{"external_id":{"arxiv":["2303.03793"]},"article_type":"original","month":"03","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning (ML) are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap encompasses key aspects of how ML is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of ML for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences."}],"quality_controlled":"1","status":"public","OA_type":"gold","scopus_import":"1","date_updated":"2026-03-02T09:10:31Z","citation":{"ista":"Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton IC, Rubinsztein-Dunlop H, Brunner D, Bai B, Ozcan A, Midtvedt D, Wang H, Li T, Sladoje N, Lindblad J, Smith JT, Ochoa M, Barroso M, Intes X, Qiu T, Yu LY, You S, Liu Y, Ziatdinov MA, Kalinin SV, Sheridan A, Manor U, Nehme E, Goldenberg O, Shechtman Y, Moberg HK, Langhammer C, Špačková B, Helgadottir S, Midtvedt B, Argun A, Thalheim T, Cichos F, Bo S, Hubatsch L, Pineda J, Manzo C, Bachimanchi H, Selander E, Homs-Corbera A, Fränzl M, De Haan K, Rivenson Y, Korczak Z, Adiels CB, Mijalkov M, Veréb D, Chang YW, Pereira JB, Matuszewski D, Kylberg G, Sintorn IM, Caicedo JC, Cimini BA, Lediju Bell MA, Saraiva BM, Jacquemet G, Henriques R, Ouyang W, Le T, Gómez-De-Mariscal E, Sage D, Muñoz-Barrutia A, Lindqvist EJ, Bergman J. 2026. Roadmap on deep learning for microscopy. Jphys Photonics. 8(1), 012501.","chicago":"Volpe, Giovanni, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, et al. “Roadmap on Deep Learning for Microscopy.” <i>Jphys Photonics</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">https://doi.org/10.1088/2515-7647/ae0fd1</a>.","mla":"Volpe, Giovanni, et al. “Roadmap on Deep Learning for Microscopy.” <i>Jphys Photonics</i>, vol. 8, no. 1, 012501, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">10.1088/2515-7647/ae0fd1</a>.","ieee":"G. Volpe <i>et al.</i>, “Roadmap on deep learning for microscopy,” <i>Jphys Photonics</i>, vol. 8, no. 1. IOP Publishing, 2026.","apa":"Volpe, G., Wählby, C., Tian, L., Hecht, M., Yakimovich, A., Monakhova, K., … Bergman, J. (2026). Roadmap on deep learning for microscopy. <i>Jphys Photonics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">https://doi.org/10.1088/2515-7647/ae0fd1</a>","short":"G. Volpe, C. Wählby, L. Tian, M. Hecht, A. Yakimovich, K. Monakhova, L. Waller, I.F. Sbalzarini, C.A. Metzler, M. Xie, K. Zhang, I.C. Lenton, H. Rubinsztein-Dunlop, D. Brunner, B. Bai, A. Ozcan, D. Midtvedt, H. Wang, T. Li, N. Sladoje, J. Lindblad, J.T. Smith, M. Ochoa, M. Barroso, X. Intes, T. Qiu, L.Y. Yu, S. You, Y. Liu, M.A. Ziatdinov, S.V. Kalinin, A. Sheridan, U. Manor, E. Nehme, O. Goldenberg, Y. Shechtman, H.K. Moberg, C. Langhammer, B. Špačková, S. Helgadottir, B. Midtvedt, A. Argun, T. Thalheim, F. Cichos, S. Bo, L. Hubatsch, J. Pineda, C. Manzo, H. Bachimanchi, E. Selander, A. Homs-Corbera, M. Fränzl, K. De Haan, Y. Rivenson, Z. Korczak, C.B. Adiels, M. Mijalkov, D. Veréb, Y.W. Chang, J.B. Pereira, D. Matuszewski, G. Kylberg, I.M. Sintorn, J.C. Caicedo, B.A. Cimini, M.A. Lediju Bell, B.M. Saraiva, G. Jacquemet, R. Henriques, W. Ouyang, T. Le, E. Gómez-De-Mariscal, D. Sage, A. Muñoz-Barrutia, E.J. Lindqvist, J. Bergman, Jphys Photonics 8 (2026).","ama":"Volpe G, Wählby C, Tian L, et al. Roadmap on deep learning for microscopy. <i>Jphys Photonics</i>. 