[{"article_type":"original","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","title":"Dense 4D nanoscale reconstruction of living brain tissue","scopus_import":"1","month":"08","date_published":"2023-08-01T00:00:00Z","_id":"13267","year":"2023","intvolume":"        20","date_updated":"2026-04-07T12:58:30Z","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"author":[{"orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba"},{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"full_name":"Wei, Donglai","first_name":"Donglai","last_name":"Wei"},{"full_name":"Lin, Zudi","first_name":"Zudi","last_name":"Lin"},{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson"},{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"full_name":"Beyer, Johanna","last_name":"Beyer","first_name":"Johanna"},{"full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Jahr, Wiebke","orcid":"0000-0003-0201-2315","last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"first_name":"Seth G.N.","last_name":"Grant","full_name":"Grant, Seth G.N."},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"}],"date_created":"2023-07-23T22:01:13Z","project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"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","call_identifier":"H2020"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":20,"oa":1,"OA_type":"hybrid","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"file_date_updated":"2025-02-26T08:01:57Z","page":"1256-1265","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.).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41592-023-01936-6","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"citation":{"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>","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>","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.","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>.","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>.","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.","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."},"isi":1,"day":"01","file":[{"content_type":"application/pdf","file_size":14103039,"success":1,"file_id":"19088","file_name":"2023_NatureMethods_Velicky.pdf","date_updated":"2025-02-26T08:01:57Z","creator":"dernst","access_level":"open_access","checksum":"a68e845780a82ea36d0d4d3212a87c10","relation":"main_file","date_created":"2025-02-26T08:01:57Z"}],"corr_author":"1","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Nature Methods","ddc":["570"],"OA_place":"publisher","related_material":{"record":[{"status":"public","id":"12817","relation":"research_data"},{"relation":"shorter_version","id":"14770","status":"public"},{"id":"11943","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"18674"}],"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}]},"has_accepted_license":"1","publisher":"Springer Nature"},{"abstract":[{"lang":"eng","text":"Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue."}],"publication":"bioRxiv","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","oa":1,"related_material":{"record":[{"relation":"later_version","id":"13267","status":"public"},{"relation":"dissertation_contains","status":"public","id":"12470"}]},"OA_place":"repository","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"date_updated":"2026-05-05T22:30:35Z","corr_author":"1","type":"preprint","publication_status":"draft","author":[{"orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky"},{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","first_name":"Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"full_name":"Troidl, Jakob","first_name":"Jakob","last_name":"Troidl"},{"last_name":"Beyer","first_name":"Johanna","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"last_name":"Broichhagen","first_name":"Johannes","full_name":"Broichhagen, Johannes"},{"full_name":"Grant, Seth G. N.","last_name":"Grant","first_name":"Seth G. N."},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"}],"date_created":"2022-08-23T11:07:59Z","date_published":"2022-05-09T00:00:00Z","title":"Saturated reconstruction of living brain tissue","doi":"10.1101/2022.03.16.484431","month":"05","_id":"11943","citation":{"ieee":"P. Velicky <i>et al.</i>, “Saturated reconstruction of living brain tissue,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, 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, BioRxiv (n.d.).","mla":"Velicky, Philipp, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Wei, D., Lin, Z., Watson, J., … Danzl, J. G. (n.d.). Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>","ista":"Velicky P, Miguel Villalba E, Michalska JM, 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. Saturated reconstruction of living brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Donglai Wei, Zudi Lin, Jake Watson, Jakob Troidl, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.16.484431"}],"year":"2022","day":"09","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public"},{"year":"2018","_id":"6195","citation":{"short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018.","ieee":"M. Pozzi <i>et al.</i>, “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.","mla":"Pozzi, Maria, et al. <i>Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains</i>. 8461106, IEEE, 2018, doi:<a href=\"https://doi.org/10.1109/icra.2018.8461106\">10.1109/icra.2018.8461106</a>.","ista":"Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.","chicago":"Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. <a href=\"https://doi.org/10.1109/icra.2018.8461106\">https://doi.org/10.1109/icra.2018.8461106</a>.","apa":"Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., &#38; Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. <a href=\"https://doi.org/10.1109/icra.2018.8461106\">https://doi.org/10.1109/icra.2018.8461106</a>","ama":"Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:<a href=\"https://doi.org/10.1109/icra.2018.8461106\">10.1109/icra.2018.8461106</a>"},"day":"10","isi":1,"title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains","scopus_import":"1","doi":"10.1109/icra.2018.8461106","month":"09","date_published":"2018-09-10T00:00:00Z","article_number":"8461106","status":"public","conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2018-05-25","location":"Brisbane, Australia","start_date":"2018-05-21"},"article_processing_charge":"No","language":[{"iso":"eng"}],"external_id":{"isi":["000446394503031"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"IEEE","oa_version":"None","abstract":[{"lang":"eng","text":"In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers."}],"quality_controlled":"1","author":[{"full_name":"Pozzi, Maria","first_name":"Maria","last_name":"Pozzi"},{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba"},{"last_name":"Deimel","first_name":"Raphael","full_name":"Deimel, Raphael"},{"first_name":"Monica","last_name":"Malvezzi","full_name":"Malvezzi, Monica"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brock, Oliver","first_name":"Oliver","last_name":"Brock"},{"full_name":"Prattichizzo, Domenico","first_name":"Domenico","last_name":"Prattichizzo"}],"date_created":"2019-04-04T09:50:38Z","type":"conference","publication_status":"published","date_updated":"2023-09-19T14:49:03Z","department":[{"_id":"BeBi"}],"publication_identifier":{"isbn":["9781538630815"]}},{"date_published":"2016-07-01T00:00:00Z","month":"07","scopus_import":"1","title":"Computational design of stable planar-rod structures","intvolume":"        35","year":"2016","_id":"1364","pubrep_id":"763","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"abstract":[{"text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.","lang":"eng"}],"oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000380112400056"]},"volume":35,"oa":1,"date_updated":"2025-09-22T07:42:15Z","project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599"}],"date_created":"2018-12-11T11:51:36Z","author":[{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","first_name":"Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lepoutre, Mathias","first_name":"Mathias","last_name":"Lepoutre"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"article_number":"86","doi":"10.1145/2897824.2925978","issue":"4","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599.","publist_id":"5878","day":"01","isi":1,"citation":{"ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86.","chicago":"Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>.","ama":"Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>","apa":"Miguel Villalba, E., Lepoutre, M., &#38; Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>","mla":"Miguel Villalba, Eder, et al. <i>Computational Design of Stable Planar-Rod Structures</i>. Vol. 35, no. 4, 86, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>.","short":"E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.","ieee":"E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4."},"file_date_updated":"2020-07-14T12:44:47Z","conference":{"location":"Anaheim, CA, USA","name":"ACM SIGGRAPH","end_date":"2016-07-28","start_date":"2016-07-24"},"ddc":["006"],"publisher":"ACM","has_accepted_license":"1","department":[{"_id":"BeBi"}],"corr_author":"1","alternative_title":["ACM Transactions on Graphics"],"file":[{"date_updated":"2020-07-14T12:44:47Z","file_name":"IST-2017-763-v1+1_wirebending.pdf","creator":"system","access_level":"open_access","checksum":"d00c2664a43d945df8876ea0193734e3","relation":"main_file","date_created":"2018-12-12T10:11:01Z","file_size":44766392,"content_type":"application/pdf","file_id":"4853"}],"publication_status":"published","type":"conference","quality_controlled":"1"},{"department":[{"_id":"BeBi"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Computer Graphics Forum","publisher":"Wiley-Blackwell","page":"385 - 396","acknowledgement":"This work was funded in part by grants from the Spanish Ministry of Economy (TIN2012-35840), the European Research Council (ERC Starting Grant no. 280135 Animetrics), and the EU FP7 (project no. 601165 WEARHAP).","doi":"10.1111/cgf.12840","issue":"2","citation":{"apa":"Miguel Villalba, E., Miraut, D., &#38; Otaduy, M. (2016). Modeling and estimation of energy-based hyperelastic objects. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/cgf.12840\">https://doi.org/10.1111/cgf.12840</a>","ama":"Miguel Villalba E, Miraut D, Otaduy M. Modeling and estimation of energy-based hyperelastic objects. <i>Computer Graphics Forum</i>. 2016;35(2):385-396. doi:<a href=\"https://doi.org/10.1111/cgf.12840\">10.1111/cgf.12840</a>","ista":"Miguel Villalba E, Miraut D, Otaduy M. 2016. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 35(2), 385–396.","chicago":"Miguel Villalba, Eder, David Miraut, and Miguel Otaduy. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/cgf.12840\">https://doi.org/10.1111/cgf.12840</a>.","mla":"Miguel Villalba, Eder, et al. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” <i>Computer Graphics Forum</i>, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 385–96, doi:<a href=\"https://doi.org/10.1111/cgf.12840\">10.1111/cgf.12840</a>.","ieee":"E. Miguel Villalba, D. Miraut, and M. Otaduy, “Modeling and estimation of energy-based hyperelastic objects,” <i>Computer Graphics Forum</i>, vol. 35, no. 2. Wiley-Blackwell, pp. 385–396, 2016.","short":"E. Miguel Villalba, D. Miraut, M. Otaduy, Computer Graphics Forum 35 (2016) 385–396."},"isi":1,"publist_id":"5792","day":"01","date_updated":"2025-09-18T14:24:28Z","author":[{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba"},{"full_name":"Miraut, David","first_name":"David","last_name":"Miraut"},{"full_name":"Otaduy, Miguel","first_name":"Miguel","last_name":"Otaduy"}],"date_created":"2018-12-11T11:51:53Z","oa_version":"None","abstract":[{"text":"In this paper, we present a method to model hyperelasticity that is well suited for representing the nonlinearity of real-world objects, as well as for estimating it from deformation examples. Previous approaches suffer several limitations, such as lack of integrability of elastic forces, failure to enforce energy convexity, lack of robustness of parameter estimation, or difficulty to model cross-modal effects. Our method avoids these problems by relying on a general energy-based definition of elastic properties. The accuracy of the resulting elastic model is maximized by defining an additive model of separable energy terms, which allow progressive parameter estimation. In addition, our method supports efficient modeling of extreme nonlinearities thanks to energy-limiting constraints. We combine our energy-based model with an optimization method to estimate model parameters from force-deformation examples, and we show successful modeling of diverse deformable objects, including cloth, human finger skin, and internal human anatomy in a medical imaging application.","lang":"eng"}],"volume":35,"external_id":{"isi":["000377222200036"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Modeling and estimation of energy-based hyperelastic objects","month":"05","scopus_import":"1","date_published":"2016-05-01T00:00:00Z","_id":"1414","year":"2016","intvolume":"        35"}]