Meeting Abstract
Large scale digitization projects like #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through open-source licenses. MorphoSource currently hosts almost 16,000 3D scans of eukaryotes, and the number of available specimens is expected to double in next couple years. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyze them. Yet, the road from a series of image sequences to analysis is typically fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, acquiring measurements and annotations. Users opt-to use commercial software with proprietary formats that constitutes a roadblock for data exchange, collaboration and reproducibility. Our project is extending the functionality of the 3D-Slicer with tools that biologists need to conduct 3D specimen-driven research. SlicerMorph is as an extension of Slicer that provides users with tools to conduct shape analyses and 3D visualizations. Soon, functionality will be supplemented with semi-automatic landmark generation, and with a landmark-free shape correspondence method. We are also organizing weeklong intensive workshops that cover the fundamentals of 3D imaging and morphometric analyses. Our goal is to establish a community of organismal biologists centered around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens.
