SlicerMorph

SlicerMorph provides 3D morphological analysis of biological specimens by retrieving, visualizing, annotating, measuring, and analyzing high-resolution microCT-derived volumes and models for organismal and evolutionary biology research.

Key Features:

• Repository integration: Retrieval and import of open-access 3D models and volumes from repositories and large-scale digitization projects including MorphoSource, #ScanAllFishes, and oVerte.
• Landmark annotation: Modules for annotating curve- and patch-based landmarks and generating canonical templates for comparative analyses.
• Geometric morphometrics: Support for both landmark-driven and landmark-free geometric morphometric analyses.
• Visualization and segmentation: Visualization and segmentation capabilities built on the Visualization Toolkit (VTK) and the Insight Segmentation and Registration Toolkit (ITK).
• Workflow automation: Automation of workflows from image sequence to morphospace and support for generation of 3D animations of results.
• Python scripting: Python-scriptable operations enabling customization and automation of analysis steps.
• Spatial scale and formats: Preservation of spatial scale and use of open file formats to support data exchange and reproducibility.

Scientific Applications:

• Evolutionary biology: Quantitative analysis of form and shape to study evolutionary patterns and processes.
• Comparative morphology: Comparative analysis of extinct and extant vertebrate specimens using microCT-derived 3D data.
• Biodiversity digitization studies: Analysis of large-scale digitized specimen datasets from projects such as #ScanAllFishes and oVerte.
• Morphospace analysis: Construction and exploration of morphospaces for quantitative shape analysis and visualization.

Methodology:

Extension of 3D Slicer utilizing VTK and ITK for visualization and segmentation, modules for curve- and patch-based landmark annotation, landmark-driven and landmark-free geometric morphometrics, canonical template generation, python-scriptable operations, preservation of spatial scale, and use of open file formats with support for importing and retrieving microCT volumes and models from repositories including MorphoSource.