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Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses.  This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","date_updated":"2026-04-07T13:02:36Z","citation":{"ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024).","ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54.","apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., &#38; Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>.","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>.","ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 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We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles."}],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","OA_type":"hybrid","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"type":"journal_article","publication":"ACM Transactions on Graphics","author":[{"first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak","full_name":"Synak, Peter"},{"id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","first_name":"Aleksei","full_name":"Kalinov, Aleksei","last_name":"Kalinov","orcid":"0000-0003-2189-3904"},{"id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","first_name":"Irina-Malina","last_name":"Strugaru","full_name":"Strugaru, 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The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh."}],"article_processing_charge":"No","oa_version":"Published Version","page":"39","citation":{"short":"A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking, Institute of Science and Technology Austria, 2024.","ista":"Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria.","apa":"Etemadi, A. (2024). <i>Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18301\">https://doi.org/10.15479/at:ista:18301</a>","ieee":"A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024.","ama":"Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18301\">10.15479/at:ista:18301</a>","mla":"Etemadi, Arian. <i>Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18301\">10.15479/at:ista:18301</a>.","chicago":"Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18301\">https://doi.org/10.15479/at:ista:18301</a>."},"date_updated":"2026-04-07T13:02:36Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1},{"language":[{"iso":"eng"}],"month":"05","degree_awarded":"PhD","day":"07","file_date_updated":"2021-02-11T11:17:15Z","citation":{"ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>"},"page":"183","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T14:02:12Z","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M"}],"article_processing_charge":"No","oa_version":"Published Version","_id":"6435","doi":"10.15479/AT:ISTA:6435","abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}],"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"date_created":"2019-05-13T08:58:35Z","ddc":["570","006","578","592"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"year":"2019","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"title":"Collective defenses of garden ants against a fungal pathogen","date_published":"2019-05-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"1999","relation":"part_of_dissertation"}]},"corr_author":"1","publication_status":"published","has_accepted_license":"1","department":[{"_id":"SyCr"}],"status":"public","alternative_title":["ISTA Thesis"],"file":[{"file_id":"6438","access_level":"open_access","date_updated":"2021-02-11T11:17:15Z","content_type":"application/pdf","file_name":"tesisDoctoradoBC.pdf","date_created":"2019-05-13T09:16:20Z","relation":"main_file","creator":"casillas","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","file_size":3895187,"embargo":"2020-05-08"},{"relation":"source_file","checksum":"3d221aaff7559a7060230a1ff610594f","creator":"casillas","file_size":7365118,"embargo_to":"open_access","file_id":"6439","access_level":"closed","date_updated":"2020-07-14T12:47:30Z","content_type":"application/zip","file_name":"tesisDoctoradoBC.zip","date_created":"2019-05-13T09:16:20Z"}]},{"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","type":"research_data","datarep_id":"69","oa_version":"Published Version","file":[{"file_id":"5636","date_updated":"2020-07-14T12:47:04Z","access_level":"open_access","content_type":"application/zip","file_name":"IST-2017-69-v1+2_TipTrackerZeissLSM700.zip","date_created":"2018-12-12T13:04:12Z","relation":"main_file","checksum":"a976000e6715106724a271cc9422be4a","creator":"system","file_size":1587986}],"article_processing_charge":"No","_id":"5566","doi":"10.15479/AT:ISTA:69","abstract":[{"text":"Current minimal version of TipTracker","lang":"eng"}],"has_accepted_license":"1","citation":{"chicago":"Hauschild, Robert. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:69\">https://doi.org/10.15479/AT:ISTA:69</a>.","mla":"Hauschild, Robert. <i>Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:69\">10.15479/AT:ISTA:69</a>.","ama":"Hauschild R. Live tracking of moving samples in confocal microscopy for vertically grown roots. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:69\">10.15479/AT:ISTA:69</a>","ieee":"R. Hauschild, “Live tracking of moving samples in confocal microscopy for vertically grown roots.” Institute of Science and Technology Austria, 2017.","ista":"Hauschild R. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:69\">10.15479/AT:ISTA:69</a>.","apa":"Hauschild, R. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:69\">https://doi.org/10.15479/AT:ISTA:69</a>","short":"R. 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Forward migration indexes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:75\">10.15479/AT:ISTA:75</a>"},"department":[{"_id":"Bio"}],"file":[{"file_id":"5596","date_updated":"2020-07-14T12:47:04Z","access_level":"open_access","file_name":"IST-2017-75-v1+1_FMI.m","content_type":"application/octet-stream","date_created":"2018-12-12T13:02:29Z","relation":"main_file","file_size":799,"checksum":"cb7a2fa622460eca6231d659ce590e32","creator":"system"}],"oa_version":"Published Version","article_processing_charge":"No","_id":"5570","abstract":[{"lang":"eng","text":"Matlab script to calculate the forward migration indexes (<d_y>/<L>) from TrackMate spot-statistics files."}],"doi":"10.15479/AT:ISTA:75","type":"research_data","datarep_id":"75","status":"public","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}}]