{{Short description|Consortium for microscopy image data}} {{Infobox organization | name = Open Microscopy Environment | abbreviation = OME | type = Research consortium | formation = {{start date and age|2005}}<!-- launched officially in 2005 --> | founder = Jason Swedlow, Ilya Goldberg, Peter K. Sorger | purpose = Open tools and standards for managing and sharing microscopy image data | fields = bioimage informatics; microscopy | products = OMERO; Bio-Formats; OME-TIFF; OME-Zarr | website = {{URL|https://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.
== 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.<ref name=":0">{{Cite journal |last1=Goldberg |first1=Ilya G. |last2=Allan |first2=Chris |last3=Burel |first3=Jean-Marie |last4=Creager |first4=Doug |last5=Falconi |first5=Andrea |last6=Hochheiser |first6=Harry |last7=Johnston |first7=Josiah |last8=Mellen |first8=Jeff |last9=Sorger |first9=Peter K. |last10=Swedlow |first10=Jason R. |date=2005-05-03 |title=The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging |journal=Genome Biology |language=en |volume=6 |issue=5 |pages=R47 |doi=10.1186/gb-2005-6-5-r47 |doi-access=free |issn=1474-760X |pmc=1175959 |pmid=15892875}}</ref><ref>{{Cite journal |last=Brooks |first=Michael |date=2023-10-05 |title=How open-source software could finally get the world's microscopes speaking the same language |url=https://www.nature.com/articles/d41586-023-03064-9 |journal=Nature |language=en |volume=622 |issue=7981 |pages=206–208 |doi=10.1038/d41586-023-03064-9 |bibcode=2023Natur.622..206B |issn=0028-0836|url-access=subscription }}</ref><ref>{{Cite journal |last1=Swedlow |first1=Jason R. |last2=Goldberg |first2=Ilya |last3=Brauner |first3=Erik |last4=Sorger |first4=Peter K. |date=2003-04-04 |title=Informatics and Quantitative Analysis in Biological Imaging |journal=Science |language=en |volume=300 |issue=5616 |pages=100–102 |doi=10.1126/science.1082602 |issn=0036-8075 |pmc=3522889 |pmid=12677061 |bibcode=2003Sci...300..100S }}</ref><ref>{{Cite book |last=Goldberg |first=I. |chapter=Open Microscopy Environment |date=2005 |title=2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) |publisher=IEEE |pages=380 |doi=10.1109/CSBW.2005.100 |isbn=978-0-7695-2442-9}}</ref>
The consortium published the OME-XML metadata model in 2005, which led to the file format OME-TIFF.<ref name=":0" /> In 2010, the Bio-Formats library was released, enabling conversion of proprietary file formats (such as Zeiss' .czi and Leica's .lif) to an open, interoperable format.<ref name=":1">{{Cite journal |date=2004-10-01 |title=Images to reveal all? |url=https://www.nature.com/articles/ncb1004-909 |journal=Nature Cell Biology |language=en |volume=6 |issue=10 |pages=909 |doi=10.1038/ncb1004-909 |pmid=15459713 |issn=1465-7392}}</ref><ref name=":2">{{Cite journal |last1=Linkert |first1=Melissa |last2=Rueden |first2=Curtis T. |last3=Allan |first3=Chris |last4=Burel |first4=Jean-Marie |last5=Moore |first5=Will |last6=Patterson |first6=Andrew |last7=Loranger |first7=Brian |last8=Moore |first8=Josh |last9=Neves |first9=Carlos |last10=MacDonald |first10=Donald |last11=Tarkowska |first11=Aleksandra |last12=Sticco |first12=Caitlin |last13=Hill |first13=Emma |last14=Rossner |first14=Mike |last15=Eliceiri |first15=Kevin W. |date=2010-05-31 |title=Metadata matters: access to image data in the real world |url=https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real |journal=Journal of Cell Biology |language=en |volume=189 |issue=5 |pages=777–782 |doi=10.1083/jcb.201004104 |issn=1540-8140 |pmc=2878938 |pmid=20513764}}</ref>
