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‎_sources/authors/arina_rybina.md‎

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# Arina rybina (3)
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## Building a FAIR image data ecosystem for microscopy communities
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Isabel Kemmer, Antje Keppler, Beatriz Serrano-Solano, Arina Rybina, Bugra Özdemir, Johanna Bischof, Ayoub El Ghadraoui, John E. Eriksson, Aastha Mathur
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Published 2023-03-31
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Bioimaging has now entered the era of big data with faster than ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within those datasets has brought with it several difficulties in terms of common and harmonized data handling, analysis and management practices, which are currently hampering the full potential of image data being realized. Here we outline a wide range of efforts and solutions currently being developed by the microscopy community to address these challenges on the path towards FAIR bioimage data. We also highlight how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field. 
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Tags: Include In Dalia
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[https://zenodo.org/records/7788899](https://zenodo.org/records/7788899)
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[https://doi.org/10.5281/zenodo.7788899](https://doi.org/10.5281/zenodo.7788899)
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---
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## Life Science Competence Centres: Open by Design
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Romain David, Nektarios Liaskos, Arina Rybina, Christos Arvanitidis, Anne-Sophie Bage, Carvajal-Vallejos, Patricia K., Sudeep Das, De Pascalis, Francesca, Dorothea Dörr, Katrina Exter, Petr Holub, Gurwitz, Kim Tamara, Fabio Liberante, Philippe Lieutaud, Allyson Lister, Joaquin Lopez, Bénédicte Madon, Marzia Massimi, Rafaele Matteoni, Maria Mîrza, Sarah Morgan, Bugra Oezdemir, Maria Panagiotopoulou, Christina Pavloudi, P. Melo, Ana M., Susanna-Assunta Sansone, Harald Schwalbe, Beatriz Serrano-Solano, Sorzano, Carlos Oscar, Emilio Urbinati, Jing Tang, Jonathan Tedds, Gary Saunders, Jonathan Ewbank
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Published 2025-12
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Licensed CC-BY-4.0
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Preprint in submission process to Briefings in Bioinformatics
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Abstract:
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European Life Science Research Infrastructures (LS-RIs), one of the five major RI Science Clusters in Europe, were established to provide access to cutting-edge technologies to the scientific community. Individually, and collectively as the LS-RI cluster, they contribute to the development of the European Open Science Cloud (EOSC), under the aegis of the EOSC Federation. They are actively involved in the design and implementation of Competence Centres (CCs). These aim to increase the accessibility of domain-specific knowledge and tools, enhance interoperability, facilitate sharing and harmonisation of procedures, and promote Open Science and FAIR (Findable, Accessible, Interoperable, Reusable) practices. In this paper, we report a landscape mapping of the existing resources that formed the basis for the construction of CCs. We describe the possible design of CCs and their articulation with the LS-RIs. We focus on community-based ideas and recommendations to increase the potential of CCs to address long-standing challenges in sustainability, governance, scalability, and interoperability of Open Science within EOSC and the European Research Area (ERA) more generally.This paper provides a description of the nascent LS CCs, built following a survey of needs and services of existing LS-RI communities. When fully implemented, the LS CCs will serve as dynamic hubs to foster innovation, contribute to the EOSC’s future FAIR web of data, and support ongoing developments of the EOSC Federation. They will act as drivers of collaborative and impactful LS research in Europe and beyond. We explore the underlying challenges, and propose solutions, to ensure that the establishment of CCs will add value to the LS RI community, and to the EOSC, in a sustainable way.
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[https://zenodo.org/records/17672046](https://zenodo.org/records/17672046)
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[https://doi.org/10.5281/zenodo.17672046](https://doi.org/10.5281/zenodo.17672046)
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## Preprint: "Be Sustainable", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life's Lessons
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Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
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Published 2023-09-12
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Licensed CC-BY-4.0
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"Be SURE - Be SUstainable REcommendations"The main goals and challenges for the Life Science (LS) communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable LS resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European LS Research Infrastructures (RIs), it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable FAIR data management, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.IN PRESS EMBO Journal: https://www.embopress.org/journal/14602075 AVAILABLE SOON at : https://doi.org/10.15252/embj.2023115008 
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[https://zenodo.org/records/8338931](https://zenodo.org/records/8338931)
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[https://doi.org/10.5281/zenodo.8338931](https://doi.org/10.5281/zenodo.8338931)
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‎_sources/authors/beatriz_serrano-solano.md‎

