[{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL.","date_published":"2023-01-01T00:00:00Z","doi":"10.1245/s10434-022-12459-3","date_created":"2023-01-16T09:44:36Z","page":"35-45","day":"01","publication":"Annals of Surgical Oncology","isi":1,"has_accepted_license":"1","year":"2023","title":"Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium","author":[{"first_name":"Jacek","full_name":"Glajzer, Jacek","last_name":"Glajzer"},{"first_name":"Dan Cacsire","last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire"},{"full_name":"Richter, Rolf","last_name":"Richter","first_name":"Rolf"},{"last_name":"Vergote","full_name":"Vergote, Ignace","first_name":"Ignace"},{"first_name":"Hagen","last_name":"Kulbe","full_name":"Kulbe, Hagen"},{"last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan","first_name":"Adriaan"},{"first_name":"Ilary","full_name":"Ruscito, Ilary","last_name":"Ruscito"},{"first_name":"Fabian","last_name":"Trillsch","full_name":"Trillsch, Fabian"},{"last_name":"Mustea","full_name":"Mustea, Alexander","first_name":"Alexander"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"full_name":"Gourley, Charlie","last_name":"Gourley","first_name":"Charlie"},{"last_name":"Gabra","full_name":"Gabra, Hani","first_name":"Hani"},{"first_name":"Eliane T.","last_name":"Taube","full_name":"Taube, Eliane T."},{"first_name":"Oliver","full_name":"Dorigo, Oliver","last_name":"Dorigo"},{"full_name":"Horst, David","last_name":"Horst","first_name":"David"},{"first_name":"Carlotta","full_name":"Keunecke, Carlotta","last_name":"Keunecke"},{"first_name":"Joanna","last_name":"Baum","full_name":"Baum, Joanna"},{"first_name":"Timothy","last_name":"Angelotti","full_name":"Angelotti, Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"full_name":"Braicu, Elena Ioana","last_name":"Braicu","first_name":"Elena Ioana"}],"article_processing_charge":"No","external_id":{"isi":["000852125500006"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 35–45.","ieee":"J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3","mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3."},"month":"01","intvolume":" 30","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC."}],"volume":30,"related_material":{"record":[{"id":"12115","status":"public","relation":"other"}]},"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"date_created":"2023-02-02T13:01:20Z","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","creator":"dernst","date_updated":"2023-02-02T13:01:20Z","file_size":365865,"file_id":"12490","checksum":"36a1200e1011f4b2155a8041d0308f34","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"publication_status":"published","status":"public","keyword":["Oncology","Surgery"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12205","file_date_updated":"2023-02-02T13:01:20Z","department":[{"_id":"JoDa"}],"ddc":["610"],"date_updated":"2023-09-05T15:18:37Z"},{"citation":{"ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Jacek","last_name":"Glajzer","full_name":"Glajzer, Jacek"},{"last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire","first_name":"Dan Cacsire"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"last_name":"Vergote","full_name":"Vergote, Ignace","first_name":"Ignace"},{"last_name":"Kulbe","full_name":"Kulbe, Hagen","first_name":"Hagen"},{"first_name":"Adriaan","last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan"},{"first_name":"Ilary","full_name":"Ruscito, Ilary","last_name":"Ruscito"},{"last_name":"Trillsch","full_name":"Trillsch, Fabian","first_name":"Fabian"},{"last_name":"Mustea","full_name":"Mustea, Alexander","first_name":"Alexander"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Charlie","full_name":"Gourley, Charlie","last_name":"Gourley"},{"last_name":"Gabra","full_name":"Gabra, Hani","first_name":"Hani"},{"last_name":"Taube","full_name":"Taube, Eliane T.","first_name":"Eliane T."},{"full_name":"Dorigo, Oliver","last_name":"Dorigo","first_name":"Oliver"},{"full_name":"Horst, David","last_name":"Horst","first_name":"David"},{"first_name":"Carlotta","full_name":"Keunecke, Carlotta","last_name":"Keunecke"},{"last_name":"Baum","full_name":"Baum, Joanna","first_name":"Joanna"},{"last_name":"Angelotti","full_name":"Angelotti, Timothy","first_name":"Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"last_name":"Braicu","full_name":"Braicu, Elena Ioana","first_name":"Elena Ioana"}],"article_processing_charge":"No","external_id":{"isi":["000879151800001"]},"title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","isi":1,"year":"2023","day":"01","publication":"Annals of Surgical Oncology","page":"46-47","doi":"10.1245/s10434-022-12681-z","date_published":"2023-01-01T00:00:00Z","date_created":"2023-01-12T11:56:22Z","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-09-05T15:18:36Z","department":[{"_id":"JoDa"}],"_id":"12115","type":"journal_article","article_type":"original","status":"public","keyword":["Oncology","Surgery"],"publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"12205","status":"public","relation":"other"}]},"volume":30,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1245/s10434-022-12681-z","open_access":"1"}],"month":"01","intvolume":" 30"},{"_id":"12817","status":"public","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-01-10T08:37:48Z","citation":{"ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817.","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.","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12817","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:10.15479/AT:ISTA:12817","mla":"Danzl, Johann G. Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817."},"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","file_date_updated":"2023-05-18T19:51:52Z","department":[{"_id":"JoDa"}],"author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"article_processing_charge":"No","oa_version":"Published Version","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. ","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"abstract":[{"text":"3D-reconstruction of living brain tissue down to 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, 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.","lang":"eng"}],"month":"05","publisher":"Institute of Science and Technology 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Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"author":[{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder"},{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"first_name":"Donglai","full_name":"Wei, Donglai","last_name":"Wei"},{"last_name":"Lin","full_name":"Lin, Zudi","first_name":"Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"full_name":"Beyer, Johanna","last_name":"Beyer","first_name":"Johanna"},{"first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","full_name":"Ben Simon, Yoav"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","last_name":"Cenameri"},{"first_name":"Johannes","last_name":"Broichhagen","full_name":"Broichhagen, Johannes"},{"full_name":"Grant, Seth G.N.","last_name":"Grant","first_name":"Seth G.N."