Bia-binder: A web-native cloud compute service for the bioimage analysis community

Craig T. Russell; Jean Marie Burel; Awais Athar; Simon Li; Ugis Sarkans; Jason Swedlow; Alvis Brazma; Matthew Hartley; Virginie Uhlmann

doi:10.1093/bioinformatics/btaf412

Bia-binder: A web-native cloud compute service for the bioimage analysis community

Craig T. Russell, Jean Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Jason Swedlow, Alvis Brazma, Matthew Hartley (Lead / Corresponding author), Virginie Uhlmann (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

Abstract

We introduce BioImage Archive Binder (bia-binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter Notebook coding environments hosted on EMBL-EBI's Embassy Cloud, an academically hosted compute service which provides significant computational resources. The bia-binder architecture is free, open-source and publicly available for deployment. It features fast and direct access to images in the BioImage Archive, the Image Data Resource, and the BioStudies databases. We believe that this service can play a role in mitigating the current inequalities in access to scientific resources across academia. As bia-binder produces permanent links to compiled coding environments, we foresee the service to become widely used within the community and enable exploratory research. Availability and implementation bia-binder is built and deployed using helmsman and helm and released under the MIT licence. It can be accessed at binder.bioimagearchive.org and runs on any standard web browser.

Original language	English
Article number	btaf412
Journal	Bioinformatics
Volume	41
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btaf412
Publication status	Published - 22 Jul 2025

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btaf412Licence: CC BY

Final published version
© The Author(s) 2025. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 828 KBLicence: CC BY

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title = "Bia-binder: A web-native cloud compute service for the bioimage analysis community",

abstract = "We introduce BioImage Archive Binder (bia-binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter Notebook coding environments hosted on EMBL-EBI's Embassy Cloud, an academically hosted compute service which provides significant computational resources. The bia-binder architecture is free, open-source and publicly available for deployment. It features fast and direct access to images in the BioImage Archive, the Image Data Resource, and the BioStudies databases. We believe that this service can play a role in mitigating the current inequalities in access to scientific resources across academia. As bia-binder produces permanent links to compiled coding environments, we foresee the service to become widely used within the community and enable exploratory research. Availability and implementation bia-binder is built and deployed using helmsman and helm and released under the MIT licence. It can be accessed at binder.bioimagearchive.org and runs on any standard web browser.",

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AU - Sarkans, Ugis

AU - Swedlow, Jason

AU - Brazma, Alvis

AU - Hartley, Matthew

AU - Uhlmann, Virginie

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AB - We introduce BioImage Archive Binder (bia-binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter Notebook coding environments hosted on EMBL-EBI's Embassy Cloud, an academically hosted compute service which provides significant computational resources. The bia-binder architecture is free, open-source and publicly available for deployment. It features fast and direct access to images in the BioImage Archive, the Image Data Resource, and the BioStudies databases. We believe that this service can play a role in mitigating the current inequalities in access to scientific resources across academia. As bia-binder produces permanent links to compiled coding environments, we foresee the service to become widely used within the community and enable exploratory research. Availability and implementation bia-binder is built and deployed using helmsman and helm and released under the MIT licence. It can be accessed at binder.bioimagearchive.org and runs on any standard web browser.

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Bia-binder: A web-native cloud compute service for the bioimage analysis community

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ASJC Scopus subject areas

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