{"doi":"10.15479/AT:ISTA:12817","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-10T08:37:48Z","tmp":{"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)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"department":[{"_id":"JoDa"}],"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","license":"https://creativecommons.org/licenses/by-sa/4.0/","citation":{"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>.","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>.","short":"J.G. Danzl, (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. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","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>"},"day":"19","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. ","ddc":["570"],"oa":1,"date_created":"2023-04-07T11:37:40Z","related_material":{"record":[{"id":"13267","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431"},{"last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska"},{"first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Donglai","last_name":"Wei"},{"last_name":"Lin","first_name":"Zudi"},{"first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Troidl","first_name":"Jakob"},{"last_name":"Beyer","first_name":"Johanna"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","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"},{"last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G. N. ","last_name":"Grant"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hanspeter","last_name":"Pfister"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","year":"2023","_id":"12817","type":"research_data","date_published":"2023-05-19T00:00:00Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"file_id":"13030","date_created":"2023-05-18T17:06:12Z","relation":"main_file","checksum":"c1819889e72ec86ee1bba809e19739e0","file_name":"Readme.txt","content_type":"text/plain","access_level":"open_access","file_size":651,"success":1,"date_updated":"2023-05-18T17:06:12Z","creator":"jdanzl"},{"relation":"main_file","checksum":"8f6259fc5128ffcc0cd89d25d51995c1","date_created":"2023-05-18T19:51:52Z","file_id":"13031","content_type":"image/tiff","file_name":"Fig1a_LIONESS.tif","access_level":"open_access","file_size":347448884,"success":1,"creator":"jdanzl","date_updated":"2023-05-18T19:51:52Z"},{"content_type":"image/tiff","file_name":"Fig_1b.tif","checksum":"204e8ef763b5a122fa95a594f5217d83","relation":"main_file","date_created":"2023-05-18T16:48:26Z","file_id":"13029","creator":"jdanzl","date_updated":"2023-05-18T16:48:26Z","success":1,"file_size":91626,"access_level":"open_access"},{"checksum":"dc521a4e6e80a57c100a06ba1e87c766","relation":"main_file","date_created":"2023-05-18T16:48:26Z","file_id":"13028","content_type":"image/tiff","file_name":"Fig_1c.tif","file_size":90300,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T16:48:26Z","success":1},{"date_created":"2023-05-18T16:00:06Z","file_id":"13022","checksum":"56d3d5dbe7e1f54dbecc32ad2d2cc6df","relation":"main_file","file_name":"Figure2a_low_exposure_input.tif","content_type":"image/tiff","file_size":18391928,"access_level":"open_access","date_updated":"2023-05-18T16:00:06Z","creator":"jdanzl","success":1},{"success":1,"date_updated":"2023-05-18T15:59:30Z","creator":"jdanzl","access_level":"open_access","file_size":18392017,"file_name":"Figure2a_LIONESS.tif","content_type":"image/tiff","date_created":"2023-05-18T15:59:30Z","file_id":"13021","relation":"main_file","checksum":"2c30dbd6c4db079f7fdc2eaeea5f9710"},{"access_level":"open_access","file_size":36785440,"success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:58:54Z","checksum":"799868024bf734fecaf36f4ffd843ed2","relation":"main_file","file_id":"13020","date_created":"2023-05-18T15:58:54Z","content_type":"image/tiff","file_name":"Figure2a_merge_LIONESS_EGFP.tif"},{"success":1,"date_updated":"2023-05-18T16:44:45Z","creator":"jdanzl","access