[{"year":"2023","file_date_updated":"2023-11-23T10:30:08Z","_id":"14506","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"related_material":{"record":[{"id":"13238","status":"deleted","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9969","status":"public"},{"id":"14490","status":"public","relation":"part_of_dissertation"}]},"month":"11","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios."}],"corr_author":"1","date_updated":"2026-04-07T13:29:45Z","author":[{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0001-3676-4809","last_name":"Yeo","full_name":"Yeo, Michelle X","first_name":"Michelle X"}],"file":[{"access_level":"closed","date_updated":"2023-11-23T10:29:55Z","file_name":"thesis_yeo.zip","file_size":3037720,"creator":"cchlebak","content_type":"application/x-zip-compressed","file_id":"14598","relation":"source_file","date_created":"2023-11-23T10:29:55Z","checksum":"521c72818d720a52b377207b2ee87b6a"},{"success":1,"date_created":"2023-11-23T10:30:08Z","relation":"main_file","checksum":"0ed5d16899687aecf13d843c9878c9f2","file_size":2717256,"content_type":"application/pdf","creator":"cchlebak","file_id":"14599","file_name":"thesis_yeo.pdf","access_level":"open_access","date_updated":"2023-11-23T10:30:08Z"}],"oa_version":"Published Version","date_published":"2023-11-10T00:00:00Z","doi":"10.15479/14506","day":"10","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","title":"Advances in efficiency and privacy in payment channel network analysis","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","date_created":"2023-11-10T08:10:43Z","publisher":"Institute of Science and Technology Austria","ec_funded":1,"article_processing_charge":"No","type":"dissertation","ddc":["000"],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"alternative_title":["ISTA Thesis"],"page":"162","language":[{"iso":"eng"}],"publication_status":"published","citation":{"ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","mla":"Yeo, Michelle X. <i>Advances in Efficiency and Privacy in Payment Channel Network Analysis</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>.","chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>.","apa":"Yeo, M. X. (2023). <i>Advances in efficiency and privacy in payment channel network analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria."},"supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}]},{"date_created":"2023-11-05T23:00:54Z","volume":2023,"publisher":"IEEE","article_processing_charge":"No","type":"conference","acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant 2020388). It was also partially supported by NCN Grant 2019/35/B/ST6/04138 and ERC Grant 885666.","intvolume":"      2023","conference":{"name":"ICDCS: International Conference on Distributed Computing Systems","start_date":"2023-07-18","end_date":"2023-07-21","location":"Hong Kong, China"},"isi":1,"external_id":{"isi":["001081242600053"],"arxiv":["2306.16006"]},"oa":1,"page":"603-613","language":[{"iso":"eng"}],"publication_status":"published","arxiv":1,"citation":{"ieee":"Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation games,” in <i>43rd International Conference on Distributed Computing Systems</i>, Hong Kong, China, 2023, vol. 2023, pp. 603–613.","short":"Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.","ama":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In: <i>43rd International Conference on Distributed Computing Systems</i>. Vol 2023. IEEE; 2023:603-613. doi:<a href=\"https://doi.org/10.1109/ICDCS57875.2023.00037\">10.1109/ICDCS57875.2023.00037</a>","ista":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games. 43rd International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems vol. 2023, 603–613.","apa":"Avarikioti, Z., Lizurej, T., Michalak, T., &#38; Yeo, M. X. (2023). Lightning creation games. In <i>43rd International Conference on Distributed Computing Systems</i> (Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. <a href=\"https://doi.org/10.1109/ICDCS57875.2023.00037\">https://doi.org/10.1109/ICDCS57875.2023.00037</a>","chicago":"Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo. “Lightning Creation Games.” In <i>43rd International Conference on Distributed Computing Systems</i>, 2023:603–13. IEEE, 2023. <a href=\"https://doi.org/10.1109/ICDCS57875.2023.00037\">https://doi.org/10.1109/ICDCS57875.2023.00037</a>.","mla":"Avarikioti, Zeta, et al. “Lightning Creation Games.” <i>43rd International Conference on Distributed Computing Systems</i>, vol. 2023, IEEE, 2023, pp. 603–13, doi:<a href=\"https://doi.org/10.1109/ICDCS57875.2023.00037\">10.1109/ICDCS57875.2023.00037</a>."},"_id":"14490","year":"2023","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.16006","open_access":"1"}],"scopus_import":"1","month":"10","publication":"43rd International Conference on Distributed Computing Systems","abstract":[{"text":"Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium.","lang":"eng"}],"department":[{"_id":"KrPi"}],"related_material":{"record":[{"status":"public","id":"14506","relation":"dissertation_contains"}]},"author":[{"first_name":"Zeta","full_name":"Avarikioti, Zeta","last_name":"Avarikioti"},{"last_name":"Lizurej","first_name":"Tomasz","full_name":"Lizurej, Tomasz"},{"last_name":"Michalak","full_name":"Michalak, Tomasz","first_name":"Tomasz"},{"orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","date_updated":"2026-04-07T13:29:44Z","date_published":"2023-10-11T00:00:00Z","doi":"10.1109/ICDCS57875.2023.00037","oa_version":"Preprint","day":"11","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"isbn":["9798350339864"],"eissn":["2575-8411"]},"title":"Lightning creation games"},{"intvolume":"        66","type":"journal_article","publisher":"Cambridge University Press","volume":66,"article_processing_charge":"No","date_created":"2023-06-11T22:00:40Z","citation":{"ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>.","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>.","apa":"Mohammadi, A., Pham, T., &#38; Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. 