#39 · Tools & infrastructure
Segmentation models and 3D classifiers automate morphological measurement from images
The dominant thread is automated extraction of morphological information from imaging data via segmentation or classification. SAMWOOD applies zero-shot Segment-Anything to wood microscopy images, reconstructing cell files to analyze lumen area along growth orientation. Descriptron-GBIF Annotator provides a zero-install browser platform for crowdsourced annotation of GBIF biodiversity images, using SAM2 with UBERON-linked JSON-LD exports. The phytolith preprint pairs a 2D ConvNeXt with a 3D PointNet++ to classify phytoliths and infer plant sources in archaeological samples. The methods do not converge on a single architecture. What is new is the pairing of general-purpose segmentation models with domain-specific ontologies or 3D classifiers, delivered as accessible tooling.
Preprints
Assessing 3D tree model quality and species classification using imbalance indices
Applies 3D and phylogenetic tree balance indices to Wytham Woods virtual forest models, reaching up to 81.8% species classification accuracy, with an updated R…
Descriptron-GBIF Annotator: A browser-based platform for crowdsourced morphological annotation of biodiversity images to help accelerate morphology based biodiversity data
Zero-install browser tool for crowdsourced morphological annotation of GBIF biodiversity images, using SAM2 and UBERON-linked JSON-LD exports.
SAMWOOD: An automated method to measure wood cells along growth orientation
SAMWOOD applies zero-shot Segment-Anything to segment wood cells in microscopy images, reconstructing cell files for growth-orientation and lumen-area analysis…
Topic history
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