_level":"open_access","file_size":670051576,"file_name":"Fig2c_LIONESS.tif","content_type":"image/tiff","date_created":"2023-05-18T16:44:45Z","file_id":"13025","checksum":"522fe0fe505e437d6f637f9b8059dfaa","relation":"main_file"},{"file_name":"Fig2de_LIONESS_1.tif","content_type":"image/tiff","file_id":"13024","date_created":"2023-05-18T16:23:10Z","checksum":"c9c0d873341d2f974ba799fa71a1b789","relation":"main_file","date_updated":"2023-05-18T16:23:10Z","creator":"jdanzl","success":1,"file_size":412478217,"access_level":"open_access"},{"access_level":"open_access","file_size":637360217,"success":1,"date_updated":"2023-05-18T19:48:02Z","creator":"jdanzl","date_created":"2023-05-18T19:48:02Z","file_id":"13032","checksum":"ff86ad8642c56ba1c67c814e20925a85","relation":"main_file","file_name":"Fig2de_LIONESS_2.tif","content_type":"image/tiff"},{"creator":"jdanzl","date_updated":"2023-05-18T14:39:05Z","success":1,"file_size":46563159,"access_level":"open_access","content_type":"application/zip","file_name":"Fig_3_LIONESS.zip","relation":"main_file","checksum":"32681bd33673088193fad9f9c7b79090","file_id":"12995","date_created":"2023-05-18T14:39:05Z"},{"file_name":"Fig_4_LIONESS_synaptic_markers.zip","content_type":"application/zip","date_created":"2023-05-18T15:04:40Z","file_id":"13001","relation":"main_file","checksum":"17239ed0f54ac7495e2b1daa5d0864ef","success":1,"date_updated":"2023-05-18T15:04:40Z","creator":"jdanzl","access_level":"open_access","file_size":29159397},{"checksum":"c060c898f2bf93312a4c07dfdcb745cb","relation":"main_file","file_id":"12997","date_created":"2023-05-18T14:58:09Z","content_type":"application/zip","file_name":"Fig_5a_time_series_Ca2+_imaging.zip","file_size":16563855,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T14:58:09Z","success":1},{"success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:55:44Z","access_level":"open_access","file_size":30632526,"content_type":"image/tiff","file_name":"Fig5b_LIONESS_T1.tif","checksum":"85b4c0cd099212ecf0beec3a78bb35c5","relation":"main_file","file_id":"13017","date_created":"2023-05-18T15:55:44Z"},{"access_level":"open_access","file_size":57634426,"success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:57:40Z","checksum":"eb83649a0ebc2f5ea7a0308324ebf308","relation":"main_file","file_id":"13018","date_created":"2023-05-18T15:57:40Z","content_type":"image/tiff","file_name":"Fig5b_LIONESS_T2.tif"},{"file_name":"Extended_Data_Figure 3a_low_exposure.tif","content_type":"image/tiff","file_id":"13005","date_created":"2023-05-18T15:14:33Z","checksum":"40a2d93a34f83ce37043d8414d981b3d","relation":"main_file","date_updated":"2023-05-18T15:14:33Z","creator":"jdanzl","success":1,"file_size":12512676,"access_level":"open_access"},{"file_name":"Extended_Data_Figure 3a_high_exposure.tif","content_type":"image/tiff","date_created":"2023-05-18T15:15:01Z","file_id":"13006","relation":"main_file","checksum":"516521bb400f5c058184994b57165f8b","date_updated":"2023-05-18T15:15:01Z","creator":"jdanzl","success":1,"file_size":12512678,"access_level":"open_access"},{"success":1,"date_updated":"2023-05-18T15:17:08Z","creator":"jdanzl","access_level":"open_access","file_size":50038242,"file_name":"Extended_Data_Figure 3a_restored.tif","content_type":"image/tiff","date_created":"2023-05-18T15:17:08Z","file_id":"13007","checksum":"1d3a21970307de2d84b614985ec0706d","relation":"main_file"},{"success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:56:57Z","access_level":"open_access","file_size":68298045,"content_type":"image/tiff","file_name":"Extended_Data_Figure 3b_example dataset_low_exposure_input.tif","checksum":"441575853bf667ed89cc218079cc397b","relation":"main_file","file_id":"13016","date_created":"2023-05-18T15:56:57Z"},{"file_id":"13015","date_created":"2023-05-18T15:54:43Z","checksum":"e499355760270e14bcf12bdc7960bd7a","relation":"main_file","file_name":"Extended_Data_Figure 