[{"external_id":{"pmid":["39930095"],"isi":["001416866800001"]},"intvolume":"        28","oa_version":"Published Version","day":"01","isi":1,"type":"journal_article","year":"2025","department":[{"_id":"MaJö"},{"_id":"PreCl"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"publisher":"Springer Nature","ec_funded":1,"doi":"10.1038/s41593-025-01874-w","citation":{"ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2025. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Nature Neuroscience. 28, 7278.","chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” <i>Nature Neuroscience</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41593-025-01874-w\">https://doi.org/10.1038/s41593-025-01874-w</a>.","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2025). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-025-01874-w\">https://doi.org/10.1038/s41593-025-01874-w</a>","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, Nature Neuroscience 28 (2025).","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. <i>Nature Neuroscience</i>. 2025;28. doi:<a href=\"https://doi.org/10.1038/s41593-025-01874-w\">10.1038/s41593-025-01874-w</a>","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics,” <i>Nature Neuroscience</i>, vol. 28. Springer Nature, 2025.","mla":"Vega Zuniga, Tomas A., et al. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” <i>Nature Neuroscience</i>, vol. 28, 7278, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41593-025-01874-w\">10.1038/s41593-025-01874-w</a>."},"has_accepted_license":"1","publication":"Nature Neuroscience","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1038/s41593-025-01874-w","open_access":"1"}],"pmid":1,"ddc":["570"],"author":[{"last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A"},{"orcid":"0000-0002-4792-1881","first_name":"Anton L","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","full_name":"Schmidt, Florian","id":"A2EF226A-AF19-11E9-924C-0525E6697425","last_name":"Schmidt"},{"full_name":"Jösch, Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"}],"OA_type":"hybrid","OA_place":"publisher","date_created":"2025-02-23T23:01:58Z","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"article_number":"7278","article_type":"original","abstract":[{"text":"For accurate perception and motor control, an animal must distinguish between sensory experiences elicited by external stimuli and those elicited by its own actions. The diversity of behaviors and their complex influences on the senses make this distinction challenging. Here, we uncover an action–cue hub that coordinates motor commands with visual processing in the brain’s first visual relay. We show that the ventral lateral geniculate nucleus (vLGN) acts as a corollary discharge center, integrating visual translational optic flow signals with motor copies from saccades, locomotion and pupil dynamics. The vLGN relays these signals to correct action-specific visual distortions and to refine perception, as shown for the superior colliculus and in a depth-estimation task. Simultaneously, brain-wide vLGN projections drive corrective actions necessary for accurate visuomotor control. Our results reveal an extended corollary discharge architecture that refines early visual transformations and coordinates actions via a distributed hub-and-spoke network to enable visual perception during action.","lang":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"18579","status":"public"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/high-tech-video-optimization-in-our-brain/","description":"News on ISTA Website"}]},"fulldoi":"https://doi.org/10.1038/s41593-025-01874-w","acknowledgement":"We thank Y. Ben-Simon for generously making viral vectors for retrograde tracing available, as well as J. Watson and F. Marr for reagents. We also thank R. Shigemoto, W. Młynarski and members of the Neuroethology group for their comments on the manuscript and L. Burnett for her schematic drawings. This research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility and the Imaging and Optics Facility, in particular F. Lange, M. Schunn and T. Asenov. This work was supported by European Research Council Starting Grant no. 756502 (M.J.) and European Research Council Consolidator Grant no. 101086580 (M.J.); and EMBO ALTF grant no. 1098-2017 (A.S.) and Human Frontiers Science Program grant no. LT000256/2018-L (A.S.). Open access funding provided by Institute of Science and Technology (IST Austria).","scopus_import":"1","date_published":"2025-03-01T00:00:00Z","_id":"19076","quality_controlled":"1","corr_author":"1","date_updated":"2026-06-18T18:12:08Z","status":"public","volume":28,"title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","oa":1,"project":[{"name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"756502"},{"_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses"},{"grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"}],"month":"03"},{"day":"15","oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"citation":{"ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024.","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>","mla":"Burnett, Laura, et al. <i>Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>."