantage to downloading the files themselves, as microscopy data can get large, often exceeding multiple gigabytes per file. [7]

This modularity makes it possible for other, custom applications to interact with OMERO servers, including OMERO.importer, to process images for loading in OMERO, [7] OMERO.figure (to construct publication-ready figures) [15] and the "pythonic" interface ezomero. [16]

Use cases

OMERO servers have been used in several scenarios related to research data management for microscopy. [17] Use cases include high-content screening workflows, [18] the sharing of digitized biological collections [19] and educational use for shared virtual microscopes. [20]

The Image Data Repository, an open source database of bio-image files, is built upon directly on an OMERO server. [10]

Multiple institutions around the world host OMERO servers. The list spans multiple continents, including organizations like the University of São Paulo, the Smithsonian Tropical Research Institute and the Jackson Laboratory in the Americas, [20] [19] [16] the University of Dundee, the Francis Crick Institute, the Technische Universität Dresden, the universities of Tübingen and Münster, and the Karolinska Institute in Europe, [10] [21] [22] [23] [24] [25] and RIKEN [26] in Japan.

File formats

The Open Microscopy Environment has developed standards to ensure long-term data compatibility of microscopy data using platform-independent file formats. [27] The metadata in the file formats adheres to a common model, termed the OME-Model, originally expressed in XML. [1] [28]

OME-XML is a schema-centered metadata language representing imaging provenance (e.g., microscope, lens, detector), acquisition modality, coordinate mapping, and experiment details. Attributes such as channel wavelengths, Z index, timepoint, and objective are standardized for interoperability. [1]

OME-TIFF

OME-TIFF is an open, extensible format developed by the Open Microscopy Environment (OME) consortium to address both the data and metadata needs of modern bioimaging. [29] It extends the classic TIFF structure-with its widespread library and tool support-by embedding structured OME-XML metadata within TIFF tags, particularly within the ImageDescription field of the first Image File Directory (IFD). The file specification is made available by the OME consortium. [30] Key features include:

OME-TIFF is adopted in research and academic pathology where comprehensive metadata and analysis pipeline integration are prioritized. The Bio-Formats Java library and OMERO server provide read/write and management capabilities, with desktop analysis supported by QuPath and Fiji/ImageJ. [31]

OME-Zarr

Representation of microscopy data for high-content screening using OME-Zarr. OME-Zarr format for High Content Screening (HCS).webp
Representation of microscopy data for high-content screening using OME-Zarr.

Zarr is an open standard for storing large multidimensional array data. It specifies a protocol and data format, and is designed to be "cloud ready" including random access, by dividing data into subsets referred to as chunks. [32] [33] The OME-Zarr formad is based on Zarr with extensions to enable, for example, encoding of multidimensional image pyramids. [12] [13]

The .zarr specification enables granular representation of outputs of complex experiments, such as high content screening assays. Each plate read in the microscope contains multiple wells, and to scan each well, multiple fields are needed. Each image may have up to 5 dimensions (time points, imaging channels and the three space dimensions). It may also include resolution pyramids, enabling better performance of visualization tools. As Zarr uses multiple directories for organizing data, each of these different fields can be specified and retrieved independently, for example by retrieving a custom URL from object storage databases. [13]