2023;66(4):1280-1295. doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023."},"arxiv":1,"publication_status":"published","language":[{"iso":"eng"}],"page":"1280-1295","external_id":{"arxiv":["2106.07328"],"isi":["001011963000001"]},"oa":1,"isi":1,"date_updated":"2026-04-08T13:04:49Z","author":[{"full_name":"Mohammadi, Ali","first_name":"Ali","last_name":"Mohammadi"},{"full_name":"Pham, Thang","first_name":"Thang","last_name":"Pham"},{"id":"1917d194-076e-11ed-97cd-837255f88785","last_name":"Wang","first_name":"Yiting","full_name":"Wang, Yiting","orcid":"0000-0002-2856-767X"}],"quality_controlled":"1","article_type":"original","department":[{"_id":"GradSch"}],"publication":"Canadian Mathematical Bulletin","month":"12","abstract":[{"lang":"eng","text":"Given 𝐴 ⊆𝐺⁡𝐿2⁡(𝔽𝑞), we prove that there exist disjoint subsets 𝐵,𝐶 ⊆𝐴 such that 𝐴 =𝐵 ⊔𝐶 and their additive and multiplicative energies satisfying\r\nmax⁡{𝐸+⁡(𝐵),𝐸×⁡(𝐶)}≪|𝐴|3/𝑀⁡(|𝐴|), where\r\n𝑀⁡(|𝐴|)=min⁡{𝑞4/3/|𝐴|1/3⁢(log⁡|𝐴|)2/3, |𝐴|4/5/𝑞13/5⁢(log⁡|𝐴|)27/10}.\r\n \r\nWe also study some related questions on moderate expanders over matrix rings, namely, for 𝐴,𝐵,𝐶 ⊆𝐺⁡𝐿2⁡(𝔽𝑞), we have\r\n|𝐴⁢𝐵+𝐶|, |(𝐴+𝐵)⁢𝐶|≫𝑞4,\r\n whenever |𝐴|⁢|𝐵|⁢|𝐶| ≫𝑞10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, 𝐹⁡𝑜⁢𝑟⁢𝑢⁢𝑚⁢𝑀⁢𝑎⁢𝑡⁢ℎ., 31, 951–970)."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.07328"}],"year":"2023","scopus_import":"1","_id":"13128","title":"An energy decomposition theorem for matrices and related questions","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","issue":"4","oa_version":"Preprint","date_published":"2023-12-01T00:00:00Z","doi":"10.4153/S000843952300036X"},{"scopus_import":"1","date_created":"2026-04-09T09:10:41Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.05535","open_access":"1"}],"year":"2023","OA_place":"repository","_id":"21677","abstract":[{"text":"Lasers with high intensity generally exhibit strong intensity fluctuations far above the shot-noise level. Taming this noise is pivotal to a wide range of applications, both classical and quantum. Here, we demonstrate the creation of intense light with quantum levels of noise even when starting from inputs with large amounts of excess noise. In particular, we demonstrate how intense squeezed light with intensities approaching 0.1 TW/cm^2, but noise at or below the shot noise level, can be produced from noisy inputs associated with high-power amplified laser sources (an overall noise-reduction of 30-fold). Based on a new theory of quantum noise in multimode systems, we show that the ability to generate quantum light from noisy inputs results from multimode quantum correlations, which maximally decouple the output light from the dominant noise channels in the input light. As an example, we demonstrate this effect for femtosecond pulses in nonlinear fibers, but the noise-immune correlations that enable our results are generic to many other nonlinear systems in optics and beyond.","lang":"eng"}],"type":"preprint","month":"11","article_processing_charge":"No","publication":"arXiv","date_updated":"2026-04-13T09:43:17Z","author":[{"first_name":"Shiekh Zia","full_name":"Uddin, Shiekh Zia","last_name":"Uddin"},{"last_name":"Rivera","full_name":"Rivera, Nicholas","first_name":"Nicholas"},{"first_name":"Devin","full_name":"Seyler, Devin","last_name":"Seyler"},{"last_name":"Sloan","full_name":"Sloan, Jamison","first_name":"Jamison"},{"first_name":"Yannick","full_name":"Salamin, Yannick","last_name":"Salamin"},{"id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"first_name":"Shutao","full_name":"Xu, Shutao","last_name":"Xu"},{"last_name":"Sander","first_name":"Michelle","full_name":"Sander, Michelle"},{"last_name":"Kaminer","first_name":"Ido","full_name":"Kaminer, Ido"},{"last_name":"Soljacic","first_name":"Marin","full_name":"Soljacic, Marin"}],"extern":"1","oa_version":"Preprint","article_number":"2311.05535","external_id":{"arxiv":["2311.05535"]},"oa":1,"doi":"10.48550/arXiv.2311.05535","date_published":"2023-11-09T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","OA_type":"green","publication_status":"submitted","language":[{"iso":"eng"}],"title":"Noise-immune quantum correlations of intense light","citation":{"ama":"Uddin SZ, Rivera N, Seyler D, et al. Noise-immune quantum correlations of intense light. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2311.05535\">10.48550/arXiv.2311.05535</a>","short":"S.Z. Uddin, N. Rivera, D. Seyler, J. Sloan, Y. Salamin, C. Roques-Carmes, S. Xu, M. Sander, I. Kaminer, M. Soljacic, ArXiv (n.d.).","ieee":"S. Z. Uddin <i>et al.</i>, “Noise-immune quantum correlations of intense light,” <i>arXiv</i>. .","apa":"Uddin, S. Z., Rivera, N., Seyler, D., Sloan, J., Salamin, Y., Roques-Carmes, C., … Soljacic, M. (n.d.). Noise-immune quantum correlations of intense light. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2311.05535\">https://doi.org/10.48550/arXiv.2311.05535</a>","chicago":"Uddin, Shiekh Zia, Nicholas Rivera, Devin Seyler, Jamison Sloan, Yannick Salamin, Charles Roques-Carmes, Shutao Xu, Michelle Sander, Ido Kaminer, and Marin Soljacic. “Noise-Immune Quantum Correlations of Intense Light.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2311.05535\">https://doi.org/10.48550/arXiv.2311.05535</a>.","mla":"Uddin, Shiekh Zia, et al. “Noise-Immune Quantum Correlations of Intense Light.” <i>ArXiv</i>, 2311.05535, doi:<a href=\"https://doi.org/10.48550/arXiv.2311.05535\">10.48550/arXiv.2311.05535</a>.","ista":"Uddin SZ, Rivera N, Seyler D, Sloan J, Salamin Y, Roques-Carmes C, Xu S, Sander M, Kaminer I, Soljacic M. Noise-immune quantum correlations of intense light. arXiv, 2311.05535."