Algavision: Object Recognition Tool for Phytoplankton Cells in Microscopy Images

Anotacija

Phytoplankton are microbes driving half of global primary production and are widely used model organisms in various studies. Despite advancements in high-throughput methods for acquisition of cell size and abundance data, microscopy remains widely preferred in multi-strain experiments. In this study, an instance segmentation model was trained on a dataset containing 11 strains and integrated into an image processing pipeline. The final version of the pipeline showed superiority over an established thresholding method (Avg. F1 Score 86% vs. 34%). This approach also highlights the potential of clustering unseen strains by prompting a general-purpose segmenter with low-confidence predictions.