},"keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.15479/AT:ISTA:15385","publisher":"Institute of Science and Technology Austria","type":"research_data","department":[{"_id":"MaJö"},{"_id":"PreCl"},{"_id":"SiHi"},{"_id":"RySh"},{"_id":"GaNo"}],"year":"2024","abstract":[{"lang":"eng","text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)"}],"acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ","file":[{"success":1,"checksum":"9205eb0876f0f08552dbad80d6884b4b","file_size":"1149617663","date_updated":"2024-05-15T06:09:17Z","file_name":"PatchClamp.zip","relation":"main_file","date_created":"2024-05-15T06:09:17Z","access_level":"open_access","file_id":"15396","content_type":"application/zip","creator":"mjoesch"},{"date_updated":"2024-05-15T06:09:12Z","file_size":"564903112","success":1,"creator":"mjoesch","content_type":"application/zip","access_level":"open_access","file_id":"15397","relation":"main_file","file_name":"SiliconProbe.zip","date_created":"2024-05-15T06:09:12Z"},{"access_level":"open_access","file_id":"15398","creator":"mjoesch","content_type":"application/zip","date_created":"2024-05-15T06:09:14Z","file_name":"WesternBlot.zip","relation":"main_file","date_updated":"2024-05-15T06:09:14Z","success":1,"file_size":"11685703","checksum":"49a807bbab06b5fada38f532e2176e2e"},{"file_size":"1335626779","checksum":"beeeeaa43770090f3b291209ed6b0623","success":1,"date_updated":"2024-05-15T06:09:38Z","date_created":"2024-05-15T06:09:38Z","relation":"main_file","file_name":"Behaviour.zip","content_type":"application/zip","creator":"mjoesch","access_level":"open_access","file_id":"15399"},{"success":1,"checksum":"8862ad7719388304d1d19f8e7db8bb00","file_size":18841,"date_updated":"2024-05-16T09:08:20Z","date_created":"2024-05-16T09:08:20Z","file_name":"Readme_Data.txt","relation":"main_file","file_id":"15400","access_level":"open_access","content_type":"text/plain","creator":"mjoesch"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:15385","related_material":{"record":[{"status":"public","id":"17142","relation":"used_in_publication"}]},"date_created":"2024-05-13T15:04:04Z","author":[{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura","first_name":"Laura","orcid":"0000-0002-8937-410X"},{"full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","first_name":"Peter"},{"first_name":"Olga","orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga"},{"first_name":"Tomas","orcid":"0000-0002-2634-6283","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson","full_name":"Masson, Tomas"},{"first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga"},{"first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"}],"ddc":["570"],"month":"05","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","status":"public","file_date_updated":"2024-05-16T09:08:20Z","oa":1,"date_updated":"2025-09-08T07:57:11Z","corr_author":"1","date_published":"2024-05-15T00:00:00Z","_id":"15385"},{"date_updated":"2025-09-08T07:57:11Z","DOAJ_listed":"1","quality_controlled":"1","corr_author":"1","_id":"17142","date_published":"2024-06-10T00:00:00Z","scopus_import":"1","month":"06","project":[{"name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2025-01-09T10:39:41Z","oa":1,"title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","status":"public","volume":22,"author":[{"full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","orcid":"0000-0002-8937-410X","first_name":"Laura"},{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter","orcid":"0000-0002-3509-1948"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947"},{"orcid":"0000-0002-2634-6283","first_name":"Tomas","full_name":"Masson, Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson"},{"first_name":"Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A"},{"first_name":"Ximena","full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"}],"OA_type":"gold","ddc":["570"],"pmid":1,"acknowledgement":"This work was supported by a European Research Council Starting Grant 756502 (MJ). ","file":[{"success":1,"checksum":"496e1aa4fd5b92b7e4087ecc2c964133","file_size":4016568,"date_updated":"2025-01-09T10:39:41Z","date_created":"2025-01-09T10:39:41Z","file_name":"2024_PloS_Burnett.pdf","relation":"main_file","access_level":"open_access","file_id":"18805","creator":"dernst","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.1371/journal.pbio.3002668","related_material":{"record":[{"relation":"research_data","status":"public","id":"15385"}],"link":[{"url":"https://doi.org/10.5281/zenodo.11130587","relation":"software"}]},"abstract":[{"lang":"eng","text":"Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD."