arXiv subjects

Soorya Pradeep

Publications and source records attributed to Soorya Pradeep.

3 recordsLinked to original sources

arXiv2026

The DynaCell Evaluation Suite for Dynamic 3D Virtual Staining of Live Cells

Understanding how cells respond to perturbations over time is central to cell biology and drug discovery. Live-cell imaging captures the dynamics of perturbation-induced phenotypes in individual cells. While fluorescence imaging can visualize specific molecular phenotypes, labeling and repeated illumination often affect cell health. Virtual staining offers an alternative by predicting these fluorescence images from images acquired without fluorescent labels. Although many virtual staining models have been developed, their performance on volumetric time-lapse data remains poorly characterized. We address this gap with an evaluation suite for 3D time-lapse virtual staining of live cells. The suite combines paired 3D time-lapse images acquired with and without fluorescent labels, a set of baseline models, and three metric tiers measuring pixel-level fidelity, organelle segmentation performance, and single-cell phenotype similarity. Using this evaluation suite, we study metric and model behavior across 3 cell types, 2 microscopes, 4 organelles, and 3 perturbation states. We find that regression baselines better predict the spatial localization of target organelles, whereas the generative baseline better captures the distribution of phenotypes across cells. These differences expose trade-offs between structural and phenotypic fidelity that are obscured by single-metric evaluation and suggest how virtual staining models can be developed for diverse downstream tasks such as localization, segmentation, tracking, and phenotypic profiling. We release the curated datasets, baseline checkpoints, and evaluation code as part of DynaCell, a broader framework for image-based profiling of cell-state dynamics.

cs.CV↗

arXiv2025

WaveOrder: A differentiable wave-optical framework for scalable biological microscopy with diverse modalities

Correlative computational microscopy can accelerate imaging and modeling of cellular dynamics by relaxing trade-offs inherent to dynamic imaging. Existing computational microscopy frameworks are either specialized or overly generic, limiting use to fixed configurations or domain experts. We introduce WaveOrder, a generalist wave-optical framework for imaging the architectural order of biomolecules. WaveOrder reconstructs diverse specimen properties from multi-channel acquisitions, with or without fluorescence. It provides a unified representation of linear optical properties and differentiable physics-based image formation models spanning widefield, confocal, light-sheet, and oblique label-free geometries. WaveOrder uses physics-informed ML to auto-tune model parameters and solve blind shift-variant restoration problems. This open-source, PyTorch-based framework enables scalable quantitative imaging across scales from organelles to adult zebrafish, and improves restoration of cellular structures in high-throughput experiments. We validate WaveOrder on diverse imaging applications, demonstrating its ability to recover biomolecular structure beyond the limits of existing approaches.

physics.optics↗

arXiv2025

DynaCLR: Contrastive Learning of Cellular Dynamics with Temporal Regularization

We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn robust, temporally regularized representations of cell dynamics. DynaCLR embeddings generalize effectively to in-distribution and out-of-distribution datasets, and can be used for several downstream tasks with sparse human annotations. We demonstrate efficient annotations of cell states with a human-in-the-loop using fluorescence and label-free imaging channels. DynaCLR method enables diverse downstream biological analyses: classification of cell division and infection, clustering heterogeneous cell migration patterns, cross-modal distillation of cell states from fluorescence to label-free channel, alignment of asynchronous cellular responses and broken cell tracks, and discovering organelle response due to infection. DynaCLR is a flexible method for comparative analyses of dynamic cellular responses to pharmacological, microbial, and genetic perturbations. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a GUI (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.

cs.CV↗