},"arxiv":1},{"acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","ec_funded":1,"publisher":"Elsevier","type":"journal_article","volume":79,"article_processing_charge":"Yes (via OA deal)","date_created":"2023-02-26T12:24:21Z","has_accepted_license":"1","intvolume":"        79","ddc":["570"],"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"keyword":["General Neuroscience"],"article_number":"102695","oa":1,"external_id":{"isi":["000953497700001"],"pmid":["36842274"]},"isi":1,"citation":{"ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” <i>Current Opinion in Neurobiology</i>, vol. 79, no. 4. Elsevier, 2023.","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. 2023;79(4). doi:<a href=\"https://doi.org/10.1016/j.conb.2023.102695\">10.1016/j.conb.2023.102695</a>","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2023.102695\">https://doi.org/10.1016/j.conb.2023.102695</a>","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.conb.2023.102695\">https://doi.org/10.1016/j.conb.2023.102695</a>.","mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>, vol. 79, no. 4, 102695, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.conb.2023.102695\">10.1016/j.conb.2023.102695</a>."},"language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"department":[{"_id":"SiHi"}],"abstract":[{"text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.","lang":"eng"}],"publication":"Current Opinion in Neurobiology","month":"04","scopus_import":"1","file_date_updated":"2023-08-16T12:29:06Z","year":"2023","_id":"12679","date_updated":"2025-04-15T08:23:06Z","article_type":"review","quality_controlled":"1","file":[{"date_created":"2023-08-16T12:29:06Z","relation":"main_file","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","success":1,"file_size":1787894,"creator":"dernst","content_type":"application/pdf","file_id":"14071","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","date_updated":"2023-08-16T12:29:06Z","access_level":"open_access"}],"author":[{"first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"01","issue":"4","oa_version":"Published Version","doi":"10.1016/j.conb.2023.102695","date_published":"2023-04-01T00:00:00Z","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","publication_identifier":{"issn":["0959-4388"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"04","oa_version":"Published Version","doi":"10.15479/AT:ISTA:13126","date_published":"2023-08-04T00:00:00Z","title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"link":[{"url":"https://pub.ista.ac.at/group_danzl/data/CATS/","relation":"research_data","description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. "}],"record":[{"id":"14257","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and 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Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>.","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","short":"J.G. Danzl, (2023).","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>"},"acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","type":"research_data","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","ec_funded":1,"has_accepted_license":"1","date_created":"2023-06-07T07:15:12Z","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508"},{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020"}],"ddc":["610"]},{"citation":{"mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>.","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. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","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.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","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.","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>","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."},"language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"page":"1256-1265","OA_type":"hybrid","isi":1,"oa":1,"external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"intvolume":"        20","project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"_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","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"ddc":["570"],"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.).","volume":20,"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"publisher":"Springer Nature","has_accepted_license":"1","date_created":"2023-07-23T22:01:13Z","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"title":"Dense 4D nanoscale reconstruction of living brain tissue","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","doi":"10.1038/s41592-023-01936-6","date_published":"2023-08-01T00:00:00Z","oa_version":"Published Version","file":[{"date_updated":"2025-02-26T08:01:57Z","access_level":"open_access","file_name":"2023_NatureMethods_Velicky.pdf","file_id":"19088","content_type":"application/pdf","creator":"dernst","file_size":14103039,"checksum":"a68e845780a82ea36d0d4d3212a87c10","relation":"main_file","date_created":"2025-02-26T08:01:57Z","success":1}],"quality_controlled":"1","article_type":"original","author":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"last_name":"Miguel Villalba","first_name":"Eder","full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3862-1235","first_name":"Julia M","full_name":"Michalska, Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wei","full_name":"Wei, Donglai","first_name":"Donglai"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","first_name":"Jake","full_name":"Watson, Jake","last_name":"Watson"},{"first_name":"Jakob","full_name":"Troidl, Jakob","last_name":"Troidl"},{"full_name":"Beyer, Johanna","first_name":"Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","full_name":"Ben Simon, Yoav","first_name":"Yoav"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0201-2315","last_name":"Jahr","first_name":"Wiebke","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"full_name":"Grant, Seth G.N.","first_name":"Seth G.N.","last_name":"Grant"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T12:58:30Z","corr_author":"1","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"}],"month":"08","publication":"Nature