}],"article_type":"original","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"article_number":"e3002668","date_created":"2024-06-16T22:01:05Z","OA_place":"publisher","APC_amount":"6081,83 EUR","ec_funded":1,"doi":"10.1371/journal.pbio.3002668","publisher":"Public Library of Science","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","department":[{"_id":"RySh"},{"_id":"GaNo"},{"_id":"MaJö"}],"year":"2024","type":"journal_article","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"Yes","publication":"PLoS Biology","has_accepted_license":"1","citation":{"ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 22, e3002668.","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” <i>PLoS Biology</i>, vol. 22. Public Library of Science, 2024.","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22 (2024).","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>.","mla":"Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>, vol. 22, e3002668, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>."},"external_id":{"pmid":["38857283"],"isi":["001246176800003"]},"day":"10","oa_version":"Published Version","intvolume":"        22"},{"_id":"18444","date_published":"2024-10-12T00:00:00Z","scopus_import":"1","date_updated":"2026-06-10T07:58:34Z","DOAJ_listed":"1","quality_controlled":"1","corr_author":"1","file_date_updated":"2024-10-21T12:11:10Z","oa":1,"title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","volume":15,"status":"public","month":"10","project":[{"name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716"}],"pmid":1,"ddc":["570"],"OA_type":"gold","author":[{"first_name":"Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria"},{"full_name":"Satapathy, Roshan K","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy","orcid":"0009-0006-2974-5075","first_name":"Roshan K"},{"first_name":"Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"}],"date_created":"2024-10-20T22:02:05Z","OA_place":"publisher","APC_amount":"6828 EUR","acknowledgement":"We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance with the reconstruction experiments. We would also like to thank Laura Burnett for drawing scientific illustrations used in the figures. We are particularly grateful to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing material support and technical advice. We are grateful to Daria Siekhaus, Eugenia Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory for valuable discussions and comments on the manuscript. Stocks from the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center were used in this study. The Scientific Service Units of ISTA supported the project through resources provided by the Imaging and Optics Facility, MIBA Machine Shop, and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the SPP 2205 – 429960716 (M.J.).","file":[{"date_updated":"2024-10-21T12:11:10Z","checksum":"2af4d6e7364329107aa94d072d594ce0","file_size":8276667,"success":1,"content_type":"application/pdf","creator":"dernst","file_id":"18459","access_level":"open_access","date_created":"2024-10-21T12:11:10Z","relation":"main_file","file_name":"2024_NatureComm_Pokusaeva.pdf"}],"fulldoi":"https://doi.org/10.1038/s41467-024-53173-w","related_material":{"record":[{"id":"18568","status":"public","relation":"dissertation_contains"},{"status":"public","id":"17488","relation":"research_data"}]},"abstract":[{"text":"Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations.","lang":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"article_number":"8830","article_type":"original","department":[{"_id":"MaJö"}],"year":"2024","type":"journal_article","isi":1,"doi":"10.1038/s41467-024-53173-w","publisher":"Springer Nature","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"citation":{"ista":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 15, 8830.","mla":"Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>, vol. 15, 8830, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>.","chicago":"Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>.","short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024).","apa":"Pokusaeva, V., Satapathy, R. K., Symonova, O., &#38; Jösch, M. A. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>","ama":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>","ieee":"V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024."},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"Yes","publication":"Nature Communications","has_accepted_license":"1","external_id":{"pmid":["39396050"],"isi":["001336422500001"]},"intvolume":"        15","day":"12","oa_version":"Published Version"},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","ec_funded":1,"doi":"10.15479/AT:ISTA:18579","type":"research_data","year":"2024","department":[{"_id":"MaJö"}],"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","citation":{"ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","mla":"Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>","chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>.","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024).","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024.","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>"},"oa_version":"Published