Advancing automated identification of airborne fungal spores: guidelines for cultivation and reference dataset creation

Abstract

Airborne bioparticles, including fungal spores, are of major concern for human and plant health, necessitating precise monitoring systems. While a European norm exists for manual volumetric monitoring, there's a growing interest in automated real-time methods. However, these methods rely heavily on machine learning, facing challenges due to diverse particle characteristics and limited training data availability, especially for fungal spores. This study aims to address this gap by outlining best practices for collecting reference material and creating tailored datasets for training algorithms. Using 17 fungal species from the Belgian fungi collection BCCM/IHEM, including five Alternaria species, key aspects such as in vitro cultivation, dry spore harvest, and aerosolization were addressed. Simple classification models were developed, achieving varying accuracies on different monitors. The Plair Rapid-E+ demonstrated accuracies ranging from 83.4% to 95.1% (macro average F1-score 0.61), with better recognition for Cladosporium spp. and Curvularia caricae-papayae . The SwisensPoleno Jupiter, initially achieving a macro average F1-score of 0.77 with holographic images of eight genera, improved to 0.83 when combined with fluorescence data. Accuracies ranged from 55 to 95%, with notable performance for Alternaria spp. and Curvularia caricae-papayae . Species differentiation was also shown to be possible for Cladosporium , but was more difficult for some Alternaria species, while the macro average F1-score remained good (0.72). Overall, this protocol paves the way for more efficient, standard, and accurate automatic identification of airborne fungal spores.

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