},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"year":"2023","isi":1,"publication":"Nature Methods","day":"01","page":"1256-1265","date_created":"2023-07-23T22:01:13Z","doi":"10.1038/s41592-023-01936-6","date_published":"2023-08-01T00:00:00Z","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"_id":"13267","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}],"record":[{"id":"12817","status":"public","relation":"research_data"},{"relation":"shorter_version","id":"14770","status":"public"}]},"volume":20,"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"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"scopus_import":"1","intvolume":" 20","month":"08"},{"date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"JoDa"}],"_id":"14770","status":"public","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"article_type":"letter_note","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"publication_status":"published","volume":20,"related_material":{"record":[{"relation":"extended_version","id":"13267","status":"public"}]},"issue":"8","oa_version":"None","abstract":[{"text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.","lang":"eng"}],"month":"08","intvolume":" 20","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142."},"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"}],"external_id":{"isi":["001025621500002"]},"article_processing_charge":"No","day":"01","publication":"Nature Methods","isi":1,"year":"2023","date_published":"2023-08-01T00:00:00Z","doi":"10.1038/s41592-023-01937-5","date_created":"2024-01-10T08:07:15Z","page":"1141-1142","publisher":"Springer Nature","quality_controlled":"1"},{"date_created":"2023-06-07T07:15:12Z","doi":"10.15479/AT:ISTA:13126","date_published":"2023-08-04T00:00:00Z","year":"2023","has_accepted_license":"1","day":"04","oa":1,"publisher":"Institute of Science and Technology Austria","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)","article_processing_charge":"No","author":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","citation":{"mla":"Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.","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:10.15479/AT:ISTA:13126","apa":"Danzl, J. G. (2023). 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Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. 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P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 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Nature Physics. 19, 1916–1926."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38075437"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","last_name":"Dunajova"},{"first_name":"Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu"},{"full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","first_name":"Dörte","last_name":"Brandis","full_name":"Brandis, Dörte"},{"full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"},{"full_name":"Wong, Richard W.","last_name":"Wong","first_name":"Richard W."},{"first_name":"Jens","full_name":"Elgeti, Jens","last_name":"Elgeti"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"title":"Chiral and nematic phases of flexible active filaments","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"language":[{"iso":"eng"}],"file":[{"file_id":"14916","checksum":"bc7673ca07d37309013a86166577b2f7","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-01-30T14:28:30Z","file_name":"2023_NaturePhysics_Dunajova.pdf","date_updated":"2024-01-30T14:28:30Z","file_size":22471673,"creator":"dernst"}],"ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"13116","status":"public"}]},"volume":19,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"12","date_updated":"2024-02-21T12:19:08Z","ddc":["530"],"file_date_updated":"2024-01-30T14:28:30Z","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"_id":"13314","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2023","isi":1,"publication":"Nature Biotechnology","day":"31","date_created":"2023-09-03T22:01:15Z","doi":"10.1038/s41587-023-01911-8","date_published":"2023-08-31T00:00:00Z","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"}],"citation":{"short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001065254200001"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","last_name":"Lyudchik"},{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"full_name":"Korinkova, Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Cenameri, Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino"},{"first_name":"Karl","full_name":"Roessler, Karl","last_name":"Roessler"},{"last_name":"Czech","full_name":"Czech, Thomas","first_name":"Thomas"},{"full_name":"Höftberger, Romana","last_name":"Höftberger","first_name":"Romana"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","abstract":[{"lang":"eng","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 disease."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-023-01911-8"}],"scopus_import":"1","month":"08","publication_status":"epub_ahead","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13126"}],"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}]},"_id":"14257","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-02-21T12:18:18Z","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470."},"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","author":[{"first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"day":"09","has_accepted_license":"1","year":"2023","date_published":"2023-01-09T00:00:00Z","doi":"10.15479/at:ista:12470","date_created":"2023-01-31T15:10:53Z","page":"201","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["610"],"supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"date_updated":"2023-08-31T12:26:58Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"file_date_updated":"2023-07-27T22:30:54Z","_id":"12470","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"embargo":"2023-07-09","file_id":"12471","checksum":"1a2306e5f59f52df598e7ecfadf921ac","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"20230109_PhD_thesis_JM_final.pdf","date_created":"2023-01-31T15:11:42Z","file_size":41771714,"date_updated":"2023-07-27T22:30:54Z","creator":"cchlebak"},{"file_size":66983464,"date_updated":"2023-07-10T22:30:04Z","creator":"cchlebak","file_name":"20230109_PhD_thesis_JM_final.docx","date_created":"2023-01-31T15:11:51Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_id":"12472"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11943"},{"id":"11950","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"month":"01","alternative_title":["ISTA Thesis"]}]