Version","day":"09","corr_author":"1","date_updated":"2026-06-18T18:12:08Z","date_published":"2024-12-09T00:00:00Z","_id":"18579","project":[{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"756502","name":"Circuits of Visual Attention"},{"_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses"}],"month":"12","status":"public","title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","oa":1,"file_date_updated":"2024-12-09T12:54:55Z","author":[{"first_name":"Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser","full_name":"Sumser, Anton L","first_name":"Anton L","orcid":"0000-0002-4792-1881"},{"first_name":"Olga","orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga"},{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter","orcid":"0000-0002-3509-1948"},{"id":"A2EF226A-AF19-11E9-924C-0525E6697425","last_name":"Schmidt","full_name":"Schmidt, Florian","first_name":"Florian"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"}],"ddc":["570"],"abstract":[{"text":"Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. ","lang":"eng"}],"file":[{"date_created":"2024-12-06T13:28:18Z","relation":"main_file","file_name":"electro_physiology_data.zip","content_type":"application/x-zip-compressed","creator":"symonova","access_level":"open_access","file_id":"18625","checksum":"8b13990ca1a458ae3f3ae54c2e888564","file_size":800647957,"date_updated":"2024-12-09T10:24:25Z"},{"file_id":"18636","access_level":"open_access","content_type":"application/x-zip-compressed","creator":"symonova","file_name":"NN_vLGN_Ca_data.zip","relation":"main_file","date_created":"2024-12-09T10:21:10Z","date_updated":"2024-12-09T10:21:10Z","success":1,"file_size":828410832,"checksum":"c5a4d71c5f29c009c3d96a3244532afa"},{"date_created":"2024-12-09T12:54:55Z","file_name":"readme.txt","relation":"main_file","file_id":"18637","access_level":"open_access","creator":"symonova","content_type":"text/plain","success":1,"file_size":505,"checksum":"63651df0186196969553dc48b467f6ab","date_updated":"2024-12-09T12:54:55Z"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:18579","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"19076"}]},"acknowledgement":"Freyja Lange, Michael Schunn, and Todor Asenov","OA_place":"publisher","date_created":"2024-11-22T13:48:12Z"},{"publisher":"Institute of Science and Technology Austria","corr_author":"1","date_updated":"2026-06-10T07:58:35Z","doi":"10.15479/AT:ISTA:17488","acknowledged_ssus":[{"_id":"M-Shop"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","_id":"17488","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"year":"2024","type":"research_data","date_published":"2024-09-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","project":[{"name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716"}],"has_accepted_license":"1","month":"09","oa":1,"file_date_updated":"2024-09-03T17:39:32Z","keyword":["drosophila","behaviour","locomotion","gap junctions"],"status":"public","citation":{"ieee":"R. K. Satapathy, M. A. Jösch, O. Symonova, and V. Pokusaeva, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies.” Institute of Science and Technology Austria, 2024.","ama":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>","apa":"Satapathy, R. K., Jösch, M. A., Symonova, O., &#38; Pokusaeva, V. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>","chicago":"Satapathy, Roshan K, Maximilian A Jösch, Olga Symonova, and Victoria Pokusaeva. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>.","short":"R.K. Satapathy, M.A. Jösch, O. Symonova, V. Pokusaeva, (2024).","mla":"Satapathy, Roshan K., et al. <i>Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>.","ista":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>."},"title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","author":[{"orcid":"0009-0006-2974-5075","first_name":"Roshan K","full_name":"Satapathy, Roshan K","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"},{"orcid":"0000-0003-2012-9947","first_name":"Olga","full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pokusaeva","id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria","first_name":"Victoria","orcid":"0000-0001-7660-444X"}],"ddc":["570"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:17488","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"18444"}]},"file":[{"date_updated":"2024-09-03T17:39:32Z","file_size":965778072,"checksum":"df9d6c8ddffa046c3b1639281f83cfcf","success":1,"creator":"rsatapat","content_type":"application/x-zip-compressed","access_level":"open_access","file_id":"17489","date_created":"2024-09-03T17:39:32Z","relation":"main_file","file_name":"BehaviouralData.zip"}],"oa_version":"Published Version","abstract":[{"text":"Behavioural data for Pokusaeva, Satapathy et al. Relevant information can be found in the 'README.txt' file.","lang":"eng"}],"date_created":"2024-09-03T17:42:46Z"},{"external_id":{"pmid":["36959418"],"isi":["000955258300002"]},"intvolume":"        26","day":"01","oa_version":"Published Version","type":"journal_article","isi":1,"year":"2023","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1038/s41593-023-01280-0","ec_funded":1,"publisher":"Springer Nature","citation":{"ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” <i>Nature Neuroscience</i>, vol. 26. Springer Nature, pp. 606–614, 2023.