High-throughput fluorescence microscopy using multi-frame motion deblurring.

We demonstrate multi-frame motion deblurring for gigapixel wide-field fluorescence microscopy using fast slide scanning with coded illumination. Our method illuminates the sample with multiple pulses within each exposure, in order to introduce structured motion blur. By deconvolving this known motion sequence from the set of acquired measurements, we recover the object with up to 10× higher SNR than when illuminated with a single pulse (strobed illumination), while performing acquisition at 5× higher frame-rate than a comparable stop-and-stare method. Our coded illumination sequence is optimized to maximize the reconstruction SNR. We also derive a framework for determining when coded illumination is SNR-optimal in terms of system parameters such as source illuminance, noise, and motion stage specifications. This helps system designers to choose the ideal technique for high-throughput microscopy of very large samples.

Motion-resolved quantitative phase imaging.

The temporal resolution of quantitative phase imaging with Differential Phase Contrast (DPC) is limited by the requirement for multiple illumination-encoded measurements. This inhibits imaging of fast-moving samples. We present a computational approach to model and correct for non-rigid sample motion during the DPC acquisition in order to improve temporal resolution to that of a single-shot method and enable imaging of motion dynamics at the framerate of the sensor. Our method relies on the addition of a simultaneously-acquired color-multiplexed reference signal to enable non-rigid registration of measurements prior to phase retrieval. We show experimental results where we reduce motion blur from fast-moving live biological samples.

Efficient illumination angle self-calibration in Fourier ptychography.

Fourier ptychography captures intensity images with varying source patterns (illumination angles) in order to computationally reconstruct large space-bandwidth-product images. Accurate knowledge of the illumination angles is necessary for good image quality; hence, calibration methods are crucial, despite often being impractical or slow. Here, we propose a fast, robust, and accurate self-calibration algorithm that uses only experimentally collected data and general knowledge of the illumination setup. First, our algorithm makes a fast direct estimate of the brightfield illumination angles based on image processing. Then, a more computationally intensive spectral correlation method is used inside the iterative solver to further refine the angle estimates of both brightfield and darkfield images. We demonstrate our method for correcting large and small misalignment artifacts in 2D and 3D Fourier ptychography with different source types: an LED array, a galvo-steered laser, and a high-NA quasi-dome LED illuminator.

Quantitative differential phase contrast (DPC) microscopy with computational aberration correction.

Differential Phase Contrast (DPC) microscopy is a practical method for recovering quantitative phase from intensity images captured with different source patterns in an LED array microscope. Being a partially coherent imaging method, DPC does not suffer from speckle artifacts and achieves 2× better resolution than coherent methods. Like all imaging systems, however, DPC is susceptible to aberrations. Here, we propose a method of algorithmic self-calibration for DPC where we simultaneously recover the complex-field of the sample and the spatially-variant aberrations of the system, using 4 images with different illumination source patterns. The resulting phase reconstructions are digitally aberration-corrected.

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC).

We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification-an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel.

Multi-Contrast Imaging and Digital Refocusing on a Mobile Microscope with a Domed LED Array.

We demonstrate the design and application of an add-on device for improving the diagnostic and research capabilities of CellScope--a low-cost, smartphone-based point-of-care microscope. We replace the single LED illumination of the original CellScope with a programmable domed LED array. By leveraging recent advances in computational illumination, this new device enables simultaneous multi-contrast imaging with brightfield, darkfield, and phase imaging modes. Further, we scan through illumination angles to capture lightfield datasets, which can be used to recover 3D intensity and phase images without any hardware changes. This digital refocusing procedure can be used for either 3D imaging or software-only focus correction, reducing the need for precise mechanical focusing during field experiments. All acquisition and processing is performed on the mobile phone and controlled through a smartphone application, making the computational microscope compact and portable. Using multiple samples and different objective magnifications, we demonstrate that the performance of our device is comparable to that of a commercial microscope. This unique device platform extends the field imaging capabilities of CellScope, opening up new clinical and research possibilities.

Longitudinal study of mammary epithelial and fibroblast co-cultures using optical coherence tomography reveals morphological hallmarks of pre-malignancy.

The human mammary gland is a complex and heterogeneous organ, where the interactions between mammary epithelial cells (MEC) and stromal fibroblasts are known to regulate normal biology and tumorigenesis. We aimed to longitudinally evaluate morphology and size of organoids in 3D co-cultures of normal (MCF10A) or pre-malignant (MCF10DCIS.com) MEC and hTERT-immortalized fibroblasts from reduction mammoplasty (RMF). This co-culture model, based on an isogenic panel of cell lines, can yield insights to understand breast cancer progression. However, 3D cultures pose challenges for quantitative assessment and imaging, especially when the goal is to measure the same organoid structures over time. Using optical coherence tomography (OCT) as a non-invasive method to longitudinally quantify morphological changes, we found that OCT provides excellent visualization of MEC-fibroblast co-cultures as they form ductal acini and remodel over time. Different concentrations of fibroblasts and MEC reflecting reported physiological ratios [1] were evaluated, and we found that larger, hollower, and more aspherical acini were formed only by pre-malignant MEC (MCF10DCIS.com) in the presence of fibroblasts, whereas in comparable conditions, normal MEC (MCF10A) acini remained smaller and less aspherical. The ratio of fibroblast to MEC was also influential in determining organoid phenotypes, with higher concentrations of fibroblasts producing more aspherical structures in MCF10DCIS.com. These findings suggest that stromal-epithelial interactions between fibroblasts and MEC can be modeled in vitro, with OCT imaging as a convenient means of assaying time dependent changes, with the potential for yielding important biological insights about the differences between benign and pre-malignant cells.