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Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","short":"R. Hauschild, (2024).","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>."},"year":"2024","month":"02","day":"02"},{"date_updated":"2026-07-06T12:57:43Z","corr_author":"1","abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"author":[{"orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"first_name":"Martin","last_name":"Falcke","full_name":"Falcke, Martin"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"file_date_updated":"2023-11-21T08:20:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"GNU Affero General Public License v3.0","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html","short":"GNU AGPLv3  "},"keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"type":"software","doi":"10.15479/AT:ISTA:14502","fulldoi":"https://doi.org/10.15479/AT:ISTA:14502","date_published":"2023-11-21T00:00:00Z","oa":1,"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","has_accepted_license":"1","ddc":["570"],"department":[{"_id":"FlSc"}],"status":"public","_id":"14502","publisher":"Institute of Science and Technology Austria","license":"https://choosealicense.com/licenses/agpl-3.0/","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","mla":"Dimchev, Georgi A., et al. <i>Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023."},"year":"2023","month":"11","day":"21","date_created":"2023-11-08T19:40:54Z","related_material":{"record":[{"id":"10290","relation":"used_for_analysis_in","status":"public"}]},"file":[{"content_type":"application/zip","date_updated":"2023-11-08T20:23:07Z","creator":"fschur","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","access_level":"open_access","relation":"main_file","file_name":"Computational_Toolbox_v1.2.zip","date_created":"2023-11-08T20:23:07Z","file_size":347641117,"success":1,"file_id":"14503"},{"success":1,"file_id":"14586","date_created":"2023-11-21T08:20:23Z","file_size":1522,"file_name":"Readme.txt","checksum":"14db2addbfca61a085ba301ed6f2900b","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"text/plain","date_updated":"2023-11-21T08:20:23Z"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}]},{"type":"software","tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"doi":"10.15479/AT:ISTA:9327","fulldoi":"https://doi.org/10.15479/AT:ISTA:9327","oa":1,"has_accepted_license":"1","title":"Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)","date_published":"2021-05-01T00:00:00Z","ddc":["005"],"file_date_updated":"2021-04-26T09:33:44Z","abstract":[{"text":"This archive contains the missing sweater mesh animations and displacement models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode Repository: https://git.ist.ac.at/gsperl/MADYPG","lang":"eng"}],"author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","first_name":"Georg"},{"first_name":"Rahul","full_name":"Narain, Rahul","last_name":"Narain"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","gitlab_url":"https://git.ist.ac.at/gsperl/MADYPG","date_updated":"2026-06-18T19:57:47Z","related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"9818"}]},"file":[{"creator":"gsperl","content_type":"application/zip","date_updated":"2021-04-16T14:15:12Z","relation":"main_file","checksum":"0324cb519273371708743f3282e7c081","access_level":"open_access","date_created":"2021-04-16T14:15:12Z","file_size":802586232,"file_name":"MADYPG_extra_data.zip","file_id":"9328","success":1},{"file_size":64962865,"date_created":"2021-04-26T09:33:44Z","file_name":"MADYPG.zip","file_id":"9353","creator":"pub-gitlab-bot","content_type":"application/gzip","date_updated":"2021-04-26T09:33:44Z","access_level":"open_access","checksum":"4c224551adf852b136ec21a4e13f0c1b","relation":"main_file"}],"date_created":"2021-04-16T14:26:19Z","publisher":"IST Austria","citation":{"ista":"Sperl G, Narain R, Wojtan C. 2021. 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IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9327\">https://doi.org/10.15479/AT:ISTA:9327</a>","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9327\">https://doi.org/10.15479/AT:ISTA:9327</a>.","mla":"Sperl, Georg, et al. <i>Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9327\">10.15479/AT:ISTA:9327</a>.","short":"G. Sperl, R. Narain, C. Wojtan, (2021)."