SynthMLM: A framework for interpretable analysis and synthetic localisation data generation for SMLM

Quantitative analysis of single-molecule localisation microscopy (SMLM) data remains challenging because biologically diverse, well-annotated datasets are limited, whilst nanoscale protein organisation is heterogeneous and difficult to describe with hand-tuned metrics. We present SynthMLM, a framework that infers interpretable structural descriptors from experimental SMLM data and uses these descriptors to generate synthetic localisation datasets. We demonstrate SynthMLM by generating descriptor-matched synthetic datasets corresponding to diverse experimental SMLM datasets and evaluating their agreement with real data using descriptor-level and embedding-based measures. By enabling controlled generation of synthetic localisation data, SynthMLM provides a practical resource for benchmarking SMLM analysis methods, testing algorithm failure modes, and developing machine-learning workflows where large, labelled datasets are required.