References

  1. 1 2 3 4 Goldberg, Ilya G.; Allan, Chris; Burel, Jean-Marie; Creager, Doug; Falconi, Andrea; Hochheiser, Harry; Johnston, Josiah; Mellen, Jeff; Sorger, Peter K.; Swedlow, Jason R. (2005-05-03). "The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging". Genome Biology. 6 (5): R47. doi: 10.1186/gb-2005-6-5-r47 . ISSN   1474-760X. PMC   1175959 . PMID   15892875.
  2. ↑ Brooks, Michael (2023-10-05). "How open-source software could finally get the world's microscopes speaking the same language" . Nature. 622 (7981): 206–208. Bibcode:2023Natur.622..206B. doi:10.1038/d41586-023-03064-9. ISSN   0028-0836.
  3. ↑ Swedlow, Jason R.; Goldberg, Ilya; Brauner, Erik; Sorger, Peter K. (2003-04-04). "Informatics and Quantitative Analysis in Biological Imaging". Science. 300 (5616): 100–102. Bibcode:2003Sci...300..100S. doi:10.1126/science.1082602. ISSN   0036-8075. PMC   3522889 . PMID   12677061.
  4. ↑ Goldberg, I. (2005). "Open Microscopy Environment". 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05). IEEE. p. 380. doi:10.1109/CSBW.2005.100. ISBN   978-0-7695-2442-9.
  5. 1 2 "Images to reveal all?". Nature Cell Biology. 6 (10): 909. 2004-10-01. doi:10.1038/ncb1004-909. ISSN   1465-7392. PMID   15459713.
  6. 1 2 Linkert, Melissa; Rueden, Curtis T.; Allan, Chris; Burel, Jean-Marie; Moore, Will; Patterson, Andrew; Loranger, Brian; Moore, Josh; Neves, Carlos; MacDonald, Donald; Tarkowska, Aleksandra; Sticco, Caitlin; Hill, Emma; Rossner, Mike; Eliceiri, Kevin W. (2010-05-31). "Metadata matters: access to image data in the real world". Journal of Cell Biology. 189 (5): 777–782. doi:10.1083/jcb.201004104. ISSN   1540-8140. PMC   2878938 . PMID   20513764.
  7. 1 2 3 4 5 6 Allan, Chris; Burel, Jean-Marie; Moore, Josh; Blackburn, Colin; Linkert, Melissa; Loynton, Scott; MacDonald, Donald; Moore, William J; Neves, Carlos; Patterson, Andrew; Porter, Michael; Tarkowska, Aleksandra; Loranger, Brian; Avondo, Jerome; Lagerstedt, Ingvar (March 2012). "OMERO: flexible, model-driven data management for experimental biology". Nature Methods. 9 (3): 245–253. doi:10.1038/nmeth.1896. ISSN   1548-7091. PMC   3437820 . PMID   22373911.
  8. ↑ Burel, Jean-Marie; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Tarkowska, Aleksandra (October 2015). "Publishing and sharing multi-dimensional image data with OMERO". Mammalian Genome. 26 (9–10): 441–447. doi:10.1007/s00335-015-9587-6. ISSN   0938-8990. PMC   4602067 . PMID   26223880.
  9. ↑ Li, Simon; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Lindner, Dominik; Linkert, Melissa; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra (March 2016). "Metadata management for high content screening in OMERO". Methods. 96: 27–32. doi:10.1016/j.ymeth.2015.10.006. PMC   4773399 . PMID   26476368.
  10. 1 2 3 Williams, Eleanor; Moore, Josh; Li, Simon W; Rustici, Gabriella; Tarkowska, Aleksandra; Chessel, Anatole; Leo, Simone; Antal, Bálint; Ferguson, Richard K; Sarkans, Ugis; Brazma, Alvis; Carazo Salas, Rafael E; Swedlow, Jason R (2017-08-01). "Image Data Resource: a bioimage data integration and publication platform". Nature Methods. 14 (8): 775–781. doi:10.1038/nmeth.4326. ISSN   1548-7091. PMC   5536224 . PMID   28775673.
  11. ↑ Ellenberg, Jan; Swedlow, Jason R.; Barlow, Mary; Cook, Charles E.; Sarkans, Ugis; Patwardhan, Ardan; Brazma, Alvis; Birney, Ewan (November 2018). "A call for public archives for biological image data". Nature Methods. 15 (11): 849–854. doi:10.1038/s41592-018-0195-8. ISSN   1548-7091. PMC   6884425 . PMID   30377375.
  12. 1 2 Moore, Josh; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Diel, Erin; Gault, David; Kozlowski, Kevin; Lindner, Dominik; Linkert, Melissa; Manz, Trevor; Moore, Will; Pape, Constantin; Tischer, Christian; Swedlow, Jason R. (December 2021). "OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies". Nature Methods. 18 (12): 1496–1498. doi:10.1038/s41592-021-01326-w. ISSN   1548-7091. PMC   8648559 . PMID   34845388.
  13. 1 2 3 Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M.; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E.; Gault, David; Ghosh, Satrajit S.; Gold, Ilan; Halchenko, Yaroslav O.; Hartley, Matthew (2023-09-01). "OME-Zarr: a cloud-optimized bioimaging file format with international community support". Histochemistry and Cell Biology. 160 (3): 223–251. doi:10.1007/s00418-023-02209-1. ISSN   1432-119X. PMC   10492740 . PMID   37428210.