Methods","related_material":{"record":[{"relation":"research_data","id":"12817","status":"public"},{"relation":"shorter_version","id":"14770","status":"public"},{"relation":"earlier_version","id":"11943","status":"public"},{"relation":"dissertation_contains","status":"public","id":"18674"}],"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}]},"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"OA_place":"publisher","_id":"13267","scopus_import":"1","file_date_updated":"2025-02-26T08:01:57Z","year":"2023"},{"ddc":["570"],"date_created":"2023-04-07T11:37:40Z","has_accepted_license":"1","type":"research_data","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. ","citation":{"apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>","mla":"Danzl, Johann G. <i>Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>.","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>","short":"J.G. Danzl, (2023).","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023."},"oa":1,"contributor":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431"},{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba"},{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","first_name":"Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"first_name":"Donglai","last_name":"Wei"},{"last_name":"Lin","first_name":"Zudi"},{"first_name":"Jake","last_name":"Watson","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Troidl","first_name":"Jakob"},{"first_name":"Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban"},{"first_name":"Johannes","last_name":"Broichhagen"},{"first_name":"Seth G. N. 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However, it 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). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior 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 synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"department":[{"_id":"JoDa"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","related_material":{"record":[{"status":"public","id":"13267","relation":"used_in_publication"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","date_published":"2023-05-19T00:00:00Z","doi":"10.15479/AT:ISTA:12817","oa_version":"Published Version","day":"19","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>.","apa":"Danzl, J. G., &#38; Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20(8):1141-1142. doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023."},"publication_status":"published","language":[{"iso":"eng"}],"page":"1141-1142","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"isi":1,"external_id":{"isi":["001025621500002"]},"intvolume":"        20","publisher":"Springer Nature","volume":20,"type":"journal_article","article_processing_charge":"No","date_created":"2024-01-10T08:07:15Z","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","issue":"8","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2023-08-01T00:00:00Z","doi":"10.1038/s41592-023-01937-5","oa_version":"None","author":[{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"}],"article_type":"letter_note","quality_controlled":"1","date_updated":"2026-04-14T08:34:34Z","corr_author":"1","month":"08","publication":"Nature Methods","abstract":[{"lang":"eng","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."}],"department":[{"_id":"JoDa"}],"related_material":{"record":[{"id":"13267","status":"public","relation":"extended_version"}]},"_id":"14770","year":"2023","scopus_import":"1"},{"publisher":"Institute of Science and Technology Austria","type":"dissertation","article_processing_charge":"No","ec_funded":1,"date_created":"2023-06-01T09:05:24Z","has_accepted_license":"1","project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"page":"147","oa":1,"alternative_title":["ISTA Thesis"],"citation":{"ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>"},"supervisor":[{"orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"12802","relation":"part_of_dissertation"}]},"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"abstract":[{"text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans.","lang":"eng"}],"month":"05","file_date_updated":"2023-06-07T08:41:49Z","year":"2023","OA_place":"publisher","_id":"13107","date_updated":"2026-04-14T08:34:36Z","file":[{"file_name":"Thesis_Lisa Knaus_approved_final.docx","date_updated":"2023-06-01T13:48:41Z","access_level":"closed","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","date_created":"2023-06-01T13:48:41Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"13112","creator":"lknaus","file_size":12991551},{"date_created":"2023-06-02T09:47:29Z","relation":"main_file","checksum":"6903d152aa01181d87a696085af31c83","file_size":9309015,"file_id":"13114","creator":"lknaus","content_type":"application/pdf","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","access_level":"open_access","date_updated":"2023-06-07T08:41:49Z"}],"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","full_name":"Knaus, Lisa","first_name":"Lisa"}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","day":"31","oa_version":"Published Version","doi":"10.15479/at:ista:13107","date_published":"2023-05-31T00:00:00Z","title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}]},{"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","publication_identifier":{"issn":["0092-8674"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","issue":"9","oa_version":"Published Version","date_published":"2023-04-27T00:00:00Z","doi":"10.1016/j.cell.2023.02.037","date_updated":"2026-04-14T08:34:36Z","author":[{"first_name":"Lisa","full_name":"Knaus, Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette"},{"last_name":"Malzl","first_name":"Daniel","full_name":"Malzl, Daniel"},{"first_name":"Maria","full_name":"Gerykova Bujalkova, Maria","last_name":"Gerykova Bujalkova"},{"last_name":"Smogavec","first_name":"Mateja","full_name":"Smogavec, Mateja"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A.","first_name":"Lena A."