Accurate automated photo-identification of Near Eastern and European fire salamanders

Abstract

Photo-identification underpins non-invasive capture-recapture monitoring of amphibians, but manual identification becomes slow and error-prone as reference libraries grow. Focusing on the Near Eastern fire salamander (Salamandra infraimmaculata), we developed a pipeline based on zero-shot local-feature matching (SuperPoint and LightGlue) without species-specific training and evaluated it on $2{,}440$ field photographs from Haifa and Tel Dan in northern Israel. We isolated the yellow spot pattern, scored image similarity by the number of high-confidence keypoint matches, which reduced a confound whereby many-spotted individuals accumulate spurious matches, and assigned identities across the database by two-tier clustering. Pipeline-assisted expert review corrected misidentifications, reducing the number of identities by almost a quarter. On held-out individuals, the pipeline ranked the correct individual first for $95.2\%$ of queries and recovered identities with an ARI of $0.958$. Without modification, it reached $95.1\%$ and $91.7\%$ top-1 accuracy on two datasets of the European fire salamander (Salamandra salamandra) and recognised $93.7\%$ of recaptures in one of them, compared with $38$-$77\%$ for five established programs and $93.9\%$ for visual inspection. Zero-shot local-feature matching thus offers amphibian monitoring a re-identification tool that needs no training data, transfers between related species, scales to databases of over a thousand individuals, and can audit existing databases before capture-recapture analysis.