Cargando…

Providing open imaging data at scale: An EMBL-EBI perspective

Biological imaging is one of the primary tools by which we understand living systems across scales from atoms to organisms. Rapid advances in imaging technology have increased both the spatial and temporal resolutions at which we examine those systems, as well as enabling visualisation of larger tis...

Descripción completa

Detalles Bibliográficos
Autores principales: Hartley, Matthew, Iudin, Andrii, Padwardhan, Ardan, Sarkans, Ugis, Yoldaş, Aybüke Küpcü, Kleywegt, Gerard J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492673/
https://www.ncbi.nlm.nih.gov/pubmed/37537341
http://dx.doi.org/10.1007/s00418-023-02216-2
_version_ 1785104307940491264
author Hartley, Matthew
Iudin, Andrii
Padwardhan, Ardan
Sarkans, Ugis
Yoldaş, Aybüke Küpcü
Kleywegt, Gerard J.
author_facet Hartley, Matthew
Iudin, Andrii
Padwardhan, Ardan
Sarkans, Ugis
Yoldaş, Aybüke Küpcü
Kleywegt, Gerard J.
author_sort Hartley, Matthew
collection PubMed
description Biological imaging is one of the primary tools by which we understand living systems across scales from atoms to organisms. Rapid advances in imaging technology have increased both the spatial and temporal resolutions at which we examine those systems, as well as enabling visualisation of larger tissue volumes. These advances have huge potential but also generate ever increasing amounts of imaging data that must be stored and analysed. Public image repositories provide a critical scientific service through open data provision, supporting reproducibility of scientific results, access to reference imaging datasets and reuse of data for new scientific discovery and acceleration of image analysis methods development. The scale and scope of imaging data provides both challenges and opportunities for open sharing of image data. In this article, we provide a perspective influenced by decades of provision of open data resources for biological information, suggesting areas to focus on and a path towards global interoperability.
format Online
Article
Text
id pubmed-10492673
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Springer Berlin Heidelberg
record_format MEDLINE/PubMed
spelling pubmed-104926732023-09-11 Providing open imaging data at scale: An EMBL-EBI perspective Hartley, Matthew Iudin, Andrii Padwardhan, Ardan Sarkans, Ugis Yoldaş, Aybüke Küpcü Kleywegt, Gerard J. Histochem Cell Biol Original Paper Biological imaging is one of the primary tools by which we understand living systems across scales from atoms to organisms. Rapid advances in imaging technology have increased both the spatial and temporal resolutions at which we examine those systems, as well as enabling visualisation of larger tissue volumes. These advances have huge potential but also generate ever increasing amounts of imaging data that must be stored and analysed. Public image repositories provide a critical scientific service through open data provision, supporting reproducibility of scientific results, access to reference imaging datasets and reuse of data for new scientific discovery and acceleration of image analysis methods development. The scale and scope of imaging data provides both challenges and opportunities for open sharing of image data. In this article, we provide a perspective influenced by decades of provision of open data resources for biological information, suggesting areas to focus on and a path towards global interoperability. Springer Berlin Heidelberg 2023-08-03 2023 /pmc/articles/PMC10492673/ /pubmed/37537341 http://dx.doi.org/10.1007/s00418-023-02216-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Original Paper
Hartley, Matthew
Iudin, Andrii
Padwardhan, Ardan
Sarkans, Ugis
Yoldaş, Aybüke Küpcü
Kleywegt, Gerard J.
Providing open imaging data at scale: An EMBL-EBI perspective
title Providing open imaging data at scale: An EMBL-EBI perspective
title_full Providing open imaging data at scale: An EMBL-EBI perspective
title_fullStr Providing open imaging data at scale: An EMBL-EBI perspective
title_full_unstemmed Providing open imaging data at scale: An EMBL-EBI perspective
title_short Providing open imaging data at scale: An EMBL-EBI perspective
title_sort providing open imaging data at scale: an embl-ebi perspective
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492673/
https://www.ncbi.nlm.nih.gov/pubmed/37537341
http://dx.doi.org/10.1007/s00418-023-02216-2
work_keys_str_mv AT hartleymatthew providingopenimagingdataatscaleanemblebiperspective
AT iudinandrii providingopenimagingdataatscaleanemblebiperspective
AT padwardhanardan providingopenimagingdataatscaleanemblebiperspective
AT sarkansugis providingopenimagingdataatscaleanemblebiperspective
AT yoldasaybukekupcu providingopenimagingdataatscaleanemblebiperspective
AT kleywegtgerardj providingopenimagingdataatscaleanemblebiperspective