UDIST: unsupervised disentanglement of shape and texture for multi-scale phenotypic profiling in 2D microscopy

Microscopy-based phenotypic profiling relies increasingly on autonomous, unsupervised feature extraction, yet no existing method explicitly separates shape from texture into dedicated and independent latent subspaces by architectural design. Therefore texture, encoding critical biological information such as protein distribution and intracellular organisation, remains inaccessible as an independent feature domain in standard unsupervised approaches. This represents a fundamental limitation that prevents unbiased phenotypic analysis across biological scales. Here we introduce UDIST (Unsupervised Disentanglement of Shape and Texture), a sequential dual variational autoencoder (VAE) framework that tackles this fundamental limitation by explicitly decoupling shape from texture into independent, non-overlapping latent subspaces at the single-object level. By training two VICReg-regularised VAEs on principal-axis-aligned objects, UDIST separates binary shape from continuous texture information into rotation-invariant feature spaces, enabling separate downstream analysis of both domains. We validated UDIST across biological scales, from nuclei and single cells to patient-derived intestinal organoids, using both fluorescence and brightfield imaging, revealing phenotypic differences previously hidden by morphological variation and enabling the independent analysis of shape and texture in downstream analyses including clustering and similarity measurements. UDIST provides a versatile, label-free, and unsupervised tool for multi-scale phenotypic profiling in high-content microscopy and screening.