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Romain David, Nektarios Liaskos, Arina Rybina, Christos Arvanitidis, Anne-Sophie Bage, Carvajal-Vallejos, Patricia K., Sudeep Das, De Pascalis, Francesca, Dorothea Dörr, Katrina Exter, Petr Holub, Gurwitz, Kim Tamara, Fabio Liberante, Philippe Lieutaud, Allyson Lister, Joaquin Lopez, Bénédicte Madon, Marzia Massimi, Rafaele Matteoni, Maria Mîrza, Sarah Morgan, Bugra Oezdemir, Maria Panagiotopoulou, Christina Pavloudi, P. Melo, Ana M., Susanna-Assunta Sansone, Harald Schwalbe, Beatriz Serrano-Solano, Sorzano, Carlos Oscar, Emilio Urbinati, Jing Tang, Jonathan Tedds, Gary Saunders, Jonathan Ewbank
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Preprint in submission process to GigaScience journal
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Preprint in submission process to Briefings in Bioinformatics
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European Life Science Research Infrastructures (LS-RIs), one of the five major RI Science Clusters in Europe, were established to provide access to cutting-edge technologies to the scientific community. Individually, and collectively as the LS-RI cluster, they contribute to the development of the European Open Science Cloud (EOSC), under the aegis of the EOSC Federation. They are actively involved in the design and implementation of Competence Centres (CCs). These aim to increase the accessibility of domain-specific knowledge and tools, enhance interoperability, facilitate sharing and harmonisation of procedures, and promote Open Science and FAIR (Findable, Accessible, Interoperable, Reusable) practices. In this paper, we report a landscape mapping of the existing resources that formed the basis for the construction of CCs. We describe the possible design of CCs and their articulation with the LS-RIs. We focus on community-based ideas and recommendations to increase the potential of CCs to address long-standing challenges in sustainability, governance, scalability, and interoperability of Open Science within EOSC and the European Research Area (ERA) more generally.This paper provides a description of the nascent LS CCs, built following a survey of needs and services of existing LS-RI communities. When fully implemented, the LS CCs will serve as dynamic hubs to foster innovation, contribute to the EOSC’s future FAIR web of data, and support ongoing developments of the EOSC Federation. They will act as drivers of collaborative and impactful LS research in Europe and beyond. We explore the underlying challenges, and propose solutions, to ensure that the establishment of CCs will add value to the LS RI community, and to the EOSC, in a sustainable way.
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[https://zenodo.org/records/15798751](https://zenodo.org/records/15798751)
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[https://zenodo.org/records/17672046](https://zenodo.org/records/17672046)
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[https://doi.org/10.5281/zenodo.15798751](https://doi.org/10.5281/zenodo.15798751)
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[https://doi.org/10.5281/zenodo.17672046](https://doi.org/10.5281/zenodo.17672046)
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## Preprint: "Be Sustainable", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life's Lessons
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Romain David, Arina Rybina, jean-marie burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
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Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
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‎_sources/authors/bugra_oezdemir.md‎