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>, vol. 26, Springer Nature, 2023, pp. 606–14, doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>."},"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"Yes (in subscription journal)","publication":"Nature Neuroscience","ddc":["570"],"pmid":1,"author":[{"first_name":"Divyansh","orcid":"0000-0001-7400-6665","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Divyansh"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F"},{"full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser","orcid":"0000-0002-4792-1881","first_name":"Anton L"},{"full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","first_name":"Olga"},{"first_name":"Jan","orcid":"0000-0002-6198-2939","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","last_name":"Svaton","full_name":"Svaton, Jan"},{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"}],"date_created":"2023-01-23T14:14:19Z","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types."}],"article_type":"original","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","related_material":{"record":[{"id":"12370","status":"public","relation":"research_data"},{"id":"18574","status":"public","relation":"dissertation_contains"}]},"fulldoi":"https://doi.org/10.1038/s41593-023-01280-0","file":[{"file_size":6144866,"checksum":"a33d91e398e548f34003170e10988368","success":1,"date_updated":"2023-10-04T11:40:51Z","relation":"main_file","file_name":"2023_NatureNeuroscience_Gupta.pdf","date_created":"2023-10-04T11:40:51Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_id":"14395"}],"date_published":"2023-04-01T00:00:00Z","scopus_import":"1","_id":"12349","date_updated":"2026-09-11T22:30:35Z","corr_author":"1","quality_controlled":"1","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","status":"public","volume":26,"file_date_updated":"2023-10-04T11:40:51Z","page":"606-614","oa":1,"month":"04","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017"}]},{"citation":{"mla":"Symonova, Olga, et al. <i>Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>."},"status":"public","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","month":"06","article_processing_charge":"No","date_published":"2015-06-01T00:00:00Z","type":"research_data_reference","_id":"9737","year":"2015","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0127657.s001","date_updated":"2025-09-23T08:30:43Z","date_created":"2021-07-28T06:20:13Z","day":"01","oa_version":"Published Version","fulldoi":"https://doi.org/10.1371/journal.pone.0127657.s001","related_material":{"record":[{"id":"1793","status":"public","relation":"used_in_publication"}]},"author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947"},{"last_name":"Topp","full_name":"Topp, Christopher","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"}]},{"date_updated":"2025-09-23T08:30:43Z","corr_author":"1","quality_controlled":"1","_id":"1793","date_published":"2015-06-01T00:00:00Z","scopus_import":"1","publist_id":"5318","month":"06","file_date_updated":"2020-07-14T12:45:16Z","pubrep_id":"454","oa":1,"title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","volume":10,"status":"public","author":[{"first_name":"Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga"},{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"file":[{"date_created":"2018-12-12T10:15:30Z","relation":"main_file","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","creator":"system","content_type":"application/pdf","access_level":"open_access","file_id":"5150","file_size":1850825,"checksum":"d20f26461ca575276ad3ed9ce4bfc787","date_updated":"2020-07-14T12:45:16Z"}],"fulldoi":"https://doi.org/10.1371/journal.pone.0127657","related_material":{"record":[{"status":"public","relation":"research_data","id":"9737"}]},"abstract":[{"lang":"eng","text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth."}],"article_number":"e0127657","date_created":"2018-12-11T11:54:02Z","doi":"10.1371/journal.pone.0127657","publisher":"Public Library of Science","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"year":"2015","issue":"6","type":"journal_article","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","publication":"PLoS One","has_accepted_license":"1","citation":{"apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” <i>PLoS One</i>, vol. 10, no. 6. Public Library of Science, 2015.","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. 2015;10(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657."