arXiv subjects

Shaowei Jiang

Publications and source records attributed to Shaowei Jiang.

32 records · Page 2Linked to original sources

arXiv2020

Virtual brightfield and fluorescence staining for Fourier ptychography via unsupervised deep learning

Fourier ptychographic microscopy (FPM) is a computational approach geared towards creating high-resolution and large field-of-view images without mechanical scanning. To acquire color images of histology slides, it often requires sequential acquisitions with red, green, and blue illuminations. The color reconstructions often suffer from coherent artifacts that are not presented in regular incoherent microscopy images. As a result, it remains a challenge to employ FPM for digital pathology applications, where resolution and color accuracy are of critical importance. Here we report a deep learning approach for performing unsupervised image-to-image translation of FPM reconstructions. A cycle-consistent adversarial network with multiscale structure similarity loss is trained to perform virtual brightfield and fluorescence staining of the recovered FPM images. In the training stage, we feed the network with two sets of unpaired images: 1) monochromatic FPM recovery, and 2) color or fluorescence images captured using a regular microscope. In the inference stage, the network takes the FPM input and outputs a virtually stained image with reduced coherent artifacts and improved image quality. We test the approach on various samples with different staining protocols. High-quality color and fluorescence reconstructions validate its effectiveness.

eess.IV↗

arXiv2020

Super-resolved multispectral lensless microscopy via angle-tilted, wavelength-multiplexed ptychographic modulation

We report an angle-tilted, wavelength-multiplexed ptychographic modulation approach for multispectral lensless on-chip microscopy. In this approach, we illuminate the specimen with lights at 5 wavelengths simultaneously. A prism is added at the illumination path for spectral dispersion. Lightwaves at different wavelengths, thus, hit the specimen at slightly different incident angles, breaking the ambiguities in mixed state ptychographic reconstruction. At the detection path, we place a thin diffuser in-between the specimen and the monochromatic image sensor for encoding the spectral information into 2D intensity measurements. By scanning the sample to different x-y positions, we acquire a sequence of monochromatic images for reconstructing the 5 complex object profiles at the 5 wavelengths. An up-sampling procedure is integrated into the recovery process to bypass the resolution limit imposed by the imager pixel size. We demonstrate a half-pitch resolution of 0.55 microns using an image sensor with 1.85-micron pixel size. We also demonstrate quantitative and high-quality multispectral reconstructions of stained tissue sections for digital pathology applications.

physics.optics↗

arXiv2020

Wide-field, high-resolution lensless on-chip microscopy via near-field blind ptychographic modulation

We report a novel lensless on-chip microscopy platform based on near-field blind ptychographic modulation. In this platform, we place a thin diffuser in between the object and the image sensor for light wave modulation. By blindly scanning the unknown diffuser to different x-y positions, we acquire a sequence of modulated intensity images for quantitative object recovery. Different from previous ptychographic implementations, we employ a unit magnification configuration with a Fresnel number of ~50,000, which is orders of magnitude higher than previous ptychographic setups. The unit magnification configuration allows us to have the entire sensor area, 6.4 mm by 4.6 mm, as the imaging field of view. The ultra-high Fresnel number enables us to directly recover the positional shift of the diffuser in the phase retrieval process, addressing the positioning accuracy issue plagued in regular ptychographic experiments. In our implementation, we use a low-cost, DIY scanning stage to perform blind diffuser modulation. Precise mechanical scanning that is critical in conventional ptychography experiments is no longer needed in our setup. We further employ an up-sampling phase retrieval scheme to bypass the resolution limit set by the imager pixel size and demonstrate a half-pitch resolution of 0.78 micron. We validate the imaging performance via in vitro cell cultures, transparent and stained tissue sections, and a thick biological sample. We show that the recovered quantitative phase map can be used to perform effective cell segmentation of the dense yeast culture. We also demonstrate 3D digital refocusing of the thick biological sample based on the recovered wavefront. The reported platform provides a cost-effective and turnkey solution for large field-of-view, high-resolution, and quantitative on-chip microscopy.

eess.IV↗

arXiv2019

OpenWSI: a low-cost, high-throughput whole slide imaging system via single-frame autofocusing and open-source hardware

