Beyond Imaging: Vision Transformer Digital Twin Surrogates for 3D+T Biological Tissue Dynamics

TL;DR

This paper introduces VT-DTSN, a deep learning framework using Vision Transformers to accurately predict and reconstruct 3D+T biological tissue dynamics from imaging data, facilitating in silico biological studies.

Contribution

The work presents a novel Vision Transformer-based surrogate model for high-fidelity, time-resolved biological tissue imaging reconstruction, integrating multi-view fusion and a specialized training loss.

Findings

Achieves low error rates and high structural similarity in tissue dynamics reconstruction.

Demonstrates robustness and consistency across biological replicates.

Enables efficient in silico exploration of tissue behaviors.

Abstract

Understanding the dynamic organization and homeostasis of living tissues requires high-resolution, time-resolved imaging coupled with methods capable of extracting interpretable, predictive insights from complex datasets. Here, we present the Vision Transformer Digital Twin Surrogate Network (VT-DTSN), a deep learning framework for predictive modeling of 3D+T imaging data from biological tissue. By leveraging Vision Transformers pretrained with DINO (Self-Distillation with NO Labels) and employing a multi-view fusion strategy, VT-DTSN learns to reconstruct high-fidelity, time-resolved dynamics of a Drosophila midgut while preserving morphological and feature-level integrity across imaging depths. The model is trained with a composite loss prioritizing pixel-level accuracy, perceptual structure, and feature-space alignment, ensuring biologically meaningful outputs suitable for in silico experimentation and hypothesis testing. Evaluation across layers and biological replicates demonstrates VT-DTSN's robustness and consistency, achieving low error rates and high structural similarity while maintaining efficient inference through model optimization. This work establishes VT-DTSN as a feasible, high-fidelity surrogate for cross-timepoint reconstruction and for studying tissue dynamics, enabling computational exploration of cellular behaviors and homeostasis to complement time-resolved imaging studies in biological research.