},{"id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","last_name":"Gorkiewicz","full_name":"Gorkiewicz, Sarah","first_name":"Sarah"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"last_name":"Knittl-Frank","first_name":"Christian","full_name":"Knittl-Frank, Christian"},{"id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","full_name":"Tassinari, Marianna","first_name":"Marianna","last_name":"Tassinari"},{"first_name":"Nuno","full_name":"Maulide, Nuno","last_name":"Maulide"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"last_name":"Menche","full_name":"Menche, Jörg","first_name":"Jörg"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"}],"article_type":"original","file":[{"file_id":"12889","creator":"dernst","content_type":"application/pdf","file_size":15712841,"success":1,"checksum":"47e94fbe19e86505b429cb7a5b503ce6","relation":"main_file","date_created":"2023-05-02T09:26:21Z","access_level":"open_access","date_updated":"2023-05-02T09:26:21Z","file_name":"2023_Cell_Knaus.pdf"}],"quality_controlled":"1","corr_author":"1","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/"}],"record":[{"relation":"dissertation_contains","id":"19557","status":"public"},{"relation":"dissertation_contains","id":"13107","status":"public"}]},"month":"04","publication":"Cell","abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}],"year":"2023","scopus_import":"1","file_date_updated":"2023-05-02T09:26:21Z","_id":"12802","citation":{"ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>."},"language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"page":"1950-1967.e25","oa":1,"external_id":{"isi":["000991468700001"],"pmid":["36996814"]},"isi":1,"project":[{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"intvolume":"       186","volume":186,"article_processing_charge":"Yes (via OA deal)","type":"journal_article","publisher":"Elsevier","ec_funded":1,"acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","date_created":"2023-04-05T08:15:40Z","has_accepted_license":"1"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","day":"16","doi":"10.1146/annurev-cellbio-020823-011522","date_published":"2023-10-16T00:00:00Z","oa_version":"Published Version","publication_identifier":{"issn":["1081-0706"],"eissn":["1530-8995"]},"title":"Control of tissue development by morphogens","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling."}],"publication":"Annual Review of Cell and Developmental Biology","month":"10","department":[{"_id":"AnKi"}],"_id":"14484","file_date_updated":"2023-11-06T09:47:50Z","scopus_import":"1","year":"2023","article_type":"review","file":[{"date_updated":"2023-11-06T09:47:50Z","access_level":"open_access","file_name":"2023_AnnualReviews_Kicheva.pdf","content_type":"application/pdf","file_id":"14491","creator":"dernst","file_size":434819,"checksum":"461726014cf5907010afbd418d3c13ec","relation":"main_file","date_created":"2023-11-06T09:47:50Z","success":1}],"quality_controlled":"1","author":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"}],"date_updated":"2025-12-30T10:57:08Z","corr_author":"1","page":"91-121","isi":1,"external_id":{"pmid":["37418774"],"isi":["001082823000006"]},"oa":1,"citation":{"chicago":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">https://doi.org/10.1146/annurev-cellbio-020823-011522</a>.","apa":"Kicheva, A., &#38; Briscoe, J. (2023). Control of tissue development by morphogens. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">https://doi.org/10.1146/annurev-cellbio-020823-011522</a>","mla":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 39, Annual Reviews, 2023, pp. 91–121, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">10.1146/annurev-cellbio-020823-011522</a>.","ista":"Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 39, 91–121.","ama":"Kicheva A, Briscoe J. Control of tissue development by morphogens. <i>Annual Review of Cell and Developmental Biology</i>. 2023;39:91-121. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">10.1146/annurev-cellbio-020823-011522</a>","short":"A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39 (2023) 91–121.","ieee":"A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 39. Annual Reviews, pp. 91–121, 2023."},"pmid":1,"publication_status":"published","language":[{"iso":"eng"}],"acknowledgement":"We are grateful to Zena Hadjivasiliou for comments on this article. A.K. is supported by grants from the European Research Council under the European Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe (101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051), and by a grant from the European Research Council under the EU Horizon 2020 research and innovation program (742138).","ec_funded":1,"publisher":"Annual Reviews","volume":39,"article_processing_charge":"Yes (in subscription journal)","type":"journal_article","date_created":"2023-11-05T23:00:53Z","has_accepted_license":"1","intvolume":"        39","ddc":["570"],"project":[{"call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"}]},{"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","relation":"press_release"}],"record":[{"relation":"research_data","id":"13122","status":"public"}]},"department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification."}],"month":"05","publication":"Science","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"year":"2023","_id":"13106","date_updated":"2026-04-15T06:39:33Z","quality_controlled":"1","article_type":"original","author":[{"full_name":"Sahu, Rishabh","first_name":"Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","orcid":"0000-0003-4345-4267","last_name":"Qiu","first_name":"Liu","full_name":"Qiu, Liu"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","first_name":"William J","last_name":"Hease"},{"last_name":"Arnold","first_name":"Georg M","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y.","full_name":"Minoguchi, Y.","last_name":"Minoguchi"},{"full_name":"Rabl, P.","first_name":"P.","last_name":"Rabl"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M"}],"corr_author":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"18","issue":"6646","oa_version":"Preprint","doi":"10.1126/science.adg3812","date_published":"2023-05-18T00:00:00Z","title":"Entangling microwaves with light","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","volume":380,"publisher":"American Association for the Advancement of Science","ec_funded":1,"article_processing_charge":"No","type":"journal_article","date_created":"2023-05-31T11:39:24Z","intvolume":"       380","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"keyword":["Multidisciplinary"],"page":"718-721","external_id":{"arxiv":["2301.03315"],"pmid":["37200415"],"isi":["000996515200004"]},"oa":1,"isi":1,"citation":{"ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. <i>Science</i>. 2023;380(6646):718-721. doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","ieee":"R. Sahu <i>et al.</i>, “Entangling microwaves with light,” <i>Science</i>, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” <i>Science</i>. 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Science. 380(6646), 718–721."},"arxiv":1,"language":[{"iso":"eng"}],"publication_status":"published","pmid":1},{"corr_author":"1","date_updated":"2026-04-15T06:39:32Z","author":[{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","last_name":"Sahu","first_name":"Rishabh","full_name":"Sahu, Rishabh"}],"year":"2023","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"date_created":"2023-06-06T06:46:16Z","_id":"13122","department":[{"_id":"JoFi"}],"related_material":{"record":[{"status":"public","id":"13106","relation":"used_in_publication"}]},"article_processing_charge":"No","publisher":"Zenodo","month":"03","type":"research_data_reference","abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"R. Sahu, (2023).","ama":"Sahu R. Entangling microwaves with light. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>","mla":"Sahu, Rishabh. <i>Entangling Microwaves with Light</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>."},"title":"Entangling microwaves with light","oa":1,"oa_version":"Published Version","date_published":"2023-03-31T00:00:00Z","doi":"10.5281/ZENODO.7789417","day":"31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"has_accepted_license":"1","date_created":"2023-07-16T22:01:08Z","acknowledgement":"The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.","volume":14,"type":"journal_article","publisher":"Springer Nature","article_processing_charge":"No","intvolume":"        14","ddc":["530"],"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"article_number":"3968","external_id":{"pmid":["37407570"],"isi":["001024729900009"]},"oa":1,"isi":1,"pmid":1,"publication_status":"published","language":[{"iso":"eng"}],"citation":{"ama":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>","short":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023).","ieee":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>.","mla":"Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>, vol. 14, 3968, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>.","apa":"Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., &#38; Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>","ista":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968."},"scopus_import":"1","file_date_updated":"2023-07-18T08:43:07Z","year":"2023","_id":"13227","related_material":{"record":[{"relation":"dissertation_contains","id":"17133","status":"public"}]},"department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","text":"Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis."}],"month":"07","publication":"Nature Communications","corr_author":"1","date_updated":"2026-04-15T06:39:57Z","article_type":"original","quality_controlled":"1","file":[{"success":1,"checksum":"a85773b5fe23516f60f7d5d31b55c200","relation":"main_file","date_created":"2023-07-18T08:43:07Z","content_type":"application/pdf","file_id":"13248","creator":"dernst","file_size":2899592,"file_name":"2023_NatureComm_Hassani.pdf","access_level":"open_access","date_updated":"2023-07-18T08:43:07Z"}],"author":[{"full_name":"Hassani, Farid","first_name":"Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"first_name":"Lucky","full_name":"Kapoor, Lucky","last_name":"Kapoor","orcid":"0000-0001-8319-2148","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","doi":"10.1038/s41467-023-39656-2","date_published":"2023-07-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"05","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours","publication_identifier":{"eissn":["2041-1723"]}},{"date_created":"2023-06-30T08:07:43Z","has_accepted_license":"1","type":"dissertation","article_processing_charge":"No","ec_funded":1,"publisher":"Institute of Science and Technology Austria","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"ddc":["537","535","539"],"alternative_title":["ISTA Thesis"],"oa":1,"page":"202","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"language":[{"iso":"eng"}],"publication_status":"published","supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"}],"citation":{"ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>.","ista":"Sahu R. 2023. Cavity quantum electrooptics. 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For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. 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Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria."