Microscopic imaging of anisotropic samples has many important applications in cytopathology. The endogenous contrast from the polarization properties of a specimen, such as its birefringence, provides valuable diagnostic information for several deadly diseases, including cardiac amyloidosis and squamous cell carcinoma, for example. In the past, polarized light microscopy (PLM) has been widely used as a diagnostic tool during the clinical review. However, in analogy with the standard microscope, the PLM typically has a restricted spatial-bandwidth product (SBP). As a consequence, one can either image a large area with low resolution or see the details of a very small area of the sample at the resolutions required for accurate analysis. To address the SBP issue of the PLM, we propose a computational microscopy method, termed vectorial Fourier ptychography, to illuminate the specimen with polarized light from different angles and detects different polarization states of the diffracted light. By illuminating a specimen with plane waves from different angles, our vectorial Fourier ptychography method effectively modulates the high-spatial-frequency components of the specimen into lower frequencies that can be detected by the optical system. With a Jones calculus-based forward model and a second-order phase retrieval method, we can reconstruct high-resolution, wide field-of-view(FOV) amplitude, phase, birefringence, retardance, and diattenuation of the specimen. To assess the reconstruction accuracy of our method, we imaged polystyrene beads submerged in immersion oils of different refractive index, as well as monosodium urate crystals. Further, To validate the diattenuation reconstruction accuracy, we reconstruct a USAF resolution test chart with a half blocked by a linear polarizer. These experiments confirm quantitatively accurate reconstruction results with a 1.25 um full-pitch resolution over a FOV of 6.6 x 4.4 mm^2, which is 5 times higher than the native (brightfield) resolution of the non-computational optical system. Finally, we demonstrate our technique by producing high SBP polarization images of several anisotropic biologic samples, includes collagen tissue, congo red stained cardiac tissue, and a bean root sample.
Fluorescence imaging is used throughout biological research to identify subcellular structures, detect neural activity, and differentiate cell types. Multi-channel fluorescence is a challenging subset of fluorescence imaging where multiple fluorescent modes are emitted simultaneously, allowing the detection of a multitude of elements within the specimen (for example, multiple types of neurons). In our work, we demonstrate a learned sensing approach to realize virtual multi-channel fluorescence, by jointly optimizing image illumination and a deep learning neural network that infers labels from brightfield images. We used our setup to demonstrate the influence of key design decisions, such as model architecture, choice of loss function, and amount of input images, on the final optical design. We expect that our work can provide a better understanding of building machine learning based imaging systems and demonstrate the scalability of our illumination optimization technique.
We present a novel approach, based on the use of an array of cameras with custom optics, which can capture snapshot stereoscopic gigapixel images across 1cm2 area at 1-micrometer half-pitch resolution. Our system uses a large space-bandwidth product objective lens to form an intermediate image, which is captured by 96 micro-cameras arranged in a flat array. Each camera records a 10-megapixel image from a unique section of the sample, which are then stitched to produce the final composite. Our system is well suited for applications in digital pathology and in vitro cell-cultures imaging.
We propose a new sensitive diffuse correlation spectroscopy(DCS) method that can probe and identify different decorrelation events happens in sub-second, by acquiring parallelized measurements from 12 fiber detectors placed at different positions on the tissue-phantom surface with a 32 ×32 SPAD array, and process the data with deep learning methods. Both experimental and simulation phantom studies are conducted to evaluate the performance of our system in classifying and imaging decorrelation patterns presented under a 5mm thick tissue phantom made with rapidly decorrelating scattering media.
We present a simple low-cost microscope that uses a vectorial extension of Fourier ptychography to recover the absorption, phase and polarization properties of a sample at high-NA across a wide field-of-view. Our principle is validated by experimentally imaging quantitative test targets as well as a plant root and rabbit spinal cord cross-sections, with which we demonstrate the ability to record complex specimen birefringence over 10.4 mm2 field-of-view at 0.73um resolution. Our new Fourier ptychographic approach also enables the measurement and correction of polarization-dependent pupil aberrations. We hope this simplicity helps adapt joint polarization and phase imaging to a wider array of applications.