},"external_id":{"isi":["000356630900069"]},"oa_version":"Published Version","day":"01","intvolume":"        10"},{"date_created":"2018-12-11T11:59:47Z","fulldoi":"https://doi.org/10.1073/pnas.1304354110","abstract":[{"text":"Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped &gt;1,400 3D root models and &gt;57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.","lang":"eng"}],"pmid":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/"}],"author":[{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali"},{"first_name":"Jill","last_name":"Anderson","full_name":"Anderson, Jill"},{"first_name":"Cheng","last_name":"Lee","full_name":"Lee, Cheng"},{"first_name":"Paul","full_name":"Zurek, Paul","last_name":"Zurek"},{"full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","first_name":"Olga"},{"full_name":"Zheng, Ying","last_name":"Zheng","first_name":"Ying"},{"full_name":"Bucksch, Alexander","last_name":"Bucksch","first_name":"Alexander"},{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"first_name":"Taras","last_name":"Galkovskyi","full_name":"Galkovskyi, Taras"},{"full_name":"Moore, Brad","last_name":"Moore","first_name":"Brad"},{"first_name":"John","last_name":"Harer","full_name":"Harer, John"},{"first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Mitchell Olds","full_name":"Mitchell Olds, Thomas","first_name":"Thomas"},{"full_name":"Weitz, Joshua","last_name":"Weitz","first_name":"Joshua"},{"first_name":"Philip","last_name":"Benfey","full_name":"Benfey, Philip"}],"page":"E1695 - E1704","oa":1,"title":"3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture","status":"public","volume":110,"month":"04","_id":"2822","date_published":"2013-04-30T00:00:00Z","publist_id":"3979","scopus_import":"1","date_updated":"2025-09-29T13:57:21Z","quality_controlled":"1","intvolume":"       110","day":"30","oa_version":"Submitted Version","external_id":{"pmid":["25673779"],"isi":["000318682300008"]},"citation":{"ista":"Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704.","ama":"Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. <i>PNAS</i>. 2013;110(18):E1695-E1704. doi:<a href=\"https://doi.org/10.1073/pnas.1304354110\">10.1073/pnas.1304354110</a>","ieee":"C. Topp <i>et al.</i>, “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” <i>PNAS</i>, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013.","chicago":"Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1304354110\">https://doi.org/10.1073/pnas.1304354110</a>.","apa":"Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1304354110\">https://doi.org/10.1073/pnas.1304354110</a>","short":"C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704.","mla":"Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” <i>PNAS</i>, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:<a href=\"https://doi.org/10.1073/pnas.1304354110\">10.1073/pnas.1304354110</a>."},"article_processing_charge":"No","publication":"PNAS","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"issue":"18","year":"2013","type":"journal_article","isi":1,"doi":"10.1073/pnas.1304354110","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published"},{"day":"06","oa_version":"Submitted Version","type":"conference","year":"2012","department":[{"_id":"HeEd"},{"_id":"MaJö"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_status":"published","publisher":"IEEE","doi":"10.1109/ISVD.2012.11","citation":{"ista":"Edelsbrunner H, Symonova O. 2012. The adaptive topology of a digital image. ISVD: International Symposium on Voronoi Diagrams in Science and Engineering, 41–48.","ieee":"H. Edelsbrunner and O. Symonova, “The adaptive topology of a digital image,” presented at the ISVD: International Symposium on Voronoi Diagrams in Science and Engineering, New Brunswick, NJ, USA , 2012, pp. 41–48.","ama":"Edelsbrunner H, Symonova O. The adaptive topology of a digital image. In: IEEE; 2012:41-48. doi:<a href=\"https://doi.org/10.1109/ISVD.2012.11\">10.1109/ISVD.2012.11</a>","apa":"Edelsbrunner, H., &#38; Symonova, O. (2012). The adaptive topology of a digital image (pp. 41–48). Presented at the ISVD: International Symposium on Voronoi Diagrams in Science and Engineering, New Brunswick, NJ, USA : IEEE. <a href=\"https://doi.org/10.1109/ISVD.2012.11\">https://doi.org/10.1109/ISVD.2012.11</a>","chicago":"Edelsbrunner, Herbert, and Olga Symonova. “The Adaptive Topology of a Digital Image,” 41–48. IEEE, 2012. <a href=\"https://doi.org/10.1109/ISVD.2012.11\">https://doi.org/10.1109/ISVD.2012.11</a>.","short":"H. Edelsbrunner, O. Symonova, in:, IEEE, 2012, pp. 41–48.","mla":"Edelsbrunner, Herbert, and Olga Symonova. <i>The Adaptive Topology of a Digital Image</i>. IEEE, 2012, pp. 41–48, doi:<a href=\"https://doi.org/10.1109/ISVD.2012.11\">10.1109/ISVD.2012.11</a>."},"conference":{"start_date":"2012-06-27","name":"ISVD: International Symposium on Voronoi Diagrams in Science and Engineering","end_date":"2012-06-29","location":"New Brunswick, NJ, USA "},"has_accepted_license":"1","ddc":["000"],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947"}],"date_created":"2018-12-11T12:00:15Z","abstract":[{"lang":"eng","text":"In order to enjoy a digital version of the Jordan Curve Theorem, it is common to use the closed topology for the foreground and the open topology for the background of a 2-dimensional binary image. In this paper, we introduce a single topology that enjoys this theorem for all thresholds decomposing a real-valued image into foreground and background. This topology is easy to construct and it generalizes to n-dimensional images."