Leveraging Phytolith Research using Artificial Intelligence

TL;DR

This paper introduces Sorometry, an AI pipeline that automates phytolith analysis using multimodal imaging and machine learning, significantly improving classification accuracy and enabling large-scale paleoecological studies.

Contribution

The paper presents a novel AI-driven platform combining 2D and 3D analysis for phytolith classification, enhancing accuracy and throughput over traditional manual methods.

Findings

Achieved 77.9% accuracy across 24 morphotypes

Integrated 3D data improves complex morphotype classification

Enabled plant source prediction in mixed archaeological samples

Abstract

Phytolith analysis is a crucial tool for reconstructing past vegetation and human activities, but traditional methods are severely limited by labour-intensive, time-consuming manual microscopy. To address this bottleneck, we present Sorometry: a comprehensive end-to-end artificial intelligence pipeline for the high-throughput digitisation, inference, and interpretation of phytoliths. Our workflow processes z-stacked optical microscope scans to automatically generate synchronised 2D orthoimages and 3D point clouds of individual microscopic particles. We developed a multimodal fusion model that combines ConvNeXt for 2D image analysis and PointNet++ for 3D point cloud analysis, supported by a graphical user interface for expert annotation and review. Tested on reference collections and archaeological samples from the Bolivian Amazon, our fusion model achieved a global classification accuracy of 77.9\% across 24 diagnostic morphotypes and 84.5% for segmentation quality. Crucially, the integration of 3D data proved essential for distinguishing complex morphotypes (such as grass silica short cell phytoliths) whose diagnostic features are often obscured by their orientation in 2D projections. Beyond individual object classification, Sorometry incorporates Bayesian finite mixture modelling to predict overall plant source contributions at the assemblage level, successfully identifying specific plants like maize and palms in complex mixed samples. This integrated platform transforms phytolith research into an "omics"-scale discipline, dramatically expanding analytical capacity, standardising expert judgements, and enabling reproducible, population-level characterisations of archaeological and paleoecological assemblages.