{"entity": "researcher", "timestamp": "2026-08-14T12:24:39.869Z", "family": "Paul-Gilloteaux", "given": "Perrine", "initials": "P", "orcid": "0000-0002-4822-165X", "affiliations": ["Universit\u00e9 de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, F-44000, France.", "Universit\u00e9 de Nantes, CHU Nantes, Inserm, CNRS, SFR Sant\u00e9, Inserm UMS 016, CNRS UMS 3556, Nantes, F-44000, France."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a"}}, "publications": [{"entity": "publication", "iuid": "bb241ed48fe94700bafa1c93cc2bba33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb241ed48fe94700bafa1c93cc2bba33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb241ed48fe94700bafa1c93cc2bba33"}}, "title": "The crucial role of bioimage analysts in scientific research and publication.", "authors": [{"family": "Cimini", "given": "Beth A", "initials": "BA", "orcid": "0000-0001-9640-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/db23220ace18412a872eeedc98b6ca3d.json"}}, {"family": "Bankhead", "given": "Peter", "initials": "P", "orcid": "0000-0003-4851-8813", "researcher": {"href": "https://publications.scilifelab.se/researcher/677800a098f9480aad3629a35a6d7145.json"}}, {"family": "D'Antuono", "given": "Rocco", "initials": "R", "orcid": "0000-0003-0180-6500", "researcher": {"href": "https://publications.scilifelab.se/researcher/19a219cdf18a48c581c66844eed7f888.json"}}, {"family": "Fazeli", "given": "Elnaz", "initials": "E", "orcid": "0000-0002-0770-0777", "researcher": {"href": "https://publications.scilifelab.se/researcher/18bdf85441724603af3433b9ca2671a7.json"}}, {"family": "Fernandez-Rodriguez", "given": "Julia", "initials": "J", "orcid": "0000-0003-4522-0966", "researcher": {"href": 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"0000-0002-1352-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/b504b532ff944ab9ab72329adc6282fd.json"}}, {"family": "Uhlmann", "given": "Virginie", "initials": "V", "orcid": "0000-0002-2859-9241", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4215607e1ed4f18b2809de6c5e34df6.json"}}, {"family": "Umney", "given": "Oliver", "initials": "O", "orcid": "0009-0005-2321-9413", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ed29415dcf34d69b863d06e8edaa256.json"}}, {"family": "Wiggins", "given": "Laura", "initials": "L", "orcid": "0000-0003-4615-2379", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbdc5616fe8542638669cbd647c46bb9.json"}}, {"family": "Eliceiri", "given": "Kevin W", "initials": "KW", "orcid": "0000-0001-8678-670X", "researcher": {"href": "https://publications.scilifelab.se/researcher/acb896fcca6a49b096068c3b5294624d.json"}}], "type": "journal article", "published": "2024-10-15", "journal": {"title": "J. Cell. Sci.", "issn": "1477-9137", "volume": "137", "issue": "20", "issn-l": "0021-9533"}, "abstract": "Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality and efficiency and can significantly advance scientific discovery. However, a lack of training resources, limited career paths and insufficient recognition of the contributions made by bioimage analysts prevent the full realization of this potential. This Perspective - the result of the recent The Company of Biologists Workshop 'Effectively Communicating Bioimage Analysis', which aimed to summarize the global BIA landscape, categorize obstacles and offer possible solutions - proposes strategies to bring about a cultural shift towards recognizing the value of BIA by standardizing tools, improving training and encouraging formal credit for contributions. We also advocate for increased funding, standardized practices and enhanced collaboration, and we conclude with a call to action for all stakeholders to join efforts in advancing BIA.", "doi": "10.1242/jcs.262322", "pmid": "39475207", "labels": {"BioImage Informatics": "Collaborative", "Integrated Microscopy Technologies Gothenburg": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "362545"}], "notes": [], "created": "2024-11-13T10:08:24.614Z", "modified": "2024-11-15T12:02:35.328Z"}, {"entity": "publication", "iuid": "123c7ce0304c4077b97f1dac22148d57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/123c7ce0304c4077b97f1dac22148d57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/123c7ce0304c4077b97f1dac22148d57"}}, "title": "Correlated multimodal imaging in life sciences: lessons learnt", "authors": [{"family": "Rudraiah", "given": "Pavitra Sokke", "initials": "PS"}, {"family": "Camacho", "given": "Rafael", "initials": "R", "orcid": "0000-0003-2325-6407", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a7a8cfe28634821984b078ce3246343.json"}}, {"family": "Fernandez-Rodriguez", "given": "Julia", "initials": "J", "orcid": "0000-0003-4522-0966", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bd9c743e99d479cb752aeec947acab3.json"}}, {"family": "Fixler", "given": "Dror", "initials": "D"}, {"family": "Grimm", "given": "Jan", "initials": "J"}, {"family": "Gruber", "given": "Florian", "initials": "F"}, {"family": "Kala\u0161", "given": "Mat\u00fa\u0161", "initials": "M", "orcid": "0000-0002-1509-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee56816d10554890a6045b9705974854.json"}}, {"family": "Kremslehner", "given": "Christopher", "initials": "C"}, {"family": "Kuntner", "given": "Claudia", "initials": "C"}, {"family": "Kuzdas-Wood", "given": "Daniela", "initials": "D"}, {"family": "Lindblad", "given": "Joakim", "initials": "J", "orcid": "0000-0001-7312-8222", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6b66ce110794e1fb312b82e790646b4.json"}}, {"family": "Mannheim", "given": "Julia G", "initials": "JG"}, {"family": "Marchetti-Deschmann", "given": "Martina", "initials": "M"}, {"family": "Paul-Gilloteaux", "given": "Perrine", "initials": "P", "orcid": "0000-0002-4822-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a.json"}}, {"family": "Sampaio", "given": "Paula", "initials": "P"}, {"family": "Sandbichler", "given": "Peter", "initials": "P"}, {"family": "Sartori-Rupp", "given": "Anna", "initials": "A"}, {"family": "Sladoje", "given": "Nata\u0161a", "initials": "N"}, {"family": "Verkade", "given": "Paul", "initials": "P"}, {"family": "Walter", "given": "Andreas", "initials": "A"}, {"family": "Zoratto", "given": "Samuele", "initials": "S"}], "type": "journal-article", "published": "2024-07-30", "journal": {"title": "Front. Biomater. Sci.", "issn": "2813-3749", "volume": "3", "issn-l": null}, "abstract": null, "doi": "10.3389/fbiom.2024.1338115", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-15T12:10:32.853Z", "modified": "2025-12-04T19:38:49.888Z"}, {"entity": "publication", "iuid": "de4d7e55211c439e95a4878e3ab8842e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de4d7e55211c439e95a4878e3ab8842e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de4d7e55211c439e95a4878e3ab8842e"}}, "title": "Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists.", "authors": [{"family": "Martins", "given": "Gabriel G", "initials": "GG", "orcid": "0000-0002-6506-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/c04a08e246854401b529158afe9de318.json"}}, {"family": "Cordeli\u00e8res", "given": "Fabrice P", "initials": "FP", "orcid": "0000-0002-5383-5816", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd3da472e85b4b19897bc513e443219f.json"}}, {"family": "Colombelli", "given": "Julien", "initials": "J", "orcid": "0000-0002-2784-4276", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e92116688467197a2eaadb170eb12.json"}}, {"family": "D'Antuono", "given": "Rocco", "initials": "R", "orcid": "0000-0003-0180-6500", "researcher": {"href": "https://publications.scilifelab.se/researcher/19a219cdf18a48c581c66844eed7f888.json"}}, {"family": "Golani", "given": "Ofra", "initials": "O", "orcid": "0000-0002-9793-236X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e239b26ad266407eb249be51f728f2ef.json"}}, {"family": "Guiet", "given": "Romain", "initials": "R", "orcid": "0000-0001-6715-4897", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e318b0b510843c194d0f1c6b852bceb.json"}}, {"family": "Haase", "given": "Robert", "initials": "R", "orcid": "0000-0001-5949-2327", "researcher": {"href": "https://publications.scilifelab.se/researcher/f99dc020f05f479cafa0aede600157f0.json"}}, {"family": "Klemm", "given": "Anna H", "initials": "AH", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "Louveaux", "given": "Marion", "initials": "M", "orcid": "0000-0002-1794-3748", "researcher": {"href": "https://publications.scilifelab.se/researcher/3901ec2c7f1345f6974d7eae9766a502.json"}}, {"family": "Paul-Gilloteaux", "given": "Perrine", "initials": "P", "orcid": "0000-0002-4822-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a.json"}}, {"family": "Tinevez", "given": "Jean-Yves", "initials": "JY", "orcid": "0000-0002-0998-4718", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed604822457048af8051bcb4e11da3a6.json"}}, {"family": "Miura", "given": "Kota", "initials": "K", "orcid": "0000-0001-6926-191X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2924dc08df743e188b5ead9a88449a6.json"}}], "type": "journal