Recent advancements in whole slide imaging (WSI) have moved pathology closer to digital practice. Existing systems require precise mechanical control and the cost is prohibitive for most individual pathologists. Here we report a low-cost and high-throughput WSI system termed OpenWSI. The reported system is built using off-the-shelf components including a programmable LED array, a photographic lens, and a low-cost computer numerical control (CNC) router. Different from conventional WSI platforms, our system performs real-time single-frame autofocusing using color-multiplexed illumination. For axial positioning control, we perform coarse adjustment using the CNC router and precise adjustment using the ultrasonic motor ring in the photographic lens. By using a 20X objective lens, we show that the OpenWSI system has a resolution of ~0.7 microns. It can acquire whole slide images of a 225-mm^2 region in ~2 mins, with throughput comparable to existing high-end platforms. The reported system offers a turnkey solution to transform the high-end WSI platforms into one that can be made broadly available and utilizable without loss of capacity.

eess.IV↗

arXiv2019

Ptychographic modulation engine (PME): a low-cost DIY microscope add-on for coherent super-resolution imaging

Imaging of biological cells and tissues often relies on fluorescent labels, which offer high contrast with molecular specificity. The use of exogenous labeling agents, however, may alter the normal physiology of the bio-specimens. Complementary to the established fluorescence microscopy, label-free quantitative phase imaging provides an objective morphological measurement tool for bio-specimens and is free of variability introduced by contrast agents. Here we report a simple and low-cost microscope add-on, termed Ptychographic Modulation Engine (PME), for super-resolution quantitative phase imaging. In this microscope add-on module, we attach a diffuser to a 3D-printed holder that can be mechanically moved to different x-y positions. We then use two vibrational motors to introduce random positional shifts to the diffuser. The add-on module can be placed between the objective lens and the specimen in most existing microscope platforms. Thanks to the diffuser modulation process, the otherwise inaccessible high-resolution object information can now be encoded into the captured images. In the ptychographic phase retrieval process, we jointly recover the complex object wavefront, the complex diffuser profile, and the unknown positional shifts of the diffuser. We demonstrate a 4-fold resolution gain over the diffraction limit of the employed 2X objective lens. We also test our approach for in-vivo cell imaging, where we are able to adjust the focus after the data has been captured. The reported microscope add-on provides a turnkey solution for super-resolution quantitative phase imaging. It may find applications in label-free bio-imaging where both large field-of-view and high resolution are needed.

physics.ins-det↗

arXiv2019

PgNN: Physics-guided Neural Network for Fourier Ptychographic Microscopy

Fourier ptychography (FP) is a newly developed computational imaging approach that achieves both high resolution and wide field of view by stitching a series of low-resolution images captured under angle-varied illumination. So far, many supervised data-driven models have been applied to solve inverse imaging problems. These models need massive amounts of data to train, and are limited by the dataset characteristics. In FP problems, generic datasets are always scarce, and the optical aberration varies greatly under different acquisition conditions. To address these dilemmas, we model the forward physical imaging process as an interpretable physics-guided neural network (PgNN), where the reconstructed image in the complex domain is considered as the learnable parameters of the neural network. Since the optimal parameters of the PgNN can be derived by minimizing the difference between the model-generated images and real captured angle-varied images corresponding to the same scene, the proposed PgNN can get rid of the problem of massive training data as in traditional supervised methods. Applying the alternate updating mechanism and the total variation regularization, PgNN can flexibly reconstruct images with improved performance. In addition, the Zernike mode is incorporated to compensate for optical aberrations to enhance the robustness of FP reconstructions. As a demonstration, we show our method can reconstruct images with smooth performance and detailed information in both simulated and experimental datasets. In particular, when validated in an extension of a high-defocus, high-exposure tissue section dataset, PgNN outperforms traditional FP methods with fewer artifacts and distinguishable structures.

eess.IV↗

arXiv2019

Super-resolution microscopy via ptychographic structured modulation of a diffuser

We report a new coherent imaging technique, termed ptychographic structured modulation (PSM), for quantitative super-resolution microscopy. In this technique, we place a thin diffuser (i.e., a scattering lens) in between the sample and the objective lens to modulate the complex light waves from the object. The otherwise inaccessible high-resolution object information can thus be encoded into the captured images. We then employ a ptychographic phase retrieval process to jointly recover the exit wavefront of the complex object and the unknown diffuser profile. Unlike the illumination-based super-resolution approach, the recovered image of our approach depends upon how the complex wavefront exits the sample - not enters it. Therefore, the sample thickness becomes irrelevant during reconstruction. After recovery, we can propagate the super-resolution complex wavefront to any position along the optical axis. We validate our approach using a resolution target, a quantitative phase target, a two-layer sample, and a thick PDMS sample. We demonstrate a 4.5-fold resolution gain over the diffraction limit. We also show that a 4-fold resolution gain can be achieved with as few as ~30 images. The reported approach may provide a quantitative super-resolution strategy for coherent light, X-ray, and electron imaging.