},"year":"2021","gitlab_commit_id":"6a77e7e22769230ae5f5edaa090fb4b828e57573","month":"05","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"status":"public","_id":"9327"},{"date_updated":"2026-10-26T23:30:43Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2021-10-08T08:46:04Z","author":[{"first_name":"José","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"orcid":"0000-0003-4710-2082","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia "},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0256-6529","first_name":"Xiaomin"},{"id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter","full_name":"Suter, Benjamin","first_name":"Benjamin","orcid":"0000-0002-9885-6936"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"oa":1,"has_accepted_license":"1","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","date_published":"2021-12-16T00:00:00Z","ddc":["005"],"type":"software","tmp":{"name":"GNU General Public License 3.0","short":"GPL 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html"},"doi":"10.15479/AT:ISTA:10110","fulldoi":"https://doi.org/10.15479/AT:ISTA:10110","status":"public","_id":"10110","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"month":"12","day":"16","publisher":"IST Austria","citation":{"mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>"},"year":"2021","date_created":"2021-10-08T06:44:22Z","file":[{"checksum":"f92f8931cad0aa7e411c1715337bf408","access_level":"open_access","relation":"main_file","creator":"cchlebak","content_type":"application/x-zip-compressed","date_updated":"2021-10-08T08:46:04Z","success":1,"file_id":"10114","date_created":"2021-10-08T08:46:04Z","file_size":332990101,"file_name":"patternseparation-main (1).zip"}],"related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/"}],"record":[{"status":"public","id":"10816","relation":"used_for_analysis_in"}]}},{"title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","has_accepted_license":"1","oa":1,"date_published":"2020-08-24T00:00:00Z","doi":"10.15479/AT:ISTA:8181","fulldoi":"https://doi.org/10.15479/AT:ISTA:8181","type":"software","tmp":{"name":"The 3-Clause BSD License","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-08-24T15:43:52Z","author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert"}],"corr_author":"1","date_updated":"2024-10-09T21:05:14Z","file":[{"date_created":"2020-08-24T15:43:49Z","file_size":6577,"file_name":"centriolesDistance.m","success":1,"file_id":"8290","creator":"rhauschild","content_type":"text/plain","date_updated":"2020-08-24T15:43:49Z","checksum":"878c60885ce30afb59a884dd5eef451c","access_level":"open_access","relation":"main_file"},{"checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","access_level":"open_access","relation":"main_file","creator":"rhauschild","date_updated":"2020-08-24T15:43:52Z","content_type":"text/plain","success":1,"file_id":"8291","date_created":"2020-08-24T15:43:52Z","file_size":2680,"file_name":"goTracking.m"}],"date_created":"2020-07-28T16:24:37Z","day":"24","month":"08","license":"https://opensource.org/licenses/BSD-3-Clause","citation":{"short":"R. Hauschild, (2020).","mla":"Hauschild, Robert. <i>Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>.","ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>","ama":"Hauschild R. Amplified centrosomes in dendritic cells promote immune cell effector functions. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>","ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>."},"year":"2020","publisher":"IST Austria","_id":"8181","status":"public","department":[{"_id":"Bio"}]},{"file_date_updated":"2020-09-08T14:26:33Z","author":[{"orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"}],"abstract":[{"lang":"eng","text":"Automated root growth analysis and tracking of root tips. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T21:05:14Z","corr_author":"1","tmp":{"name":"The 3-Clause BSD License","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD"},"type":"software","fulldoi":"https://doi.org/10.15479/AT:ISTA:8294","doi":"10.15479/AT:ISTA:8294","date_published":"2020-09-10T00:00:00Z","title":"RGtracker","oa":1,"has_accepted_license":"1","ddc":["570"],"publisher":"IST Austria","citation":{"ama":"Hauschild R. RGtracker. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>","ista":"Hauschild R. 2020. RGtracker, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>.","ieee":"R. Hauschild, “RGtracker.” IST Austria, 2020.","apa":"Hauschild, R. (2020). RGtracker. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">https://doi.org/10.15479/AT:ISTA:8294</a>","chicago":"Hauschild, Robert. “RGtracker.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">https://doi.org/10.15479/AT:ISTA:8294</a>.","mla":"Hauschild, Robert. <i>RGtracker</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>.","short":"R. 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