},"_id":"12900","OA_place":"publisher","year":"2023","file_date_updated":"2023-07-06T11:37:40Z","month":"05","abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"related_material":{"record":[{"status":"public","id":"13175","relation":"new_edition"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9114","relation":"part_of_dissertation"}]},"corr_author":"1","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"8cbdab9c37ee55e591092a6f66b272c4","relation":"source_file","date_created":"2023-05-09T08:45:14Z","file_id":"12928","creator":"rsahu","content_type":"application/x-zip-compressed","embargo_to":"open_access","file_size":36767177,"file_name":"thesis.zip","access_level":"closed","date_updated":"2023-06-06T22:30:03Z"},{"file_name":"thesis_pdfa_final.pdf","date_updated":"2023-07-06T11:37:40Z","access_level":"closed","checksum":"439659ead46618147309be39d9dd5a8c","date_created":"2023-05-09T08:51:17Z","relation":"main_file","content_type":"application/pdf","creator":"rsahu","file_id":"12929","file_size":17501990}],"date_updated":"2026-04-15T06:43:26Z","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12900","oa_version":"Published Version","day":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-030-5"]},"title":"Cavity quantum electrooptics","degree_awarded":"PhD"},{"article_processing_charge":"No","type":"journal_article","volume":31,"publisher":"Optica Publishing Group","date_created":"2026-03-30T12:22:48Z","intvolume":"        31","ddc":["530"],"page":"24260-24272","OA_type":"gold","external_id":{"arxiv":["2302.01712"],"pmid":["37475257"]},"oa":1,"arxiv":1,"citation":{"ista":"Li WF, Arya G, Roques-Carmes C, Lin Z, Johnson SG, Soljačić M. 2023. Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics. Optics Express. 31(15), 24260–24272.","chicago":"Li, William F., Gaurav Arya, Charles Roques-Carmes, Zin Lin, Steven G. Johnson, and Marin Soljačić. “Transcending Shift-Invariance in the Paraxial Regime via End-to-End Inverse Design of Freeform Nanophotonics.” <i>Optics Express</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/oe.492553\">https://doi.org/10.1364/oe.492553</a>.","mla":"Li, William F., et al. “Transcending Shift-Invariance in the Paraxial Regime via End-to-End Inverse Design of Freeform Nanophotonics.” <i>Optics Express</i>, vol. 31, no. 15, Optica Publishing Group, 2023, pp. 24260–72, doi:<a href=\"https://doi.org/10.1364/oe.492553\">10.1364/oe.492553</a>.","apa":"Li, W. F., Arya, G., Roques-Carmes, C., Lin, Z., Johnson, S. G., &#38; Soljačić, M. (2023). Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics. <i>Optics Express</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/oe.492553\">https://doi.org/10.1364/oe.492553</a>","ieee":"W. F. Li, G. Arya, C. Roques-Carmes, Z. Lin, S. G. Johnson, and M. Soljačić, “Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics,” <i>Optics Express</i>, vol. 31, no. 15. Optica Publishing Group, pp. 24260–24272, 2023.","short":"W.F. Li, G. Arya, C. Roques-Carmes, Z. Lin, S.G. Johnson, M. Soljačić, Optics Express 31 (2023) 24260–24272.","ama":"Li WF, Arya G, Roques-Carmes C, Lin Z, Johnson SG, Soljačić M. Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics. <i>Optics Express</i>. 2023;31(15):24260-24272. doi:<a href=\"https://doi.org/10.1364/oe.492553\">10.1364/oe.492553</a>"},"language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","abstract":[{"text":"Traditional optical elements and conventional metasurfaces obey shift-invariance in the paraxial regime. For imaging systems obeying paraxial shift-invariance, a small shift in input angle causes a corresponding shift in the sensor image. Shift-invariance has deep implications for the design and functionality of optical devices, such as the necessity of free space between components (as in compound objectives made of several curved surfaces). We present a method for nanophotonic inverse design of compact imaging systems whose resolution is not constrained by paraxial shift-invariance. Our method is end-to-end, in that it integrates density-based full-Maxwell topology optimization with a fully iterative elastic-net reconstruction algorithm. By the design of nanophotonic structures that scatter light in a non-shift-invariant manner, our optimized nanophotonic imaging system overcomes the limitations of paraxial shift-invariance, achieving accurate, noise-robust image reconstruction beyond shift-invariant resolution.","lang":"eng"}],"publication":"Optics Express","month":"07","OA_place":"publisher","_id":"21639","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1364/OE.492553","open_access":"1"}],"year":"2023","quality_controlled":"1","article_type":"original","author":[{"full_name":"Li, William F.","first_name":"William F.","last_name":"Li"},{"full_name":"Arya, Gaurav","first_name":"Gaurav","last_name":"Arya"},{"id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","first_name":"Charles","full_name":"Roques-Carmes, Charles"},{"first_name":"Zin","full_name":"Lin, Zin","last_name":"Lin"},{"full_name":"Johnson, Steven G.","first_name":"Steven G.","last_name":"Johnson"},{"last_name":"Soljačić","full_name":"Soljačić, Marin","first_name":"Marin"}],"extern":"1","date_updated":"2026-04-27T07:32:36Z","issue":"15","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","doi":"10.1364/oe.492553","date_published":"2023-07-10T00:00:00Z","oa_version":"Published Version","DOAJ_listed":"1","publication_identifier":{"eissn":["1094-4087"]},"title":"Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"citation":{"ista":"Yang Y, Roques-Carmes C, Kooi SE, Tang H, Beroz J, Mazur E, Kaminer I, Joannopoulos JD, Soljačić M. 2023. Photonic flatband resonances for free-electron radiation. Nature. 613, 42–47.","chicago":"Yang, Yi, Charles Roques-Carmes, Steven E. Kooi, Haoning Tang, Justin Beroz, Eric Mazur, Ido Kaminer, John D. Joannopoulos, and Marin Soljačić. “Photonic Flatband Resonances for Free-Electron Radiation.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-022-05387-5\">https://doi.org/10.1038/s41586-022-05387-5</a>.","apa":"Yang, Y., Roques-Carmes, C., Kooi, S. E., Tang, H., Beroz, J., Mazur, E., … Soljačić, M. (2023). Photonic flatband resonances for free-electron radiation. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05387-5\">https://doi.org/10.1038/s41586-022-05387-5</a>","mla":"Yang, Yi, et al. “Photonic Flatband Resonances for Free-Electron Radiation.” <i>Nature</i>, vol. 613, Springer Nature, 2023, pp. 42–47, doi:<a href=\"https://doi.org/10.1038/s41586-022-05387-5\">10.1038/s41586-022-05387-5</a>.","ieee":"Y. Yang <i>et al.