Kevin C. Zhou

Lucas Kreiss, Shaowei Jiang, Xiang Li et al. · pku

Until recently, conventional biochemical staining had the undisputed status as well-established benchmark for most biomedical problems related to clinical diagnostics, fundamental research and biotechnology. Despite this role as gold-standard, staining protocols face several challenges, such as a need for extensive, manual processing of samples, substantial time delays, altered tissue homeostasis, limited choice of contrast agents for a given sample, 2D imaging instead of 3D tomography and many more. Label-free optical technologies, on the other hand, do not rely on exogenous and artificial markers, by exploiting intrinsic optical contrast mechanisms, where the specificity is typically less obvious to the human observer. Over the past few years, digital staining has emerged as a promising concept to use modern deep learning for the translation from optical contrast to established biochemical contrast of actual stainings. In this review article, we provide an in-depth analysis of the current state-of-the-art in this field, suggest methods of good practice, identify pitfalls and challenges and postulate promising advances towards potential future implementations and applications.

Shiqi Xu, Wenhui Liu, Xi Yang et al.

Fast noninvasive probing of spatially varying decorrelating events, such as cerebral blood flow beneath the human skull, is an essential task in various scientific and clinical settings. One of the primary optical techniques used is diffuse correlation spectroscopy (DCS), whose classical implementation uses a single or few single-photon detectors, resulting in poor spatial localization accuracy and relatively low temporal resolution. Here, we propose a technique termed Classifying Rapid decorrelation Events via Parallelized single photon dEtection (CREPE)}, a new form of DCS that can probe and classify different decorrelating movements hidden underneath turbid volume with high sensitivity using parallelized speckle detection from a $32\times32$ pixel SPAD array. We evaluate our setup by classifying different spatiotemporal-decorrelating patterns hidden beneath a 5mm tissue-like phantom made with rapidly decorrelating dynamic scattering media. Twelve multi-mode fibers are used to collect scattered light from different positions on the surface of the tissue phantom. To validate our setup, we generate perturbed decorrelation patterns by both a digital micromirror device (DMD) modulated at multi-kilo-hertz rates, as well as a vessel phantom containing flowing fluid. Along with a deep contrastive learning algorithm that outperforms classic unsupervised learning methods, we demonstrate our approach can accurately detect and classify different transient decorrelation events (happening in 0.1-0.4s) underneath turbid scattering media, without any data labeling. This has the potential to be applied to noninvasively monitor deep tissue motion patterns, for example identifying normal or abnormal cerebral blood flow events, at multi-Hertz rates within a compact and static detection probe.

Kevin C. Zhou, Mark Harfouche, Maxwell Zheng et al.

We present a large-scale computational 3D topographic microscope that enables 6-gigapixel profilometric 3D imaging at micron-scale resolution across $>$110 cm$^2$ areas over multi-millimeter axial ranges. Our computational microscope, termed STARCAM (Scanning Topographic All-in-focus Reconstruction with a Computational Array Microscope), features a parallelized, 54-camera architecture with 3-axis translation to capture, for each sample of interest, a multi-dimensional, 2.1-terabyte (TB) dataset, consisting of a total of 224,640 9.4-megapixel images. We developed a self-supervised neural network-based algorithm for 3D reconstruction and stitching that jointly estimates an all-in-focus photometric composite and 3D height map across the entire field of view, using multi-view stereo information and image sharpness as a focal metric. The memory-efficient, compressed differentiable representation offered by the neural network effectively enables joint participation of the entire multi-TB dataset during the reconstruction process. To demonstrate the broad utility of our new computational microscope, we applied STARCAM to a variety of decimeter-scale objects, with applications ranging from cultural heritage to industrial inspection.

Shiqi Xu, Xiang Dai, Xi Yang et al.