}],"fulldoi":"https://doi.org/10.1109/ISVD.2012.11","file":[{"file_id":"4765","access_level":"open_access","creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:09:41Z","file_name":"IST-2016-545-v1+1_2012-P-10-AdaptiveTopology.pdf","relation":"main_file","date_updated":"2020-07-14T12:45:52Z","file_size":760548,"checksum":"444869a4e8abf07834f88b6e5cb5e9c3"}],"scopus_import":1,"publist_id":"3844","date_published":"2012-08-06T00:00:00Z","_id":"2903","corr_author":"1","quality_controlled":"1","date_updated":"2024-10-09T20:54:57Z","status":"public","title":"The adaptive topology of a digital image","oa":1,"page":"41 - 48","pubrep_id":"545","file_date_updated":"2020-07-14T12:45:52Z","month":"08"},{"extern":"1","external_id":{"isi":["000309114300001"]},"intvolume":"        12","oa_version":"Published Version","day":"26","year":"2012","isi":1,"type":"journal_article","publisher":"BioMed Central","doi":"10.1186/1471-2229-12-116","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"publication_status":"published","citation":{"ieee":"T. Galkovskyi <i>et al.</i>, “GiA Roots: Software for the high throughput analysis of plant root system architecture,” <i>BMC Plant Biology</i>, vol. 12. BioMed Central, 2012.","ama":"Galkovskyi T, Mileyko Y, Bucksch A, et al. GiA Roots: Software for the high throughput analysis of plant root system architecture. <i>BMC Plant Biology</i>. 2012;12. doi:<a href=\"https://doi.org/10.1186/1471-2229-12-116\">10.1186/1471-2229-12-116</a>","short":"T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C. Topp, A. Iyer Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey, J. Weitz, BMC Plant Biology 12 (2012).","chicago":"Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles Price, Chrostopher Topp, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” <i>BMC Plant Biology</i>. BioMed Central, 2012. <a href=\"https://doi.org/10.1186/1471-2229-12-116\">https://doi.org/10.1186/1471-2229-12-116</a>.","apa":"Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C., … Weitz, J. (2012). GiA Roots: Software for the high throughput analysis of plant root system architecture. <i>BMC Plant Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2229-12-116\">https://doi.org/10.1186/1471-2229-12-116</a>","mla":"Galkovskyi, Taras, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” <i>BMC Plant Biology</i>, vol. 12, 116, BioMed Central, 2012, doi:<a href=\"https://doi.org/10.1186/1471-2229-12-116\">10.1186/1471-2229-12-116</a>.","ista":"Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C, Iyer Pascuzzi A, Zurek P, Fang S, Harer J, Benfey P, Weitz J. 2012. GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. 12, 116."},"publication":"BMC Plant Biology","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","has_accepted_license":"1","ddc":["005","514","516"],"author":[{"first_name":"Taras","full_name":"Galkovskyi, Taras","last_name":"Galkovskyi"},{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"first_name":"Alexander","full_name":"Bucksch, Alexander","last_name":"Bucksch"},{"last_name":"Moore","full_name":"Moore, Brad","first_name":"Brad"},{"full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947","first_name":"Olga"},{"first_name":"Charles","last_name":"Price","full_name":"Price, Charles"},{"first_name":"Chrostopher","last_name":"Topp","full_name":"Topp, Chrostopher"},{"full_name":"Iyer Pascuzzi, Anjali","last_name":"Iyer Pascuzzi","first_name":"Anjali"},{"first_name":"Paul","last_name":"Zurek","full_name":"Zurek, Paul"},{"last_name":"Fang","full_name":"Fang, Suqin","first_name":"Suqin"},{"last_name":"Harer","full_name":"Harer, John","first_name":"John"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"},{"last_name":"Weitz","full_name":"Weitz, Joshua","first_name":"Joshua"}],"date_created":"2018-12-11T11:46:46Z","file":[{"content_type":"application/pdf","creator":"system","access_level":"open_access","file_id":"4953","relation":"main_file","file_name":"IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf","date_created":"2018-12-12T10:12:35Z","date_updated":"2020-07-14T12:46:35Z","checksum":"0c629e36acd5f2878ff7dd088d67d494","file_size":1691436}],"fulldoi":"https://doi.org/10.1186/1471-2229-12-116","article_number":"116","abstract":[{"lang":"eng","text":"Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis."}],"_id":"492","scopus_import":"1","publist_id":"7328","date_published":"2012-07-26T00:00:00Z","quality_controlled":"1","date_updated":"2025-09-30T08:36:34Z","oa":1,"file_date_updated":"2020-07-14T12:46:35Z","pubrep_id":"946","volume":12,"status":"public","title":"GiA Roots: Software for the high throughput analysis of plant root system architecture","month":"07"}]