DynaCell: an Evaluation Framework for Dynamic 3D Virtual Staining of Live Cells

Imaging of dynamic cellular responses to perturbations requires live-cell measurements, posing a challenge for fluorescence-based assays that can visualize molecular phenotypes by specific labeling but often affect cell health. Virtual staining helps by predicting fluorescence-like signals from label-free microscopy. Although many models have been developed for this task, their performance on volumetric time-lapse data remains poorly characterized. We address this gap by introducing DynaCell, an evaluation framework for 3D time-lapse virtual staining of live cells, comprising a new paired label-free and fluorescence 3D time-lapse imaging dataset, a suite of baseline models, and a three-tier metric panel measuring pixel-level fidelity, organelle segmentation performance, and single-cell phenotypic similarity. Using DynaCell, we study model behavior across 2 cell types and microscopes, 4 organelles, and 3 perturbation states. We find that regression baselines better predict the spatial localization of target organelles and are more robust to label-free input distribution shifts, while the generative baseline better captures population-level phenotype distribution across cells and organelles. These differences expose trade-offs between preservation of structural and phenotypic fidelity that are obscured by single-metric evaluation, and suggest how virtual staining can support downstream tasks such as localization, segmentation, tracking, and phenotypic profiling. DynaCell provides reusable data, code, checkpoints, and documentation for assessing virtual stains for live-cell biological measurements.