article published yes Philipp Velicky author 39BDC62C-F248-11E8-B48F-1D18A9856A870000-0002-2340-7431 Eder Miguel Villalba author 3FB91342-F248-11E8-B48F-1D18A9856A870000-0001-5665-0430 Julia M Michalska author 443DB6DE-F248-11E8-B48F-1D18A9856A870000-0003-3862-1235 Julia Lyudchik author 46E28B80-F248-11E8-B48F-1D18A9856A87 Donglai Wei author Zudi Lin author Jake Watson author 63836096-4690-11EA-BD4E-32803DDC885E0000-0002-8698-3823 Jakob Troidl author Johanna Beyer author Yoav Ben Simon author 43DF3136-F248-11E8-B48F-1D18A9856A87 Christoph M Sommer author 4DF26D8C-F248-11E8-B48F-1D18A9856A870000-0003-1216-9105 Wiebke Jahr author 425C1CE8-F248-11E8-B48F-1D18A9856A870000-0003-0201-2315 Alban Cenameri author 9ac8f577-2357-11eb-997a-e566c5550886 Johannes Broichhagen author Seth G.N. Grant author Peter M Jonas author 353C1B58-F248-11E8-B48F-1D18A9856A870000-0001-5001-4804 Gaia Novarino author 3E57A680-F248-11E8-B48F-1D18A9856A870000-0002-7673-7178 Hanspeter Pfister author Bernd Bickel author 49876194-F248-11E8-B48F-1D18A9856A870000-0001-6511-9385 Johann G Danzl author 42EFD3B6-F248-11E8-B48F-1D18A9856A870000-0001-8559-3973 PeJo department GaNo department BeBi department JoDa department Bio department Optical control of synaptic function via adhesion molecules project Molecular Drug Targets project Synaptic communication in neuronal microcircuits project High content imaging to decode human immune cell interactions in health and allergic disease project International IST Doctoral Program project MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling project Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models project Biophysics and circuit function of a giant cortical glutamatergic synapse project Synaptic computations of the hippocampal CA3 circuitry project High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration project 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. https://research-explorer.ista.ac.at/download/13267/19088/2023_NatureMethods_Velicky.pdf application/pdfno Springer Nature2023 eng 1548-7091 1548-7105 37429995 00102562150000110.1038/s41592-023-01936-6 201256-1265 https://research-explorer.ista.ac.at/record/12817 https://research-explorer.ista.ac.at/record/14770 https://research-explorer.ista.ac.at/record/18674 https://research-explorer.ista.ac.at/record/11943 https://github.com/danzllab/LIONESS 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>. 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> 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. 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. 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>. 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> 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. 132672023-07-23T22:01:13Z2026-07-06T12:49:46Z