Biological Congruence: Evaluating Microscopy Generation Across Representations

arXiv:2611.01850v1 Announce Type: new Abstract: Generative models increasingly produce realistic microscopy images, yet conventional evaluation primarily characterizes visual fidelity and distributional coverage rather than the biological information represented by synthetic data. We introduce biological congruence as an evaluation principle describing whether biologically relevant information forms a coherent description across representations and remains consistent with its empirical biological context. To study this principle, we develop a text-conditioned diffusion framework that jointly generates microscopy images and instance masks, exposing the same generated biological state through conditioning, visual appearance, and instance structure. Across prompt--mask, prompt--image, image--mask, and population-level analyses, we find strongly feature-dependent behavior: density and confluency are consistently preserved, morphology exhibits recurrent disagreement, while nearest-neighbor distance reveals that strong image--mask agreement can coexist with weaker conditioning and population fidelity. Stress testing increasingly unsupported phenotype combinations further shows that target controllability can increase while untargeted phenotypes reorganize and the complete generated state moves toward configurations better supported by real data. These findings demonstrate that generative quality, controllability, cross-representation agreement, and population fidelity capture complementary properties, motivating biological congruence as a relational perspective for evaluating scientific generative models.