We report Tensorial Tomographic Differential Phase-Contrast microscopy (T2DPC), a quantitative label-free tomographic imaging method for simultaneous measurement of phase and anisotropy. T2DPC extends differential phase-contrast microscopy, a quantitative phase imaging technique, to highlight the vectorial nature of light. The method solves for permittivity tensor of anisotropic samples from intensity measurements acquired with a standard microscope equipped with an LED matrix, a circular polarizer, and a polarization-sensitive camera. We demonstrate accurate volumetric reconstructions of refractive index, birefringence, and orientation for various validation samples, and show that the reconstructed polarization structures of a biological specimen are predictive of pathology.

Xing Yao, Vinayak Pathak, Haoran Xi et al.

This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth product (SBP) of conventional microscopes. Here, we show both in simulation and experiment that overlapped imaging and co-designed analysis software can achieve accurate detection of diagnostically-relevant features for several applications, including counting of white blood cells and the malaria parasite, leading to multi-fold increase in detection and processing throughput with minimal reduction in accuracy.

Shiqi Xu, Xi Yang, Wenhui Liu et al.

Noninvasive optical imaging through dynamic scattering media has numerous important biomedical applications but still remains a challenging task. While standard diffuse imaging methods measure optical absorption or fluorescent emission, it is also well-established that the temporal correlation of scattered coherent light diffuses through tissue much like optical intensity. Few works to date, however, have aimed to experimentally measure and process such temporal correlation data to demonstrate deep-tissue video reconstruction of decorrelation dynamics. In this work, we utilize a single-photon avalanche diode (SPAD) array camera to simultaneously monitor the temporal dynamics of speckle fluctuations at the single-photon level from 12 different phantom tissue surface locations delivered via a customized fiber bundle array. We then apply a deep neural network to convert the acquired single-photon measurements into video of scattering dynamics beneath rapidly decorrelating tissue phantoms. We demonstrate the ability to reconstruct images of transient (0.1-0.4s) dynamic events occurring up to 8 mm beneath a decorrelating tissue phantom with millimeter-scale resolution, and highlight how our model can flexibly extend to monitor flow speed within buried phantom vessels.

Kevin C. Zhou, Colin Cooke, Jaehee Park et al.

We present a feature-free photogrammetric technique that enables quantitative 3D mesoscopic (mm-scale height variation) imaging with tens-of-micron accuracy from sequences of images acquired by a smartphone at close range (several cm) under freehand motion without additional hardware. Our end-to-end, pixel-intensity-based approach jointly registers and stitches all the images by estimating a coaligned height map, which acts as a pixel-wise radial deformation field that orthorectifies each camera image to allow homographic registration. The height maps themselves are reparameterized as the output of an untrained encoder-decoder convolutional neural network (CNN) with the raw camera images as the input, which effectively removes many reconstruction artifacts. Our method also jointly estimates both the camera's dynamic 6D pose and its distortion using a nonparametric model, the latter of which is especially important in mesoscopic applications when using cameras not designed for imaging at short working distances, such as smartphone cameras. We also propose strategies for reducing computation time and memory, applicable to other multi-frame registration problems. Finally, we demonstrate our method using sequences of multi-megapixel images captured by an unstabilized smartphone on a variety of samples (e.g., painting brushstrokes, circuit board, seeds).

Colin L. Cooke, Fanjie Kong, Amey Chaware et al.

This paper introduces a new method of data-driven microscope design for virtual fluorescence microscopy. Our results show that by including a model of illumination within the first layers of a deep convolutional neural network, it is possible to learn task-specific LED patterns that substantially improve the ability to infer fluorescence image information from unstained transmission microscopy images. We validated our method on two different experimental setups, with different magnifications and different sample types, to show a consistent improvement in performance as compared to conventional illumination methods. Additionally, to understand the importance of learned illumination on inference task, we varied the dynamic range of the fluorescent image targets (from one to seven bits), and showed that the margin of improvement for learned patterns increased with the information content of the target. This work demonstrates the power of programmable optical elements at enabling better machine learning algorithm performance and at providing physical insight into next generation of machine-controlled imaging systems.