article", "published": "2021-04-30", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "334", "issn-l": "2046-1402"}, "abstract": "NEUBIAS, the European Network of Bioimage Analysts, was created in 2016 with the goal of improving the communication and the knowledge transfer among the various stakeholders involved in the acquisition, processing and analysis of biological image data, and to promote the establishment and recognition of the profession of Bioimage Analyst. One of the most successful initiatives of the NEUBIAS programme was its series of 15 training schools, which trained over 400 new Bioimage Analysts, coming from over 40 countries. Here we outline the rationale behind the innovative three-level program of the schools, the curriculum, the trainer recruitment and turnover strategy, the outcomes for the community and the career path of analysts, including some success stories. We discuss the future of the materials created during this programme and some of the new initiatives emanating from the community of NEUBIAS-trained analysts, such as the NEUBIAS Academy. Overall, we elaborate on how this training programme played a key role in collectively leveraging Bioimaging and Life Science research by bringing the latest innovations into structured, frequent and intensive training activities, and on why we believe this should become a model to further develop in Life Sciences.", "doi": "10.12688/f1000research.25485.1", "pmid": "34164115", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8215561"}], "notes": [], "created": "2021-11-29T12:35:36.781Z", "modified": "2021-11-29T12:35:37.127Z"}, {"entity": "publication", "iuid": "859de35c946e4369a5530fc3194f10d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/859de35c946e4369a5530fc3194f10d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/859de35c946e4369a5530fc3194f10d1"}}, "title": "Bioimage analysis workflows: community resources to navigate through a complex ecosystem.", "authors": [{"family": "Paul-Gilloteaux", "given": "Perrine", "initials": "P", "orcid": "0000-0002-4822-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a.json"}}, {"family": "Tosi", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0001-8348-2778", "researcher": {"href": "https://publications.scilifelab.se/researcher/94b7debd554a44b590a5c4bd2b802c82.json"}}, {"family": "H\u00e9rich\u00e9", "given": "Jean-Karim", "initials": "JK"}, {"family": "Gaignard", "given": "Alban", "initials": "A"}, {"family": "M\u00e9nager", "given": "Herv\u00e9", "initials": "H"}, {"family": "Mar\u00e9e", "given": "Rapha\u00ebl", "initials": "R"}, {"family": "Baecker", "given": "Volker", "initials": "V", "orcid": "0000-0002-9129-6403", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5884e3569e5470f8d0a1fe960a85c1c.json"}}, {"family": "Klemm", "given": "Anna", "initials": "A", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "Kala\u0161", "given": "Mat\u00fa\u0161", "initials": "M", "orcid": "0000-0002-1509-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee56816d10554890a6045b9705974854.json"}}, {"family": "Zhang", "given": "Chong", "initials": "C"}, {"family": "Miura", "given": "Kota", "initials": "K"}, {"family": "Colombelli", "given": "Julien", "initials": "J", "orcid": "0000-0002-2784-4276", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e92116688467197a2eaadb170eb12.json"}}], "type": "journal article", "published": "2021-04-26", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "320", "issn-l": "2046-1402"}, "abstract": "Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them. One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows. The emergence of \"big data\" in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR.", "doi": "10.12688/f1000research.52569.1", "pmid": "34136134", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8182692"}], "notes": [], "created": "2021-11-29T12:35:24.298Z", "modified": "2021-11-29T12:35:24.493Z"}]}