Adaptive 3D descattering with a dynamic synthesis network.

Deep learning has been broadly applied to imaging in scattering applications. A common framework is to train a descattering network for image recovery by removing scattering artifacts. To achieve the best results on a broad spectrum of scattering conditions, individual "expert" networks need to be trained for each condition. However, the expert's performance sharply degrades when the testing condition differs from the training. An alternative brute-force approach is to train a "generalist" network using data from diverse scattering conditions. It generally requires a larger network to encapsulate the diversity in the data and a sufficiently large training set to avoid overfitting. Here, we propose an adaptive learning framework, termed dynamic synthesis network (DSN), which dynamically adjusts the model weights and adapts to different scattering conditions. The adaptability is achieved by a novel "mixture of experts" architecture that enables dynamically synthesizing a network by blending multiple experts using a gating network. We demonstrate the DSN in holographic 3D particle imaging for a variety of scattering conditions. We show in simulation that our DSN provides generalization across a continuum of scattering conditions. In addition, we show that by training the DSN entirely on simulated data, the network can generalize to experiments and achieve robust 3D descattering. We expect the same concept can find many other applications, such as denoising and imaging in scattering media. Broadly, our dynamic synthesis framework opens up a new paradigm for designing highly adaptive deep learning and computational imaging techniques.

Large-scale holographic particle 3D imaging with the beam propagation model.

We develop a novel algorithm for large-scale holographic reconstruction of 3D particle fields. Our method is based on a multiple-scattering beam propagation method (BPM) combined with sparse regularization that enables recovering dense 3D particles of high refractive index contrast from a single hologram. We show that the BPM-computed hologram generates intensity statistics closely matching with the experimental measurements and provides up to 9× higher accuracy than the single-scattering model. To solve the inverse problem, we devise a computationally efficient algorithm, which reduces the computation time by two orders of magnitude as compared to the state-of-the-art multiple-scattering based technique. We demonstrate the superior reconstruction accuracy in both simulations and experiments under different scattering strengths. We show that the BPM reconstruction significantly outperforms the single-scattering method in particular for deep imaging depths and high particle densities.

Anatomical Modeling of Brain Vasculature in Two-Photon Microscopy by Generalizable Deep Learning.

Objective and Impact Statement. Segmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here, we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. Introduction. Vascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems and is able to segment large-scale angiograms. Methods. We employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and total variation regularization on the network's output. Its effectiveness is demonstrated on experimentally acquired in vivo angiograms from mouse brains of dimensions up to 808×808×702 µm. Results. To demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art. Conclusion. Our work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning-based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.

High-throughput intensity diffraction tomography with a computational microscope.

We demonstrate a motion-free intensity diffraction tomography technique that enables the direct inversion of 3D phase and absorption from intensity-only measurements for weakly scattering samples. We derive a novel linear forward model featuring slice-wise phase and absorption transfer functions using angled illumination. This new framework facilitates flexible and efficient data acquisition, enabling arbitrary sampling of the illumination angles. The reconstruction algorithm performs 3D synthetic aperture using a robust computation and memory efficient slice-wise deconvolution to achieve resolution up to the incoherent limit. We demonstrate our technique with thick biological samples having both sparse 3D structures and dense cell clusters. We further investigate the limitation of our technique when imaging strongly scattering samples. Imaging performance and the influence of multiple scattering is evaluated using a 3D sample consisting of stacked phase and absorption resolution targets. This computational microscopy system is directly built on a standard commercial microscope with a simple LED array source add-on, and promises broad applications by leveraging the ubiquitous microscopy platforms with minimal hardware modifications.