SAMMBA is a high-throughput pipeline for isolating and phenotyping macroalgal strains

Despite successful preservation efforts, macroalgal diversity remains under-represented in global biobanks. A major limitation is the extreme morphological diversity of seaweed thalli, which hinders standardized isolation and phenotyping and often requires taxon-specific protocols. Here we present SAMMBA (Seaweed Automatable Microplate Microscopy for Breeding Approaches), an end-to-end pipeline for the high-throughput isolation, phenotyping and storage of macroalgal propagules in 384-well plates. By optimizing live-cell manipulation for chlorophyll autofluorescence (CAF) imaging and segmentation, multiple unialgal propagules can be isolated by dilution-based workflows. In a single plate, we obtained 68 singlet gametophyte fragments of Laminaria ochroleuca (17.7%) and 60 meiospores of Phyllariopsis purpurascens (31.25%). We demonstrated taxonomic and morphological versatility by isolating 60 unialgal cultures from three distinct Rhodophyta morphotypes (filamentous, crustose and foliose) and 10 strains of Ulva sp., also in a single plate. Furthermore, CAF-based area increase over 30 days enabled high-precision estimates of specific growth rates, yielding 0.130 ± 0.006 and 0.117 ± 0.01 day −1 for male and female L. ochroleuca gametophytes, respectively ( n = 768; p = 1.27e −53 ). This precision substantially increases experimental reproducibility and statistical power compared to conventional methods, supporting high-throughput recovery of unialgal strains without motorized platforms, while remaining fully compatible with automation. SAMMBA expands operational capacity for strain discovery and phenotyping, providing a scalable foundation for phenomics, domestication workflows, and standardized macroalgal biobanking. We outline how the platform can benefit multiple areas of phycological research and facilitate the development of improved strains that can support aquaculture and restoration efforts. • Establishment of a flexible and accessible pipeline for high-throughput seaweed strain isolation in multi-well plates; • Optimization of a high-throughput phenotyping analysis via machine-learning segmentation of chlorophyll fluorescence microscopy images; • Provides open and reproducible tools for large-scale germplasm biobanking and breeding strategies.