</i>, “Photonic flatband resonances for free-electron radiation,” <i>Nature</i>, vol. 613. Springer Nature, pp. 42–47, 2023.","short":"Y. Yang, C. Roques-Carmes, S.E. Kooi, H. Tang, J. Beroz, E. Mazur, I. Kaminer, J.D. Joannopoulos, M. Soljačić, Nature 613 (2023) 42–47.","ama":"Yang Y, Roques-Carmes C, Kooi SE, et al. Photonic flatband resonances for free-electron radiation. <i>Nature</i>. 2023;613:42-47. doi:<a href=\"https://doi.org/10.1038/s41586-022-05387-5\">10.1038/s41586-022-05387-5</a>"},"arxiv":1,"pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","OA_type":"green","page":"42-47","external_id":{"arxiv":["2110.03550"],"pmid":["36600060"]},"oa":1,"ddc":["530"],"intvolume":"       613","article_processing_charge":"No","volume":613,"type":"journal_article","publisher":"Springer Nature","date_created":"2026-03-30T12:22:47Z","title":"Photonic flatband resonances for free-electron radiation","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"day":"04","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Preprint","date_published":"2023-01-04T00:00:00Z","doi":"10.1038/s41586-022-05387-5","date_updated":"2026-04-27T09:10:26Z","extern":"1","author":[{"last_name":"Yang","first_name":"Yi","full_name":"Yang, Yi"},{"id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"last_name":"Kooi","first_name":"Steven E.","full_name":"Kooi, Steven E."},{"full_name":"Tang, Haoning","first_name":"Haoning","last_name":"Tang"},{"last_name":"Beroz","first_name":"Justin","full_name":"Beroz, Justin"},{"last_name":"Mazur","first_name":"Eric","full_name":"Mazur, Eric"},{"full_name":"Kaminer, Ido","first_name":"Ido","last_name":"Kaminer"},{"first_name":"John D.","full_name":"Joannopoulos, John D.","last_name":"Joannopoulos"},{"full_name":"Soljačić, Marin","first_name":"Marin","last_name":"Soljačić"}],"article_type":"original","quality_controlled":"1","publication":"Nature","month":"01","abstract":[{"text":"Flatbands have become a cornerstone of contemporary condensed-matter physics\r\nand photonics. In electronics, flatbands entail comparable energy bandwidth and\r\nCoulomb interaction, leading to correlated phenomena such as the fractional\r\nquantum Hall effect and recently those in magic-angle systems. In photonics, they\r\nenable properties including slow light1 and lasing2. Notably, flatbands support\r\nsupercollimation—diffractionless wavepacket propagation—in both systems3,4.\r\nDespite these intense parallel efforts, flatbands have never been shown to affect the\r\ncore interaction between free electrons and photons. Their interaction, pivotal for\r\nfree-electron lasers5, microscopy and spectroscopy6,7, and particle accelerators8,9,\r\nis, in fact, limited by a dimensionality mismatch between localized electrons and\r\nextended photons. Here we reveal theoretically that photonic flatbands can overcome\r\nthis mismatch and thus remarkably boost their interaction. We design flatband\r\nresonances in a silicon-on-insulator photonic crystal slab to control and enhance the\r\nassociated free-electron radiation by tuning their trajectory and velocity. We observe\r\nsignatures of flatband enhancement, recording a two-order increase from the\r\nconventional diffraction-enabled Smith–Purcell radiation. The enhancement enables\r\npolarization shaping of free-electron radiation and characterization of photonic\r\nbands through electron-beam measurements. Our results support the use of\r\nflatbands as test beds for strong light–electron interaction, particularly relevant for\r\nefficient and compact free-electron light sources and accelerators.","lang":"eng"}],"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2110.03550"}],"scopus_import":"1","_id":"21547","OA_place":"repository"},{"title":"Learning photons go backward","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"oa_version":"None","date_published":"2023-04-28T00:00:00Z","doi":"10.1126/science.adh0724","day":"28","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","issue":"6643","date_updated":"2026-04-27T08:47:22Z","extern":"1","author":[{"last_name":"Roques-Carmes","first_name":"Charles","full_name":"Roques-Carmes, Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"}],"article_type":"original","quality_controlled":"1","year":"2023","scopus_import":"1","_id":"21585","publication":"Science","month":"04","abstract":[{"lang":"eng","text":"Efficient learning algorithms are implemented in a silicon photonic neural network chip"}],"publication_status":"published","language":[{"iso":"eng"}],"citation":{"ieee":"C. Roques-Carmes, “Learning photons go backward,” <i>Science</i>, vol. 380, no. 6643. American Association for the Advancement of Science, pp. 341–342, 2023.","ama":"Roques-Carmes C. Learning photons go backward. <i>Science</i>. 2023;380(6643):341-342. doi:<a href=\"https://doi.org/10.1126/science.adh0724\">10.1126/science.adh0724</a>","short":"C. Roques-Carmes, Science 380 (2023) 341–342.","mla":"Roques-Carmes, Charles. “Learning Photons Go Backward.” <i>Science</i>, vol. 380, no. 6643, American Association for the Advancement of Science, 2023, pp. 341–42, doi:<a href=\"https://doi.org/10.1126/science.adh0724\">10.1126/science.adh0724</a>.","chicago":"Roques-Carmes, Charles. “Learning Photons Go Backward.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adh0724\">https://doi.org/10.1126/science.adh0724</a>.","apa":"Roques-Carmes, C. (2023). Learning photons go backward. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adh0724\">https://doi.org/10.1126/science.adh0724</a>","ista":"Roques-Carmes C. 2023. Learning photons go backward. Science. 380(6643), 341–342."},"OA_type":"closed access","page":"341-342","ddc":["530"],"intvolume":"       380","date_created":"2026-03-30T12:22:48Z","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","volume":380,"type":"journal_article"}]