2026;8(1). doi:<a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">10.1088/2515-7647/ae0fd1</a>"},"article_number":"012501","file_date_updated":"2026-03-02T09:05:53Z","arxiv":1,"publication":"Jphys Photonics","_id":"21370","department":[{"_id":"ScWa"}],"date_created":"2026-03-01T23:01:39Z","ddc":["530"],"volume":8,"oa":1,"date_published":"2026-03-01T00:00:00Z","day":"01","DOAJ_listed":"1","oa_version":"Published Version","article_processing_charge":"Yes","title":"Roadmap on deep learning for microscopy","publication_identifier":{"eissn":["2515-7647"]},"PlanS_conform":"1","issue":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","creator":"dernst","file_size":16789781,"access_level":"open_access","date_updated":"2026-03-02T09:05:53Z","file_id":"21375","success":1,"checksum":"172720f1f0c5c9d06a282e52023a0030","file_name":"2026_JPhysPhotonics_Volpe.pdf","date_created":"2026-03-02T09:05:53Z","relation":"main_file"}],"author":[{"full_name":"Volpe, Giovanni","first_name":"Giovanni","last_name":"Volpe"},{"last_name":"Wählby","full_name":"Wählby, Carolina","first_name":"Carolina"},{"full_name":"Tian, Lei","first_name":"Lei","last_name":"Tian"},{"full_name":"Hecht, Michael","first_name":"Michael","last_name":"Hecht"},{"first_name":"Artur","full_name":"Yakimovich, Artur","last_name":"Yakimovich"},{"first_name":"Kristina","full_name":"Monakhova, Kristina","last_name":"Monakhova"},{"first_name":"Laura","full_name":"Waller, Laura","last_name":"Waller"},{"last_name":"Sbalzarini","first_name":"Ivo F.","full_name":"Sbalzarini, Ivo F."},{"last_name":"Metzler","full_name":"Metzler, Christopher A.","first_name":"Christopher A."},{"last_name":"Xie","full_name":"Xie, Mingyang","first_name":"Mingyang"},{"first_name":"Kevin","full_name":"Zhang, Kevin","last_name":"Zhang"},{"full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","first_name":"Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb","last_name":"Lenton"},{"first_name":"Halina","full_name":"Rubinsztein-Dunlop, Halina","last_name":"Rubinsztein-Dunlop"},{"full_name":"Brunner, Daniel","first_name":"Daniel","last_name":"Brunner"},{"last_name":"Bai","first_name":"Bijie","full_name":"Bai, Bijie"},{"first_name":"Aydogan","full_name":"Ozcan, Aydogan","last_name":"Ozcan"},{"full_name":"Midtvedt, Daniel","first_name":"Daniel","last_name":"Midtvedt"},{"full_name":"Wang, Hao","first_name":"Hao","last_name":"Wang"},{"full_name":"Li, Tongyu","first_name":"Tongyu","last_name":"Li"},{"last_name":"Sladoje","full_name":"Sladoje, Nataša","first_name":"Nataša"},{"first_name":"Joakim","full_name":"Lindblad, Joakim","last_name":"Lindblad"},{"first_name":"Jason T.","full_name":"Smith, Jason T.","last_name":"Smith"},{"first_name":"Marien","full_name":"Ochoa, Marien","last_name":"Ochoa"},{"last_name":"Barroso","full_name":"Barroso, Margarida","first_name":"Margarida"},{"last_name":"Intes","first_name":"Xavier","full_name":"Intes, Xavier"},{"last_name":"Qiu","first_name":"Tong","full_name":"Qiu, Tong"},{"first_name":"Li Yu","full_name":"Yu, Li Yu","last_name":"Yu"},{"last_name":"You","full_name":"You, Sixian","first_name":"Sixian"},{"first_name":"Yongtao","full_name":"Liu, Yongtao","last_name":"Liu"},{"first_name":"Maxim A.","full_name":"Ziatdinov, Maxim A.","last_name":"Ziatdinov"},{"full_name":"Kalinin, Sergei V.","first_name":"Sergei V.","last_name":"Kalinin"},{"first_name":"Arlo","full_name":"Sheridan, Arlo","last_name":"Sheridan"},{"first_name":"Uri","full_name":"Manor, Uri","last_name":"Manor"},{"full_name":"Nehme, Elias","first_name":"Elias","last_name":"Nehme"},{"first_name":"Ofri","full_name":"Goldenberg, Ofri","last_name":"Goldenberg"},{"first_name":"Yoav","full_name":"Shechtman, Yoav","last_name":"Shechtman"},{"full_name":"Moberg, Henrik