FossilJ

FossilJ performs semi-automatic morphometric data acquisition from images of bivalve fossils to enable reproducible shape analysis in paleontological studies.

Key Features:

• ImageJ integration: Leverages ImageJ extensibility, including batch processing and the ImageJ macro language, to implement image-analysis procedures.
• Semi-automated morphometric measurements: Extracts quantitative morphometric data from fossil images, with specific application to bivalve fossils.
• Reduction of observer bias: Applies digital, mathematically founded approaches and automation to minimize subjective decisions in data collection.
• SPHARM-PDM support: Enables comparative morphometric workflows using SPHARM-PDM (Spherical Harmonic-based Point Distribution Model) applied to volumetric data.
• Interoperability with 3D Slicer and Python tools: Compatible with 3D Slicer workflows and supplemented by small Python assistant scripts developed for analyses such as coniform conodont studies on synchrotron scans.

Scientific Applications:

• Morphometrics: Quantitative shape analysis of fossils to investigate evolutionary patterns and functional morphology.
• Comparative morphometrics on volumetric scans: Comparative studies using SPHARM-PDM applied to synchrotron scans, including analyses of coniform conodonts integrated with 3D Slicer and Python assistants.

Methodology:

Integrates with ImageJ and 3D Slicer, uses ImageJ macro language and common programming languages for extensibility, applies SPHARM-PDM to synchrotron-derived volumetric data, and employs auxiliary Python scripts for specific tasks such as coniform conodont processing.