  14. 1 2 "The Open Microscopy Environment". www.openmicroscopy.org. Retrieved 2025-11-17.
  15. ↑ Wheeler, Ann; Besson, Sébastien (2017), "Presenting and Storing Data for Publication" , Standard and Super-Resolution Bioimaging Data Analysis, John Wiley & Sons, Ltd, pp. 249–268, doi:10.1002/9781119096948.ch10, ISBN   978-1-119-09694-8 , retrieved 2025-11-17
  16. 1 2 Ratamero, Erick Martins; Govek, Kiya; Langerak, Julio Mateos; Sanchez, Fernando Cervantes; Mellert, David J. (2023-07-01), Easing OMERO adoption with ezomero, doi:10.1101/2023.06.29.546930 , retrieved 2025-11-17
  17. ↑ Schmidt, Christian; Boissonnet, Tom; Dohle, Julia; Bernhardt, Karen; Ferrando-May, Elisa; Wernet, Tobias; Nitschke, Roland; Kunis, Susanne; Weidtkamp-Peters, Stefanie (2024). "A practical guide to bioimaging research data management in core facilities". Journal of Microscopy. 294 (3): 350–371. doi: 10.1111/jmi.13317 . ISSN   1365-2818.
  18. ↑ Massei, Riccardo; Busch, Wibke; Serrano-Solano, Beatriz; Bernt, Matthias; Scholz, Stefan; Nicolay, Elena K.; Bohring, Hannes; Bumberger, Jan (2025-05-09). "High-content screening (HCS) workflows for FAIR image data management with OMERO". Scientific Reports. 15 (1) 16236. Bibcode:2025NatSR..1516236M. doi:10.1038/s41598-025-00720-0. ISSN   2045-2322. PMC   12064781 . PMID   40346117.
  19. 1 2 Jaramillo, Carlos; Punyasena, Surangi W.; de Alba, Daurys; Alveo, Roxana; Arcila, Angelica; Bermudez, Jorge; Bustos, Jonatan; Caballero-Rodriguez, Dayenari; Cardenas, Karen; Caro, David; Carvajal, Francy; Castañeda, Ivonne Marcela; Chaves, Shara; D'Apolito, Carlos; Diaz-Jaramillo, Andres (2025). "Digitizing collections to unlock the full potential of palynology: A case study with the Smithsonian palynology collection". Plants, People, Planet. n/a (n/a) ppp3.70073. doi: 10.1002/ppp3.70073 . ISSN   2572-2611.
  20. 1 2 Siviero, Fábio; Oliveira, Sérgio Ferreira de (2016-07-18). "Modernização do Ensino de Biologia Tecidual". Revista de Graduação USP (in Portuguese). 1 (1): 35–40. doi:10.11606/issn.2525-376X.v1i1p35-40. ISSN   2525-376X.
  21. ↑ "News". Crick. 2025-09-10. Retrieved 2025-11-17.
  22. ↑ Jannasch, Anett; Tulok, Silke; Okafornta, Chukwuebuka William; Kugel, Thomas; Bortolomeazzi, Michele; Boissonnet, Tom; Schmidt, Christian; Vogelsang, Andy; Dittfeld, Claudia; Tugtekin, Sems-Malte; Matschke, Klaus; Paliulis, Leocadia; Thomas, Carola; Lindemann, Dirk; Fabig, Gunar (2025). "Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users". Journal of Microscopy. 297 (1): 105–119. doi:10.1111/jmi.13360. ISSN   1365-2818. PMC   11629930 . PMID   39275979.
  23. ↑ Wanner, Julian; Cuellar, Luis Kuhn; Rausch, Luiselotte; Berendzen, Kenneth W.; Wanke, Friederike; Gabernet, Gisela; Harter, Klaus; Nahnsen, Sven (January 2024). "Nf-Root: A Best-Practice Pipeline for Deep-Learning-Based Analysis of Apoplastic pH in Microscopy Images of Developmental Zones in Plant Root Tissue". Quantitative Plant Biology. 5 e12. doi:10.1017/qpb.2024.11. ISSN   2632-8828. PMC   11706687 . PMID   39777028.
  24. ↑ "OMERO for microscopy research data management - 2022 - Wiley Analytical Science". Analytical Science Article DO Series. Retrieved 2025-11-17.
  25. ↑ "Data storage | Karolinska Institutet". ki.se. Retrieved 2025-11-17.
  26. ↑ "Workshop: OMERO Setup and Configuration for Imaging Facility Managers". Riken Bioimaging. 2024-09-13. Retrieved 2025-11-17.
  27. ↑ Hohlbein, Johannes; Diederich, Benedict; Marsikova, Barbora; Reynaud, Emmanuel G.; Holden, Séamus; Jahr, Wiebke; Haase, Robert; Prakash, Kirti (September 2022). "Open microscopy in the life sciences: quo vadis?". Nature Methods. 19 (9): 1020–1025. doi: 10.1038/s41592-022-01602-3 . ISSN   1548-7091.
  28. ↑ "Tower of Babel". Nature. 443 (7114): 1021. 2006-10-26. doi:10.1038/4431021a. ISSN   0028-0836.
  29. ↑ "The OME-TIFF format — OME Data Model and File Formats 5.6.3 documentation".
  30. ↑ "OME-TIFF specification — OME Data Model and File Formats 5.6.3 documentation".
  31. ↑ Leigh, Roger; Gault, David; Linkert, Melissa; Burel, Jean-Marie; Moore, Josh; Besson, Sébastien; Swedlow, Jason R. (2017). OME Files - an open source reference library for the OME-XML metadata model and the OME-TIFF file format (Preprint). doi:10.1101/088740.
  32. ↑ "Zarr - chunked, compressed, N-dimensional arrays". zarr.dev. Retrieved 2024-09-12.
  33. ↑ "Cloud-Optimized Geospatial Formats Guide: Zarr". guide.cloudnativegeo.org. Retrieved 2024-09-12.
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