K.","first_name":"Henrik K.","last_name":"Moberg"},{"last_name":"Langhammer","full_name":"Langhammer, Christoph","first_name":"Christoph"},{"first_name":"Barbora","full_name":"Špačková, Barbora","last_name":"Špačková"},{"last_name":"Helgadottir","full_name":"Helgadottir, Saga","first_name":"Saga"},{"first_name":"Benjamin","full_name":"Midtvedt, Benjamin","last_name":"Midtvedt"},{"first_name":"Aykut","full_name":"Argun, Aykut","last_name":"Argun"},{"last_name":"Thalheim","full_name":"Thalheim, Tobias","first_name":"Tobias"},{"last_name":"Cichos","first_name":"Frank","full_name":"Cichos, Frank"},{"last_name":"Bo","full_name":"Bo, Stefano","first_name":"Stefano"},{"first_name":"Lars","full_name":"Hubatsch, Lars","last_name":"Hubatsch"},{"full_name":"Pineda, Jesus","first_name":"Jesus","last_name":"Pineda"},{"last_name":"Manzo","first_name":"Carlo","full_name":"Manzo, Carlo"},{"last_name":"Bachimanchi","first_name":"Harshith","full_name":"Bachimanchi, Harshith"},{"last_name":"Selander","full_name":"Selander, Erik","first_name":"Erik"},{"full_name":"Homs-Corbera, Antoni","first_name":"Antoni","last_name":"Homs-Corbera"},{"first_name":"Martin","full_name":"Fränzl, Martin","last_name":"Fränzl"},{"last_name":"De Haan","first_name":"Kevin","full_name":"De Haan, Kevin"},{"last_name":"Rivenson","full_name":"Rivenson, Yair","first_name":"Yair"},{"last_name":"Korczak","first_name":"Zofia","full_name":"Korczak, Zofia"},{"first_name":"Caroline Beck","full_name":"Adiels, Caroline Beck","last_name":"Adiels"},{"last_name":"Mijalkov","full_name":"Mijalkov, Mite","first_name":"Mite"},{"first_name":"Dániel","full_name":"Veréb, Dániel","last_name":"Veréb"},{"full_name":"Chang, Yu Wei","first_name":"Yu Wei","last_name":"Chang"},{"first_name":"Joana B.","full_name":"Pereira, Joana B.","last_name":"Pereira"},{"full_name":"Matuszewski, Damian","first_name":"Damian","last_name":"Matuszewski"},{"first_name":"Gustaf","full_name":"Kylberg, Gustaf","last_name":"Kylberg"},{"last_name":"Sintorn","full_name":"Sintorn, Ida Maria","first_name":"Ida Maria"},{"full_name":"Caicedo, Juan C.","first_name":"Juan C.","last_name":"Caicedo"},{"full_name":"Cimini, Beth A.","first_name":"Beth A.","last_name":"Cimini"},{"last_name":"Lediju Bell","full_name":"Lediju Bell, Muyinatu A.","first_name":"Muyinatu A."},{"last_name":"Saraiva","first_name":"Bruno M.","full_name":"Saraiva, Bruno M."},{"full_name":"Jacquemet, Guillaume","first_name":"Guillaume","last_name":"Jacquemet"},{"last_name":"Henriques","full_name":"Henriques, Ricardo","first_name":"Ricardo"},{"last_name":"Ouyang","full_name":"Ouyang, Wei","first_name":"Wei"},{"last_name":"Le","full_name":"Le, Trang","first_name":"Trang"},{"last_name":"Gómez-De-Mariscal","first_name":"Estibaliz","full_name":"Gómez-De-Mariscal, Estibaliz"},{"last_name":"Sage","full_name":"Sage, Daniel","first_name":"Daniel"},{"last_name":"Muñoz-Barrutia","full_name":"Muñoz-Barrutia, Arrate","first_name":"Arrate"},{"last_name":"Lindqvist","full_name":"Lindqvist, Ebba Josefson","first_name":"Ebba Josefson"},{"last_name":"Bergman","full_name":"Bergman, Johanna","first_name":"Johanna"}],"type":"journal_article","publication_status":"published","OA_place":"publisher","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing","doi":"10.1088/2515-7647/ae0fd1","year":"2026","intvolume":"         8"}