Soorya Pradeep | Searcharxiv

arXiv2024

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↗

arXiv2024

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↗