We present a gigapixel-scale multi-aperture microscope capable of measuring a sample’s 3D height profile over multi-centimeter-scale fields of view with a series of single synchronized camera snapshots. Exploiting the overlap redundancy in our multi-aperture camera array microscope, we developed a novel, end-to-end photogrammetric reconstruction algorithm that simultaneously calibrates the cameras’ 3D positions and poses, stitches the acquired images, and generates a coregistered, pixel-wise 3D height map of the sample. Our work opens the door to video-rate 3D monitoring of dynamic scenes at micrometer-scale resolutions and centimeter-scale fields of view.
Fluorescence imaging has been used for decades to identify important elements in biological samples. However, the additional overhead of fixing and staining the sample limits the pervasiveness of the technique. Here we show a robust virtual fluorescence technique which uses deep learning to jointly optimize microscope design (i.e. illumination pattern) and fluorescence image reconstruction. Our results show how by combining the image capture and processing stages we can accurately and adaptively predict fluorescent images from unlabelled biological samples.
Recently developed Single-photon Avalanche Diode (SPAD) array cameras have single photon sensitivity and can provide time-of-flight information for LIDAR imaging. These SPAD cameras, however, have very few pixels and readout binary images, which are typically averaged to provide an image with sufficient dynamic range. Here, we propose to implement a modified version of Fourier ptychography (FP), a synthetic aperture technique, on SPAD cameras to reconstruct an image with much higher resolution and larger dynamic range from its binary measurements. We successfully validate this using simulated and experimental results to show its potential for recording LIDAR images at high resolution and speed.
We describe a visible-light multi-spectral system for vascular oximetry studies that can be implemented in lowand middle-income countries, using a low-cost electronics and optical elements, for instance a Raspberry Pi, a Pi camera under a resolution of 5-megapixel, 2592x1944-pixel resolution, and four different light sources at 480nm, 532nm, 593nm and 610nm on a singular structured illumination area. It is designed to quantify the vascular oxygen saturation change of the rat dorsal spinal cord, which uses a Phyton custom application that synchronize all elements to execute the imaging process in one system, powered by a portable rechargeable 5V battery pack. Aimed for drug discovery, tracking disease progression and understanding of progressive and degenerative diseases. By replacing expensive and bulky imaging systems.
Obtaining gigapixel images is a challenging task because of the aberrations present in a conventional optical system, small sensor sizes and limited data-capture rates of cameras. Multi-aperture Fourier ptychography (MAFP) was proposed recently by us to solve the issue of increasing the data acquisition bandwidth by parallelizing data capture using an array of lenses coupled with discrete detectors. We present an advanced MAFP system based on the Scheimpflug configuration to improve the MAFP system performance at high NAs. This system requires a complicated optical system due to the large number of degrees of freedom present in the system. Hence we developed a 3D-printed system which solves this issue and decreases the cost of the setup tremendously. In this manuscript we present the details of our 3D printed design and preliminary images obtained using this system.
The spatial resolution of a microscope is inversely proportionate to the sum of the objective numerical aperture (NA) and the illumination NA. Fourier Ptychography (FP) microscopy achieves high-resolution, wide-field imaging by the use of a low-NA, wide-field objective combined with time-sequential synthesis of high NA illumination using an array of LEDs. We describe reconstruction algorithms based on Fresnel propagation, rather than the traditional Fraunhofer propagation, which enables more accurate representation of LED illumination and hence reduced aberration in the image reconstruction. This also enables the new technique of Multi-Aperture Fourier Ptychography in the near-field. In this work the implementation of this algorithm is described together with some experimental results. The performance of this algorithm is validated by comparing to Fraunhofer based algorithm. More sophisticated update functions in the reconstruction procedures developed for FP are implemented with this algorithm and their performance is validated. The pupil phase can also be reconstructed during the reconstruction procedure hence allowing us to correct for the aberrations in the optical system without the need of any additional measurements.
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