{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/3d-mesh-processing-using-gamer-2-to-enable","title":"3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries","arxiv_id":"1901.11008","date":"2019-12-17","proceeding":null,"authors":[],"abstract":"Recent advances in electron microscopy have enabled the imaging of single\ncells in 3D at nanometer length scale resolutions. An uncharted frontier for in\nsilico biology is the ability to simulate cellular processes using these\nobserved geometries. Enabling such simulations requires watertight meshing of\nelectron micrograph images into 3D volume meshes, which can then form the basis\nof computer simulations of such processes using numerical techniques such as\nthe Finite Element Method. In this paper, we describe the use of our recently\nrewritten mesh processing software, GAMer 2, to bridge the gap between poorly\nconditioned meshes generated from segmented micrographs and boundary marked\ntetrahedral meshes which are compatible with simulation. We demonstrate the\napplication of a workflow using GAMer 2 to a series of electron micrographs of\nneuronal dendrite morphology explored at three different length scales and show\nthat the resulting meshes are suitable for finite element simulations. This\nwork is an important step towards making physical simulations of biological\nprocesses in realistic geometries routine. Innovations in algorithms to\nreconstruct and simulate cellular length scale phenomena based on emerging\nstructural data will enable realistic physical models and advance discovery at\nthe interface of geometry and cellular processes. We posit that a new frontier\nat the intersection of computational technologies and single cell biology is\nnow open.","url_abs":"http://arxiv.org/abs/1901.11008v3","url_pdf":"http://arxiv.org/pdf/1901.11008v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"3d-mesh-processing-using-gamer-2-to-enable","repo_url":"https://github.com/ctlee/gamer","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"physical-simulations","task_name":"Physical Simulations"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}