The OMERO.server software, for managing and sharing images, was built in 2006 using Bio-Formats to provide wide compatibility.<ref name=":3">{{Cite journal |last1=Allan |first1=Chris |last2=Burel |first2=Jean-Marie |last3=Moore |first3=Josh |last4=Blackburn |first4=Colin |last5=Linkert |first5=Melissa |last6=Loynton |first6=Scott |last7=MacDonald |first7=Donald |last8=Moore |first8=William J |last9=Neves |first9=Carlos |last10=Patterson |first10=Andrew |last11=Porter |first11=Michael |last12=Tarkowska |first12=Aleksandra |last13=Loranger |first13=Brian |last14=Avondo |first14=Jerome |last15=Lagerstedt |first15=Ingvar |date=March 2012 |title=OMERO: flexible, model-driven data management for experimental biology |journal=Nature Methods |language=en |volume=9 |issue=3 |pages=245–253 |doi=10.1038/nmeth.1896 |issn=1548-7091 |pmc=3437820 |pmid=22373911 |bibcode=2012NaMet...9..245A }}</ref> It has been continuously improved, with extensions for multi-dimensional files and high-content screening.<ref>{{Cite journal |last1=Burel |first1=Jean-Marie |last2=Besson |first2=Sébastien |last3=Blackburn |first3=Colin |last4=Carroll |first4=Mark |last5=Ferguson |first5=Richard K. |last6=Flynn |first6=Helen |last7=Gillen |first7=Kenneth |last8=Leigh |first8=Roger |last9=Li |first9=Simon |last10=Lindner |first10=Dominik |last11=Linkert |first11=Melissa |last12=Moore |first12=William J. |last13=Ramalingam |first13=Balaji |last14=Rozbicki |first14=Emil |last15=Tarkowska |first15=Aleksandra |date=October 2015 |title=Publishing and sharing multi-dimensional image data with OMERO |journal=Mammalian Genome |language=en |volume=26 |issue=9–10 |pages=441–447 |doi=10.1007/s00335-015-9587-6 |issn=0938-8990 |pmc=4602067 |pmid=26223880}}</ref><ref>{{Cite journal |last1=Li |first1=Simon |last2=Besson |first2=Sébastien |last3=Blackburn |first3=Colin |last4=Carroll |first4=Mark |last5=Ferguson |first5=Richard K. |last6=Flynn |first6=Helen |last7=Gillen |first7=Kenneth |last8=Leigh |first8=Roger |last9=Lindner |first9=Dominik |last10=Linkert |first10=Melissa |last11=Moore |first11=William J. |last12=Ramalingam |first12=Balaji |last13=Rozbicki |first13=Emil |last14=Rustici |first14=Gabriella |last15=Tarkowska |first15=Aleksandra |date=March 2016 |title=Metadata management for high content screening in OMERO |journal=Methods |language=en |volume=96 |pages=27–32 |doi=10.1016/j.ymeth.2015.10.006 |pmc=4773399 |pmid=26476368}}</ref> In 2017, OME launched The Image Data Resource, an open source database of bio-image files, built upon an OMERO server.<ref name=":4">{{Cite journal |last1=Williams |first1=Eleanor |last2=Moore |first2=Josh |last3=Li |first3=Simon W |last4=Rustici |first4=Gabriella |last5=Tarkowska |first5=Aleksandra |last6=Chessel |first6=Anatole |last7=Leo |first7=Simone |last8=Antal |first8=Bálint |last9=Ferguson |first9=Richard K |last10=Sarkans |first10=Ugis |last11=Brazma |first11=Alvis |last12=Carazo Salas |first12=Rafael E |last13=Swedlow |first13=Jason R |date=2017-08-01 |title=Image Data Resource: a bioimage data integration and publication platform |journal=Nature Methods |language=en |volume=14 |issue=8 |pages=775–781 |doi=10.1038/nmeth.4326 |issn=1548-7091 |pmc=5536224 |pmid=28775673}}</ref><ref>{{Cite journal |last1=Ellenberg |first1=Jan |last2=Swedlow |first2=Jason R. |last3=Barlow |first3=Mary |last4=Cook |first4=Charles E. |last5=Sarkans |first5=Ugis |last6=Patwardhan |first6=Ardan |last7=Brazma |first7=Alvis |last8=Birney |first8=Ewan |date=November 2018 |title=A call for public archives for biological image data |journal=Nature Methods |language=en |volume=15 |issue=11 |pages=849–854 |doi=10.1038/s41592-018-0195-8 |issn=1548-7091 |pmc=6884425 |pmid=30377375}}</ref>
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.