Simultaneous imaging of various facets of intact biological systems across multiple spatiotemporal scales would be an invaluable tool in biomedicine. However, conventional imaging modalities have stark tradeoffs precluding the fulfilment of all functional requirements.Here we propose the refractive index (RI), an intrinsic quantity governing light-matter interaction, as a means for such measurement. We show that major endogenous subcellular structures, which are conventionally accessed via exogenous fluorescence labeling, are encoded in 3D RI tomograms. We decode this information in a data-driven manner, thereby achieving multiplexed microtomography. This approach inherits the advantages of both highspecificity fluorescence imaging and label-free RI imaging. The performance, reliability, and scalability of this technology have been extensively characterized, and its application within single-cell profiling at unprecedented scales has been demonstrated..

The healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.

SummaryThe kinetics of the enzymatic hydrolysis of sucrose by invertase have been examined, with particular emphasis on high substrate concentration. Initial rates of reaction were determined by following the production of glucose directly as a function of time over a wide range of substrate concentrations (0.04M to 2.06M). The resulting data reveal a reaction rate that increases gradually until the sucrose concentration reaches about 0.2921.3, after which the reaction velocity decreases with increasing sucrose concentration. Previous workers (e.g., Xelson and Schubertl) have reported a peak reaction velocity as determined by indirect polarimetric measurements of glucose, a t a sucrose concentration of about 0.17M. These measurements, however, neglect the intermediate oligosaccharides formed by the transferase action of invertase,8-lo and assume equal amounts of glucose and fructose. According to Anderson et u1.,Io these oligosaccharides interfere by producing an erroneously low reaction rate. Experimental results of this work confirm Anderson's observations, and show a further reaction rate increase of nearly 20% between sucrose concentrations of 0.177M and 0.285M under the same conditions of temperature, pH, and enzyme concentration.Effects of substrate diffusion, solution viscosity, water concentration, and substrate inhibition were experimentally studied and the results incorporated into a kinetic model that has proven satisfactory in modeling the experimental results. This model takes into account inhibition by primary substrate, with concentration of the secondary substrate water, as a rate limiting factor at sucrose concentrations greater than 0.285M.The effects of mixing, in terms of volumetric power input, on the reaction rate have been tested. Approximately 40-fold increase in volumetric power input caused no increase in the reaction rate. These experiments have shown that bulk mass transfer is not a rate limiting factor under the experimental conditions.

We present a deep neural network to reduce coherent noise in three-dimensional quantitative phase imaging. Inspired by the cycle generative adversarial network, the denoising network was trained to learn a transform between two image domains: clean and noisy refractive index tomograms. The unique feature of this network, distinct from previous machine learning approaches employed in the optical imaging problem, is that it uses unpaired images. The learned network quantitatively demonstrated its performance and generalization capability through denoising experiments of various samples. We concluded by applying our technique to reduce the temporally changing noise emerging from focal drift in time-lapse imaging of biological cells. This reduction cannot be performed using other optical methods for denoising.

For appropriate treatments of infectious diseases, rapid identification of the pathogens is crucial. Here, we developed a rapid and label-free method for identifying common bacterial pathogens as individual bacteria by using three-dimensional quantitative phase imaging and deep learning. We achieved 95% accuracy in classifying 19 bacterial species by exploiting the rich information in three-dimensional refractive index tomograms with a convolutional neural network classifier. Extensive analysis of the features extracted by the trained classifier was carried out, which supported that our classifier is capable of learning species-dependent characteristics. We also confirmed that utilizing three-dimensional refractive index tomograms was crucial for identification ability compared to two-dimensional imaging. This method, which does not require time-consuming culture, shows high feasibility for diagnosing patients with infectious diseases who would benefit from immediate and adequate antibiotic treatment.

Objective and Impact Statement. We propose a rapid and accurate blood cell identification method exploiting deep learning and label-free refractive index (RI) tomography. Our computational approach that fully utilizes tomographic information of bone marrow (BM) white blood cell (WBC) enables us to not only classify the blood cells with deep learning but also quantitatively study their morphological and biochemical properties for hematology research. Introduction. Conventional methods for examining blood cells, such as blood smear analysis by medical professionals and fluorescence-activated cell sorting, require significant time, costs, and domain knowledge that could affect test results. While label-free imaging techniques that use a specimen’s intrinsic contrast (e.g., multiphoton and Raman microscopy) have been used to characterize blood cells, their imaging procedures and instrumentations are relatively time-consuming and complex. Methods. The RI tomograms of the BM WBCs are acquired via Mach-Zehnder interferometer-based tomographic microscope and classified by a 3D convolutional neural network. We test our deep learning classifier for the four types of bone marrow WBC collected from healthy donors (n=10): monocyte, myelocyte, B lymphocyte, and T lymphocyte. The quantitative parameters of WBC are directly obtained from the tomograms. Results. Our results show >99% accuracy for the binary classification of myeloids and lymphoids and >96% accuracy for the four-type classification of B and T lymphocytes, monocyte, and myelocytes. The feature learning capability of our approach is visualized via an unsupervised dimension reduction technique. Conclusion. We envision that the proposed cell classification framework can be easily integrated into existing blood cell investigation workflows, providing cost-effective and rapid diagnosis for hematologic malignancy.

Optical diffraction tomography measures the three-dimensional refractive index map of a specimen and visualizes biochemical phenomena at the nanoscale in a non-destructive manner. One major drawback of optical diffraction tomography is poor axial resolution due to limited access to the three-dimensional optical transfer function. This missing cone problem has been addressed through regularization algorithms that use a priori information, such as non-negativity and sample smoothness. However, the iterative nature of these algorithms and their parameter dependency make real-time visualization impossible. In this article, we propose and experimentally demonstrate a deep neural network, which we term DeepRegularizer, that rapidly improves the resolution of a three-dimensional refractive index map. Trained with pairs of datasets (a raw refractive index tomogram and a resolution-enhanced refractive index tomogram via the iterative total variation algorithm), the three-dimensional U-net-based convolutional neural network learns a transformation between the two tomogram domains. The feasibility and generalizability of our network are demonstrated using bacterial cells and a human leukaemic cell line, and by validating the model across different samples. DeepRegularizer offers more than an order of magnitude faster regularization performance compared to the conventional iterative method. We envision that the proposed data-driven approach can bypass the high time complexity of various image reconstructions in other imaging modalities.

In closed hydroponic systems, periodic readjustment of nutrient solution is necessary to continuously provide stable environment to plant roots because the interaction between plant and nutrient solution changes the rate of ions in it. The traditional method is to repeat supplying small amount of premade concentrated nutrient solution, measuring total electric conductivity and pH of the tank only. As it cannot control the collapse of ion rates, recent researches try to measure the concentration of individual components to provide insufficient ions only. However, those approaches use titrationlike heuristic approaches, which repeat adding small amount of components and measuring ion density a lot of times for a single control input. Both traditional and recent methods are not only time-consuming, but also cannot predict chemical reactions related with control inputs because the nutrient solution is a nonlinear complex system, including many precipitation reactions and complicated interactions. We present a continuous network model of the nutrient solution system, whose reactions are described as differential equations. The model predicts molar concentration of each chemical components and total dissolved solids with low error. This model also can calculate the amount of chemical compounds needed to produce a desired nutrient solution, by reverse calculation from dissolved ion concentrations.