[{"year":"2023","isi":1,"publication":"Nature Methods","day":"01","page":"1256-1265","date_created":"2023-07-23T22:01:13Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1038/s41592-023-01936-6","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"article_processing_charge":"Yes","author":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","last_name":"Miguel Villalba"},{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"last_name":"Lin","full_name":"Lin, Zudi","first_name":"Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"last_name":"Beyer","full_name":"Beyer, Johanna","first_name":"Johanna"},{"full_name":"Ben Simon, Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","last_name":"Cenameri"},{"last_name":"Broichhagen","full_name":"Broichhagen, Johannes","first_name":"Johannes"},{"first_name":"Seth G.N.","full_name":"Grant, Seth G.N.","last_name":"Grant"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057"}],"publication_status":"published","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":20,"related_material":{"record":[{"status":"public","id":"12817","relation":"research_data"},{"relation":"shorter_version","status":"public","id":"14770"}],"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"scopus_import":"1","intvolume":" 20","month":"08","date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"_id":"13267","type":"journal_article","article_type":"original","status":"public"},{"publisher":"Springer Nature","quality_controlled":"1","year":"2023","isi":1,"publication":"Nature Methods","day":"01","page":"1141-1142","date_created":"2024-01-10T08:07:15Z","doi":"10.1038/s41592-023-01937-5","date_published":"2023-08-01T00:00:00Z","citation":{"chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["001025621500002"]},"author":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"}],"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","abstract":[{"text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.","lang":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 20","month":"08","publication_status":"published","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"extended_version","id":"13267","status":"public"}]},"volume":20,"issue":"8","_id":"14770","article_type":"letter_note","type":"journal_article","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"status":"public","date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"JoDa"}]},{"project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.","chicago":"Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” Nature Methods. Springer Nature, 2022. https://doi.org/10.1038/s41592-022-01444-z.","short":"S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.","ieee":"S. Knyazev et al., “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” Nature Methods, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022.","apa":"Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-022-01444-z","ama":"Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 2022;19(4):374-380. doi:10.1038/s41592-022-01444-z","mla":"Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” Nature Methods, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:10.1038/s41592-022-01444-z."},"title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","author":[{"first_name":"Sergey","full_name":"Knyazev, Sergey","last_name":"Knyazev"},{"first_name":"Karishma","full_name":"Chhugani, Karishma","last_name":"Chhugani"},{"full_name":"Sarwal, Varuni","last_name":"Sarwal","first_name":"Varuni"},{"first_name":"Ram","last_name":"Ayyala","full_name":"Ayyala, Ram"},{"full_name":"Singh, Harman","last_name":"Singh","first_name":"Harman"},{"first_name":"Smruthi","last_name":"Karthikeyan","full_name":"Karthikeyan, Smruthi"},{"full_name":"Deshpande, Dhrithi","last_name":"Deshpande","first_name":"Dhrithi"},{"first_name":"Pelin Icer","last_name":"Baykal","full_name":"Baykal, Pelin Icer"},{"first_name":"Zoia","last_name":"Comarova","full_name":"Comarova, Zoia"},{"first_name":"Angela","full_name":"Lu, Angela","last_name":"Lu"},{"first_name":"Yuri","last_name":"Porozov","full_name":"Porozov, Yuri"},{"first_name":"Tetyana I.","full_name":"Vasylyeva, Tetyana I.","last_name":"Vasylyeva"},{"full_name":"Wertheim, Joel O.","last_name":"Wertheim","first_name":"Joel O."},{"last_name":"Tierney","full_name":"Tierney, Braden T.","first_name":"Braden T."},{"first_name":"Charles Y.","full_name":"Chiu, Charles Y.","last_name":"Chiu"},{"last_name":"Sun","full_name":"Sun, Ren","first_name":"Ren"},{"full_name":"Wu, Aiping","last_name":"Wu","first_name":"Aiping"},{"full_name":"Abedalthagafi, Malak S.","last_name":"Abedalthagafi","first_name":"Malak S."},{"last_name":"Pak","full_name":"Pak, Victoria M.","first_name":"Victoria M."},{"first_name":"Shivashankar H.","last_name":"Nagaraj","full_name":"Nagaraj, Shivashankar H."},{"full_name":"Smith, Adam L.","last_name":"Smith","first_name":"Adam L."},{"first_name":"Pavel","last_name":"Skums","full_name":"Skums, Pavel"},{"first_name":"Bogdan","full_name":"Pasaniuc, Bogdan","last_name":"Pasaniuc"},{"last_name":"Komissarov","full_name":"Komissarov, Andrey","first_name":"Andrey"},{"first_name":"Christopher E.","last_name":"Mason","full_name":"Mason, Christopher E."},{"first_name":"Eric","full_name":"Bortz, Eric","last_name":"Bortz"},{"first_name":"Philippe","full_name":"Lemey, Philippe","last_name":"Lemey"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Niko","last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko"},{"first_name":"Tommy Tsan Yuk","last_name":"Lam","full_name":"Lam, Tommy Tsan Yuk"},{"full_name":"Wu, Nicholas C.","last_name":"Wu","first_name":"Nicholas C."