<ref name=":5">{{Cite journal |last1=Moore |first1=Josh |last2=Allan |first2=Chris |last3=Besson |first3=Sébastien |last4=Burel |first4=Jean-Marie |last5=Diel |first5=Erin |last6=Gault |first6=David |last7=Kozlowski |first7=Kevin |last8=Lindner |first8=Dominik |last9=Linkert |first9=Melissa |last10=Manz |first10=Trevor |last11=Moore |first11=Will |last12=Pape |first12=Constantin |last13=Tischer |first13=Christian |last14=Swedlow |first14=Jason R. |date=December 2021 |title=OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies |journal=Nature Methods |language=en |volume=18 |issue=12 |pages=1496–1498 |doi=10.1038/s41592-021-01326-w |issn=1548-7091 |pmc=8648559 |pmid=34845388}}</ref><ref name=":6">{{Cite journal |last1=Moore |first1=Josh |last2=Basurto-Lozada |first2=Daniela |last3=Besson |first3=Sébastien |last4=Bogovic |first4=John |last5=Bragantini |first5=Jordão |last6=Brown |first6=Eva M. |last7=Burel |first7=Jean-Marie |last8=Casas Moreno |first8=Xavier |last9=de Medeiros |first9=Gustavo |last10=Diel |first10=Erin E. |last11=Gault |first11=David |last12=Ghosh |first12=Satrajit S. |last13=Gold |first13=Ilan |last14=Halchenko |first14=Yaroslav O. |last15=Hartley |first15=Matthew |date=2023-09-01 |title=OME-Zarr: a cloud-optimized bioimaging file format with international community support |url=https://doi.org/10.1007/s00418-023-02209-1 |journal=Histochemistry and Cell Biology |language=en |volume=160 |issue=3 |pages=223–251 |doi=10.1007/s00418-023-02209-1 |issn=1432-119X |pmc=10492740 |pmid=37428210}}</ref>
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.<ref name=":7">{{Cite web |title=The Open Microscopy Environment |url=https://www.openmicroscopy.org/2025/10/21/ome-transition.html |access-date=2025-11-17 |website=www.openmicroscopy.org |language=en}}</ref> 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).<ref name=":7" />
== OMERO == The OME consortium developed and maintains OMERO, a modular, open-source platform for managing microscopy data. It uses the Bio-Formats 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.<ref name=":1" /><ref name=":2" /><ref name=":3" />
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.<ref name=":3" />
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.<ref name=":3" /> This provides an advantage to downloading the files themselves, as microscopy data can get large, often exceeding multiple gigabytes per file.<ref name=":3" />
This modularity makes it possible for other, custom applications to interact with OMERO servers, including ''OMERO.importer'', to process images for loading in OMERO,<ref name=":3" /> ''OMERO.figure'' (to construct publication-ready figures)<ref>{{Citation |last1=Wheeler |first1=Ann |title=Presenting and Storing Data for Publication |date=2017 |work=Standard and Super-Resolution Bioimaging Data Analysis |pages=249–268 |url=https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119096948.ch10 |access-date=2025-11-17 |publisher=John Wiley & Sons, Ltd |language=en |doi=10.1002/9781119096948.ch10 |isbn=978-1-119-09694-8 |last2=Besson |first2=Sébastien|url-access=subscription }}</ref> and the "pythonic" interface ''ezomero''.<ref name="Easing OMERO adoption with ezomero">{{cite bioRxiv |last1=Ratamero |first1=Erick Martins |title=Easing OMERO adoption with ezomero |date=2023-07-01 |language=en |biorxiv=10.1101/2023.06.29.546930 |last2=Govek |first2=Kiya |last3=Langerak |first3=Julio Mateos |last4=Sanchez |first4=Fernando Cervantes |last5=Mellert |first5=David J.}}</ref>
=== Use cases === OMERO servers have been used in several scenarios related to research data management for microscopy.<ref>{{Cite journal |last1=Schmidt |first1=Christian |last2=Boissonnet |first2=Tom |last3=Dohle |first3=Julia |last4=Bernhardt |first4=Karen |last5=Ferrando-May |first5=Elisa |last6=Wernet |first6=Tobias |last7=Nitschke |first7=Roland |last8=Kunis |first8=Susanne |last9=Weidtkamp-Peters |first9=Stefanie |date=2024 |title=A practical guide to bioimaging research data management in core facilities |journal=Journal of Microscopy |language=en |volume=294 |issue=3 |pages=350–371 |doi=10.1111/jmi.13317 |issn=1365-2818|doi-access=free |pmid=38752662 }}</ref> Use cases include high-content screening workflows,<ref>{{Cite journal |last1=Massei |first1=Riccardo |last2=Busch |first2=Wibke |last3=Serrano-Solano |first3=Beatriz |last4=Bernt |first4=Matthias |last5=Scholz |first5=Stefan |last6=Nicolay |first6=Elena K. |last7=Bohring |first7=Hannes |last8=Bumberger |first8=Jan |date=2025-05-09 |title=High-content screening (HCS) workflows for FAIR image data management with OMERO |journal=Scientific Reports |language=en |volume=15 |issue=1 |article-number=16236 |doi=10.1038/s41598-025-00720-0 |issn=2045-2322 |pmc=12064781 |pmid=40346117 |bibcode=2025NatSR..1516236M }}</ref> the sharing of digitized biological collections<ref name=":8">{{Cite journal |last1=Jaramillo |first1=Carlos |last2=Punyasena |first2=Surangi W. |last3=de Alba |first3=Daurys |last4=Alveo |first4=Roxana |last5=Arcila |first5=Angelica |last6=Bermudez |first6=Jorge |last7=Bustos |first7=Jonatan |last8=Caballero-Rodriguez |first8=Dayenari |last9=Cardenas |first9=Karen |last10=Caro |first10=David |last11=Carvajal |first11=Francy |last12=Castañeda |first12=Ivonne Marcela |last13=Chaves |first13=Shara |last14=D'Apolito |first14=Carlos |last15=Diaz-Jaramillo |first15=Andres |title=Digitizing collections to unlock the full potential of palynology: A case study with the Smithsonian palynology collection |date=2025 |article-number=ppp3.70073 |journal=Plants, People, Planet |language=en |volume=n/a |issue=n/a |doi=10.1002/ppp3.70073 |issn=2572-2611|doi-access=free }}</ref> and educational use for shared virtual microscopes.<ref name=":9">{{Cite journal |last1=Siviero |first1=Fábio |last2=Oliveira |first2=Sérgio Ferreira de |date=2016-07-18 |title=Modernização do Ensino de Biologia Tecidual |url=https://revistas.usp.br/gradmais/article/view/117723 |journal=Revista de Graduação USP |language=pt |volume=1 |issue=1 |pages=35–40 |doi=10.11606/issn.2525-376X.v1i1p35-40 |issn=2525-376X}}</ref>
The Image Data Repository, an open source database of bio-image files, is built upon directly on an OMERO server.<ref name=":4" />
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,<ref name=":9" /><ref name=":8" /><ref name="Easing OMERO adoption with ezomero"/> the University of Dundee, the Francis Crick Institute, the Technische Universität Dresden, the universities of Tübingen and Münster, and the Karolinska Institute in Europe,<ref name=":4" /><ref>{{Cite web |date=2025-09-10 |title=News |url=https://www.crick.ac.uk/research/platforms-and-facilities/light-microscopy/news |access-date=2025-11-17 |website=Crick |language=en}}</ref><ref>{{Cite journal |last1=Jannasch |first1=Anett |last2=Tulok |first2=Silke |last3=Okafornta |first3=Chukwuebuka William |last4=Kugel |first4=Thomas |last5=Bortolomeazzi |first5=Michele |last6=Boissonnet |first6=Tom |last7=Schmidt |first7=Christian |last8=Vogelsang |first8=Andy |last9=Dittfeld |first9=Claudia |last10=Tugtekin |first10=Sems-Malte |last11=Matschke |first11=Klaus |last12=Paliulis |first12=Leocadia |last13=Thomas |first13=Carola |last14=Lindemann |first14=Dirk |last15=Fabig |first15=Gunar |date=2025 |title=Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users |journal=Journal of Microscopy |language=en |volume=297 |issue=1 |pages=105–119 |doi=10.1111/jmi.13360 |issn=1365-2818 |pmc=11629930 |pmid=39275979}}</ref><ref>{{Cite journal |last1=Wanner |first1=Julian |last2=Cuellar |first2=Luis Kuhn |last3=Rausch |first3=Luiselotte |last4=Berendzen |first4=Kenneth W. |last5=Wanke |first5=Friederike |last6=Gabernet |first6=Gisela |last7=Harter |first7=Klaus |last8=Nahnsen |first8=Sven |date=January 2024 |title=Nf-Root: A Best-Practice Pipeline for Deep-Learning-Based Analysis of Apoplastic pH in Microscopy Images of Developmental Zones in Plant Root Tissue |journal=Quantitative Plant Biology |language=en |volume=5 |article-number=e12 |doi=10.1017/qpb.2024.11 |issn=2632-8828 |pmc=11706687 |pmid=39777028}}</ref><ref>{{Cite web |title=OMERO for microscopy research data management - 2022 - Wiley Analytical Science |url=https://analyticalscience.wiley.com/content/article-do/omero-microscopy-research-data-management |access-date=2025-11-17 |website=Analytical Science Article DO Series |language=en}}</ref><ref>{{Cite web |title=Data storage {{!