SlicerMorph A toolkit for morphometric analysis of high-resolution specimen data


SOCIETY FOR INTEGRATIVE AND COMPARATIVE BIOLOGY
2021 VIRTUAL ANNUAL MEETING (VAM)
January 3 – Febuary 28, 2021

Meeting Abstract


39-11  Sat Jan 2  SlicerMorph: A toolkit for morphometric analysis of high-resolution specimen data Rolfe, SM*; Porto, A; Pieper, S; Winchester, J; Boyer, D; Summers, A; Maga, AM; University of Washington, Seattle and Seattle Children’s Research Institute, WA; Seattle Children’s Research Institute, WA; Isomics, Inc; Duke University, Durham, NC; Duke University, Durham, NC; University of Washington, Seattle ; University of Washington, Seattle and Seattle Children’s Research Institute, WA smrolfe@uw.edu

Recent advances in 3D imaging have driven collaborative, “big data” initiatives, such as #scanallfish and oVert, with the goal of making data broadly accessible to the organismal biology community. Data from these projects is shared via public repositories like MorphoSource, encouraging data reuse and removing obstacles posed by access to imaging equipment. As quantitative imaging becomes more widely available, there is a corresponding need for image analysis software that supports open, reproducible research. Open-source, community-driven platforms, such as 3D Slicer, provide a compelling solution to the challenges around publishing and maintaining accessible toolkits and workflows. We have developed SlicerMorph, an extension to the 3D Slicer platform that provides users with modules to support analysis of 3D organismal forms, including conducting geometric morphometric analysis using both landmark-driven and landmark-free approaches, annotation of 3D curves and patch-based landmarks, as well as convenience modules for 3D data retrieval, import and export. We aim to establish a community around SlicerMorph to support collaboration, sharing of data and methods, and sustainable tool development. To this end, we hold regular short courses, conduct online user meetings, and provide tutorial material. In this talk, I will address how SlicerMorph addresses challenges specific to morphometric analyses of high-resolution specimen data and highlight common workflows from data import from public repositories through visualization of statistical shape analysis and export of 3D animations.

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