},{"first_name":"Alex","last_name":"Zelikovsky","full_name":"Zelikovsky, Alex"},{"first_name":"Rob","full_name":"Knight, Rob","last_name":"Knight"},{"first_name":"Keith A.","full_name":"Crandall, Keith A.","last_name":"Crandall"},{"first_name":"Serghei","full_name":"Mangul, Serghei","last_name":"Mangul"}],"external_id":{"isi":["000781199600011"],"pmid":["35396471"]},"article_processing_charge":"No","acknowledgement":"Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"08","publication":"Nature Methods","isi":1,"year":"2022","date_published":"2022-04-08T00:00:00Z","doi":"10.1038/s41592-022-01444-z","date_created":"2022-04-17T22:01:48Z","page":"374-380","_id":"11187","status":"public","type":"journal_article","article_type":"letter_note","date_updated":"2023-08-03T06:46:09Z","department":[{"_id":"FyKo"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.","lang":"eng"}],"month":"04","intvolume":" 19","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41592-022-01444-z","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"publication_status":"published","issue":"4","volume":19,"ec_funded":1},{"volume":18,"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"publication_status":"published","month":"03","intvolume":" 18","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-021-01087-6"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"JoDa"}],"date_updated":"2023-08-07T14:19:08Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"9258","doi":"10.1038/s41592-021-01087-6","date_published":"2021-03-01T00:00:00Z","date_created":"2021-03-21T23:01:20Z","page":"226-228","day":"01","publication":"Nature Methods","isi":1,"year":"2021","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank S. van der Walt and K. Marchuk for discussion during development. This project was funded by Packard Fellowship and Chan Zuckerberg Biohub Investigator Awards to L.W.; STROBE: A NSF Science and Technology Center; an NSF Graduate Research Fellowship awarded to H.P.; a Berkeley Institute for Data Science/UCSF Bakar Computational Health Sciences Institute Fellowship awarded to H.P. with support from the Koret Foundation, the Gordon and Betty Moore Foundation, and the Alfred P. Sloan Foundation to the University of California, Berkeley. K.W.E., B.L. and M.T. were funded by the Chan Zuckerberg Initiative and NIH grant P41GM135019.","title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","author":[{"full_name":"Pinkard, Henry","last_name":"Pinkard","first_name":"Henry"},{"full_name":"Stuurman, Nico","last_name":"Stuurman","first_name":"Nico"},{"full_name":"Ivanov, Ivan E.","last_name":"Ivanov","first_name":"Ivan E."},{"last_name":"Anthony","full_name":"Anthony, Nicholas M.","first_name":"Nicholas M."},{"first_name":"Wei","last_name":"Ouyang","full_name":"Ouyang, Wei"},{"full_name":"Li, Bin","last_name":"Li","first_name":"Bin"},{"last_name":"Yang","full_name":"Yang, Bin","first_name":"Bin"},{"first_name":"Mark A.","last_name":"Tsuchida","full_name":"Tsuchida, Mark A."},{"first_name":"Bryant","full_name":"Chhun, Bryant","last_name":"Chhun"},{"first_name":"Grace","last_name":"Zhang","full_name":"Zhang, Grace"},{"first_name":"Ryan","full_name":"Mei, Ryan","last_name":"Mei"},{"first_name":"Michael","last_name":"Anderson","full_name":"Anderson, Michael"},{"last_name":"Shepherd","full_name":"Shepherd, Douglas P.","first_name":"Douglas P."},{"first_name":"Ian","full_name":"Hunt-Isaak, Ian","last_name":"Hunt-Isaak"},{"first_name":"Raymond L.","last_name":"Dunn","full_name":"Dunn, Raymond L."},{"full_name":"Jahr, Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"last_name":"Kato","full_name":"Kato, Saul","first_name":"Saul"},{"full_name":"Royer, Loïc A.","last_name":"Royer","first_name":"Loïc A."},{"last_name":"Thiagarajah","full_name":"Thiagarajah, Jay R.","first_name":"Jay R."},{"last_name":"Eliceiri","full_name":"Eliceiri, Kevin W.","first_name":"Kevin W."},{"last_name":"Lundberg","full_name":"Lundberg, Emma","first_name":"Emma"},{"full_name":"Mehta, Shalin B.","last_name":"Mehta","first_name":"Shalin B."},{"last_name":"Waller","full_name":"Waller, Laura","first_name":"Laura"}],"external_id":{"pmid":["33674797"],"isi":["000625600600007"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L. 2021. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 18(3), 226–228.","chicago":"Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” Nature Methods. Springer Nature, 2021. https://doi.org/10.1038/s41592-021-01087-6.","apa":"Pinkard, H., Stuurman, N., Ivanov, I. E., Anthony, N. M., Ouyang, W., Li, B., … Waller, L. (2021). Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-021-01087-6","ama":"Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 2021;18(3):226-228. doi:10.1038/s41592-021-01087-6","ieee":"H. Pinkard et al., “Pycro-Manager: Open-source software for customized and reproducible microscope control,” Nature Methods, vol. 18, no. 3. Springer Nature, pp. 226–228, 2021.","short":"H. Pinkard, N. Stuurman, I.E. Ivanov, N.M. Anthony, W. Ouyang, B. Li, B. Yang, M.A. Tsuchida, B. Chhun, G. Zhang, R. Mei, M. Anderson, D.P. Shepherd, I. Hunt-Isaak, R.L. Dunn, W. Jahr, S. Kato, L.A. Royer, J.R. Thiagarajah, K.W. Eliceiri, E. Lundberg, S.B. Mehta, L. Waller, Nature Methods 18 (2021) 226–228.","mla":"Pinkard, Henry, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” Nature Methods, vol. 18, no. 3, Springer Nature, 2021, pp. 226–28, doi:10.1038/s41592-021-01087-6."}}]