3b_example dataset_merge_LIONESS_EGFP.tif","content_type":"image/tiff","file_size":136597524,"access_level":"open_access","date_updated":"2023-05-18T15:54:43Z","creator":"jdanzl","success":1},{"content_type":"image/tiff","file_name":"Extended_Data_Figure 3b_dataset_1_merge_LIONESS_EGFP.tif","relation":"main_file","checksum":"add9f1adc6763091233dbe8504f1c396","date_created":"2023-05-18T15:50:19Z","file_id":"13014","success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:50:19Z","access_level":"open_access","file_size":76103800},{"creator":"jdanzl","date_updated":"2023-05-18T15:51:20Z","success":1,"file_size":49810007,"access_level":"open_access","content_type":"image/tiff","file_name":"Extended_Data_Figure 3b_dataset_2_merge_LIONESS_EGFP.tif","relation":"main_file","checksum":"311719efb1c68d7243be557b779173f2","date_created":"2023-05-18T15:51:20Z","file_id":"13013"},{"file_name":"Extended_Data_Figure 3b_dataset_3_merge_LIONESS_EGFP.tif","content_type":"image/tiff","file_id":"13010","date_created":"2023-05-18T15:32:55Z","relation":"main_file","checksum":"8d5d9d859f8d099bb3b877c4e455f699","date_updated":"2023-05-18T15:32:55Z","creator":"jdanzl","success":1,"file_size":169060658,"access_level":"open_access"},{"file_name":"Extended_Data_Figure 3b_dataset_4_merge_LIONESS_EGFP.tif","content_type":"image/tiff","date_created":"2023-05-18T15:47:03Z","file_id":"13011","checksum":"79eca23cc5e2fc1fe26e03e1bba2e90f","relation":"main_file","date_updated":"2023-05-18T15:47:03Z","creator":"jdanzl","success":1,"file_size":169060658,"access_level":"open_access"},{"success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:47:47Z","access_level":"open_access","file_size":244861000,"content_type":"image/tiff","file_name":"Extended_Data_Figure 3b_dataset_5_merge_LIONESS_EGFP.tif","relation":"main_file","checksum":"107bf2e0f8a14b4bd0169c9104765171","file_id":"13012","date_created":"2023-05-18T15:47:47Z"},{"file_size":76795968,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T14:36:34Z","success":1,"relation":"main_file","checksum":"b71e4a090dd9a8048aee847ae47624f0","file_id":"12994","date_created":"2023-05-18T14:36:34Z","content_type":"application/zip","file_name":"Extended_Data_Fig_4_LIONESS_TIF_stacks.zip"},{"file_name":"Extended_Data_Fig5b.tif","content_type":"image/tiff","file_id":"13023","date_created":"2023-05-18T16:09:31Z","relation":"main_file","checksum":"ea011c3d1966ba79a62e8cf775e595c5","date_updated":"2023-05-18T16:09:31Z","creator":"jdanzl","success":1,"file_size":288330201,"access_level":"open_access"},{"access_level":"open_access","file_size":255976297,"success":1,"date_updated":"2023-05-18T15:21:29Z","creator":"jdanzl","file_id":"13003","date_created":"2023-05-18T15:21:29Z","relation":"main_file","checksum":"1c56b5b324b6270b0df72a77e1e9d6f1","file_name":"Extended_Data_Fig_6_TIF_stacks.zip","content_type":"application/zip"},{"file_id":"13002","date_created":"2023-05-18T15:08:20Z","checksum":"89150ebb0044ead282b9048e55cd3961","relation":"main_file","file_name":"Extended_Data_Fig_7.zip","content_type":"application/zip","file_size":70694476,"access_level":"open_access","date_updated":"2023-05-18T15:08:20Z","creator":"jdanzl","success":1},{"access_level":"open_access","file_size":57634426,"success":1,"creator":"jdanzl","date_updated":"2023-05-18T16:46:36Z","relation":"main_file","checksum":"81e79a6d4e6745dce63cdad94bfcdca4","file_id":"13026","date_created":"2023-05-18T16:46:36Z","content_type":"image/tiff","file_name":"Extended_Data_Fig_8b_T1.tif"},{"date_created":"2023-05-18T16:48:26Z","file_id":"13027","checksum":"53da2b10969a185239b317be0ffa61ef","relation":"main_file","file_name":"Extended_Data_Fig_8b_T2.tif","content_type":"image/tiff","file_size":57634426,"access_level":"open_access","date_updated":"2023-05-18T16:48:26Z","creator":"jdanzl","success":1},{"file_name":"Extended_Data_Fig_8c_png.zip","content_type":"application/zip","file