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# Bugra oezdemir (3)
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## Life Science Competence Centres: Open by Design
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Romain David, Nektarios Liaskos, Arina Rybina, Christos Arvanitidis, Anne-Sophie Bage, Carvajal-Vallejos, Patricia K., Sudeep Das, De Pascalis, Francesca, Dorothea Dörr, Katrina Exter, Petr Holub, Gurwitz, Kim Tamara, Fabio Liberante, Philippe Lieutaud, Allyson Lister, Joaquin Lopez, Bénédicte Madon, Marzia Massimi, Rafaele Matteoni, Maria Mîrza, Sarah Morgan, Bugra Oezdemir, Maria Panagiotopoulou, Christina Pavloudi, P. Melo, Ana M., Susanna-Assunta Sansone, Harald Schwalbe, Beatriz Serrano-Solano, Sorzano, Carlos Oscar, Emilio Urbinati, Jing Tang, Jonathan Tedds, Gary Saunders, Jonathan Ewbank
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Published 2025-12
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Licensed CC-BY-4.0
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Preprint in submission process to Briefings in Bioinformatics
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Abstract:
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European Life Science Research Infrastructures (LS-RIs), one of the five major RI Science Clusters in Europe, were established to provide access to cutting-edge technologies to the scientific community. Individually, and collectively as the LS-RI cluster, they contribute to the development of the European Open Science Cloud (EOSC), under the aegis of the EOSC Federation. They are actively involved in the design and implementation of Competence Centres (CCs). These aim to increase the accessibility of domain-specific knowledge and tools, enhance interoperability, facilitate sharing and harmonisation of procedures, and promote Open Science and FAIR (Findable, Accessible, Interoperable, Reusable) practices. In this paper, we report a landscape mapping of the existing resources that formed the basis for the construction of CCs. We describe the possible design of CCs and their articulation with the LS-RIs. We focus on community-based ideas and recommendations to increase the potential of CCs to address long-standing challenges in sustainability, governance, scalability, and interoperability of Open Science within EOSC and the European Research Area (ERA) more generally.This paper provides a description of the nascent LS CCs, built following a survey of needs and services of existing LS-RI communities. When fully implemented, the LS CCs will serve as dynamic hubs to foster innovation, contribute to the EOSC’s future FAIR web of data, and support ongoing developments of the EOSC Federation. They will act as drivers of collaborative and impactful LS research in Europe and beyond. We explore the underlying challenges, and propose solutions, to ensure that the establishment of CCs will add value to the LS RI community, and to the EOSC, in a sustainable way.
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[https://zenodo.org/records/17672046](https://zenodo.org/records/17672046)
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[https://doi.org/10.5281/zenodo.17672046](https://doi.org/10.5281/zenodo.17672046)
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---
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## Modular training resources for bioimage analysis
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Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Gonzalez Tirado, Sebastian, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
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Published 2025-01-21
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The newly developed image data formats course was taught for the first time: https://github.com/NEUBIAS/training-resources/blob/master/courses/2025_01_EMBL_image_data_formats.md
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Tags: Exclude From Dalia
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[https://zenodo.org/records/14710820](https://zenodo.org/records/14710820)
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[https://doi.org/10.5281/zenodo.14710820](https://doi.org/10.5281/zenodo.14710820)
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## OME-Zarr course
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Bugra Oezdemir, Christian Tischer
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Licensed UNKNOWN
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Content type: Tutorial
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[https://git.embl.de/oezdemir/course_scripts#ome-zarr-course](https://git.embl.de/oezdemir/course_scripts#ome-zarr-course)
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‎_sources/authors/chris_allan.md‎

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## OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies
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Josh Moore, Chris Allan, Sébastien Besson, jean-marie burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
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Josh Moore, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
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## The Open Microscopy Environment (OME) Data Model and XML file - open tools for informatics and quantitative analysis in biological imaging
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Ilya G. Goldberg, Chris Allan, jean-marie burel, Doug Creager, Andrea Falconi, et. al
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Ilya G. Goldberg, Chris Allan, Jean-Marie Burel, Doug Creager, Andrea Falconi, et. al
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‎_sources/authors/christian_tischer.md‎

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# Christian tischer (15)
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# Christian tischer (16)
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## A Hitchhiker's guide through the bio-image analysis software universe
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Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer
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[https://github.com/tischi/presentation-image-analysis](https://github.com/tischi/presentation-image-analysis)
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## Bioimage ANalysis Desktop Source Code
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Yi Sun, Christian Tischer, Jean-Karim Hériché
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Published 2025-11-21
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The BAND platform offers cloud based desktops accessible with a web browser so that you can work on your data from anywhere with an internet connection.
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This project is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659
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[https://zenodo.org/records/17671971](https://zenodo.org/records/17671971)
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[https://doi.org/10.5281/zenodo.17671971](https://doi.org/10.5281/zenodo.17671971)
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## CellProfiler Practical NeuBIAS Lisbon 2017
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Josh Moore, Chris Allan, Sébastien Besson, jean-marie burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
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Josh Moore, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
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‎_sources/authors/constantin_pape.md‎

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## OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies
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Josh Moore, Chris Allan, Sébastien Besson, jean-marie burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
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Josh Moore, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
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‎_sources/authors/cornelia_wetzker.md‎

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# Cornelia wetzker (9)
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# Cornelia wetzker (10)
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## A Glimpse of the Open-Source FLIM Analysis Software Tools FLIMfit, FLUTE and napari-flim-phasor-plotter
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Anca Margineanu, Chiara Stringari, Marcelo Zoccoler, Cornelia Wetzker
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## [SaxFDMTagung2025] Share your Bioimage Data with the World
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Cornelia Wetzker, Riccardo Massei, Michael Schlierf
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Published 2025-11-20
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This poster presents motivations and strategies to share bioimage data in life science research. It presents NFDI4BIOIMAGE as a consortium in research data management in bioimaging and bioimage analysis and its data stewardship team.
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The consortium NFDI4BIOIMAGE is funded by DFG grant number NFDI 46/1, project number 501864659.
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[https://zenodo.org/records/17659149](https://zenodo.org/records/17659149)
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[https://doi.org/10.5281/zenodo.17659149](https://doi.org/10.5281/zenodo.17659149)
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