}} Karolinska Institutet |url=https://ki.se/en/research/research-infrastructure-and-environments/core-facilities-for-research/live-cell-imaging-core-facility-lci/data-storage-0 |access-date=2025-11-17 |website=ki.se |language=en}}</ref> and RIKEN<ref>{{Cite web |date=2024-09-13 |title=Workshop: OMERO Setup and Configuration for Imaging Facility Managers |url=https://bioimaging.riken.jp/workshop/20241104/ |access-date=2025-11-17 |website=Riken Bioimaging |language=en}}</ref> 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.<ref>{{Cite journal |last1=Hohlbein |first1=Johannes |last2=Diederich |first2=Benedict |last3=Marsikova |first3=Barbora |last4=Reynaud |first4=Emmanuel G. |last5=Holden |first5=Séamus |last6=Jahr |first6=Wiebke |last7=Haase |first7=Robert |last8=Prakash |first8=Kirti |date=September 2022 |title=Open microscopy in the life sciences: quo vadis? |journal=Nature Methods |language=en |volume=19 |issue=9 |pages=1020–1025 |doi=10.1038/s41592-022-01602-3 |issn=1548-7091|doi-access=free |pmid=36008630 }}</ref> The metadata in the file formats adheres to a common model, termed the OME-Model, originally expressed in XML.<ref name=":0" /><ref>{{Cite journal |date=2006-10-26 |title=Tower of Babel |url=https://www.nature.com/articles/4431021a |journal=Nature |language=en |volume=443 |issue=7114 |pages=1021 |doi=10.1038/4431021a |issn=0028-0836}}</ref>
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.<ref name=":0" />
=== 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.<ref>{{cite web |title=The OME-TIFF format — OME Data Model and File Formats 5.6.3 documentation |url=https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/}}</ref> 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.<ref>{{cite web |title=OME-TIFF specification — OME Data Model and File Formats 5.6.3 documentation |url=https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/specification.html}}</ref> Key features include:
* Pyramidal multi-resolution support: OME-TIFF uses TIFF’s SubIFD mechanism (Tag 330) to represent image pyramids, supporting rapid image navigation. Each level may use its own compression (JPEG, JPEG 2000, etc.), and BigTIFF extensions are supported for large file sizes. * Multi-dimensionality: Supports Z-stacks, time series, multichannel imaging, and 3D/4D data organization. * OME ecosystem: The Bio-Formats Java library and OMERO server provide read/write and management capabilities for OME-TIFF images, with desktop analysis supported by QuPath, Fiji/ImageJ, and others617. * Validation and archiving: The format is openly specified, making it suitable for long-term research data stewardship, regulatory submission, and reproducible AI workflows.
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.<ref>{{cite bioRxiv |title=OME Files - an open source reference library for the OME-XML metadata model and the OME-TIFF file format |last1=Leigh |first1=Roger |last2=Gault |first2=David |last3=Linkert |first3=Melissa |last4=Burel |first4=Jean-Marie |last5=Moore |first5=Josh |last6=Besson |first6=Sébastien |last7=Swedlow |first7=Jason R. |date=2017 |biorxiv=10.1101/088740 }}</ref>
=== OME-Zarr === [[File:OME-Zarr_format_for_High_Content_Screening_(HCS).webp|thumb|298x298px|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.<ref name="zarr-specs">{{cite web |title=Zarr - chunked, compressed, N-dimensional arrays |url=https://zarr.dev/ |access-date=2024-09-12 |website=zarr.dev}}</ref><ref name="cloudnativegeo">{{cite web |title=Cloud-Optimized Geospatial Formats Guide: Zarr |url=https://guide.cloudnativegeo.org/zarr/intro.html |access-date=2024-09-12 |website=guide.cloudnativegeo.org}}</ref> The OME-Zarr formad is based on Zarr with extensions to enable, for example, encoding of multidimensional image pyramids.<ref name=":5" /><ref name=":6" />
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.<ref name=":6" />
== References == {{Reflist}}
Category:Free and open-source software organizations Category:Microscopy organizations