_id":"12999","date_created":"2023-05-18T15:02:09Z","relation":"main_file","checksum":"9a97ccd3eb0c75a5c4f142e5dadc0fb3","success":1,"date_updated":"2023-05-18T15:02:09Z","creator":"jdanzl","access_level":"open_access","file_size":2942961},{"file_size":11949362,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T15:17:38Z","success":1,"checksum":"baaee60e695160118ea2167c6cb91775","relation":"main_file","file_id":"13008","date_created":"2023-05-18T15:17:38Z","content_type":"image/tiff","file_name":"Extended_Data_Fig9c_LIONESS.tif"},{"checksum":"095a980d0d746bc2277b0586dbb9d652","relation":"main_file","date_created":"2023-05-18T15:02:00Z","file_id":"12998","content_type":"application/zip","file_name":"Extended_Data_Fig_10_LIONESS_tif_xy_view.zip","file_size":72553526,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T15:02:00Z","success":1},{"access_level":"open_access","file_size":72906090,"success":1,"date_updated":"2023-05-18T14:22:43Z","creator":"jdanzl","date_created":"2023-05-18T14:22:43Z","file_id":"12992","relation":"main_file","checksum":"343b87c4842eab9e5086f248668dec84","file_name":"Extended_Data_Fig_10_LIONESS_tif_xz_view.zip","content_type":"application/zip"},{"relation":"main_file","checksum":"c3d4970e5185f72cb89f36005e83a556","date_created":"2023-05-18T15:14:01Z","file_id":"13004","content_type":"application/zip","file_name":"Supplementary_Fig_4.zip","access_level":"open_access","file_size":428208,"success":1,"creator":"jdanzl","date_updated":"2023-05-18T15:14:01Z"},{"file_name":"Supplementary_Fig_8.zip","content_type":"application/zip","file_id":"12991","date_created":"2023-05-18T14:32:29Z","checksum":"f451852622f8ba8992582ab9b57c49e5","relation":"main_file","date_updated":"2023-05-18T14:32:29Z","creator":"jdanzl","success":1,"file_size":230506869,"access_level":"open_access"},{"creator":"jdanzl","date_updated":"2023-05-18T16:00:15Z","success":1,"file_size":40406386,"access_level":"open_access","content_type":"image/tiff","file_name":"Suppl_Fig_11_LIONESS.tif","relation":"main_file","checksum":"874b524f38fad6b86be14326bb5aa706","date_created":"2023-05-18T16:00:15Z","file_id":"13019"},{"access_level":"open_access","file_size":357705621,"success":1,"date_updated":"2023-05-18T14:57:18Z","creator":"jdanzl","file_id":"12996","date_created":"2023-05-18T14:57:18Z","checksum":"7ab5cc6c581c463d1d7e430399b8b384","relation":"main_file","file_name":"Supplementary_Fig_12.zip","content_type":"application/zip"},{"relation":"main_file","checksum":"9763330288c2d544a3e1d7bc12657ee8","file_id":"13009","date_created":"2023-05-18T15:39:45Z","content_type":"image/tiff","file_name":"Supplementary_Fig_13.tif","file_size":617709326,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T15:39:45Z","success":1},{"file_size":9387873,"access_level":"open_access","creator":"jdanzl","date_updated":"2023-05-18T14:19:48Z","success":1,"relation":"main_file","checksum":"1e83b64e220694942ccf0ca70f17e33b","date_created":"2023-05-18T14:19:48Z","file_id":"12990","content_type":"application/zip","file_name":"GCaMP_recording_overview_time_series_Suppl_Video_5.zip"},{"content_type":"application/zip","file_name":"CARE model.zip","relation":"main_file","checksum":"fc7208299e6393e69b31a0051fa5ac2e","file_id":"12993","date_created":"2023-05-18T15:13:55Z","creator":"jdanzl","date_updated":"2023-05-18T15:13:55Z","success":1,"file_size":1218458059,"access_level":"open_access"},{"access_level":"open_access","file_size":19052980,"success":1,"date_updated":"2023-05-18T15:03:10Z","creator":"jdanzl","file_id":"13000","date_created":"2023-05-18T15:03:10Z","relation":"main_file","checksum":"47db2185ff2c6ba9b059c9b1a8882832","file_name":"Segmentation model.zip","content_type":"application/zip"}],"has_accepted_license":"1","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"}],"status":"public","author":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-05-18T19:51:52Z"}