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arXiv2019

Rapid and robust whole slide imaging based on LED-array illumination and color-multiplexed single-shot autofocusing

Background: The use of whole slide imaging (WSI) for digital pathology has recently been cleared for primary diagnosis in the US. A conventional WSI system scans the tissue slide to different positions and acquires the digital images. In a typical implementation, a focus map is created prior to the scanning process, leading to significant overhead time and a necessity for high positional accuracy of the mechanical system. The resulting cost of WSI system is often prohibitive for frozen section procedure during surgery. Methods: We report a novel WSI scheme based on a programmable LED array for sample illumination. In between two regular brightfield image acquisitions, we acquire one additional image by turning on a red and a green LED for color multiplexed illumination. We then identify the translational shift of the red- and green-channel images by maximizing the image mutual information or cross-correlation. The resulting translational shift is used for dynamic focus correction in the scanning process. Since we track the differential focus during adjacent acquisitions, there is no positional repeatability requirement in our scheme. Results: We demonstrate a prototype WSI platform with a mean focusing error of ~0.3 microns. Different from previous implementations, this prototype platform requires no focus map surveying, no secondary camera or additional optics, and allows for continuous sample motion in the focus tracking process. Conclusions: A programmable LED array can be used for color-multiplexed single-shot autofocusing in WSI. The reported scheme may enable the development of cost-effective WSI platforms without positional repeatability requirement. It may also provide a turnkey solution for other high-content microscopy applications.

eess.IV↗

arXiv2019

Full-field Fourier ptychography (FFP): spatially varying pupil modeling and its application for rapid field-dependent aberration metrology

Digital aberration measurement and removal play a prominent role in computational imaging platforms aimed at achieving simple and compact optical arrangements. A recent important class of such platforms is Fourier ptychography, which is geared towards efficiently creating gigapixel images with high resolution and large field of view (FOV). In current FP implementations, pupil aberration is often recovered at each small segment of the entire FOV. This reconstruction strategy fails to consider the field-dependent nature of the optical pupil. Given the power series expansion of the wavefront aberration, the spatially varying pupil can be fully characterized by tens of coefficients over the entire FOV. With this observation, we report a Full-field Fourier Ptychography (FFP) scheme for rapid and robust aberration metrology. The meaning of 'full-field' in FFP is referred to the recovering of the 'full-field' coefficients that govern the field-dependent pupil over the entire FOV. The optimization degrees of freedom are at least two orders of magnitude lower than the previous implementations. We show that the image acquisition process of FFP can be completed in ~1s and the spatially varying aberration of the entire FOV can be recovered in ~35s using a CPU. The reported approach may facilitate the further development of Fourier ptychography. Since no moving part or calibration target is needed in this approach, it may find important applications in aberration metrology. The derivation of the full-field coefficients and its extension for Zernike modes also provide a general tool for analyzing spatially varying aberrations in computational imaging systems.

physics.optics↗

arXiv2019

Field-portable quantitative lensless microscopy based on translated speckle illumination and sub-sampled ptychographic phase retrieval

We report a compact, cost-effective and field-portable lensless imaging platform for quantitative microscopy. In this platform, the object is placed on top of an image sensor chip without using any lens. We use a low-cost galvo scanner to rapidly scan an unknown laser speckle pattern on the object. To address the positioning repeatability and accuracy issues, we directly recover the positional shifts of the speckle pattern based on the phase correlation of the captured images. To bypass the resolution limit set by the imager pixel size, we employ a sub-sampled ptychographic phase retrieval process to recover the complex object. We validate our approach using a resolution target, a phase target, and a biological sample. Our results show that accurate, high-quality complex images can be obtained from a lensless dataset with as few as ~10 images. We also demonstrate the reported approach to achieve a 6.4 mm by 4.6 mm field of view and a half pitch resolution of 1 miron. The reported approach may provide a quantitative lensless imaging strategy for addressing point-of-care, global-health, and telemedicine related challenges.

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arXiv2019

Near-field Fourier ptychography: super-resolution phase retrieval via speckle illumination

Achieving high spatial resolution is the goal of many imaging systems. Designing a high-resolution lens with diffraction-limited performance over a large field of view remains a difficult task in imaging system design. On the other hand, creating a complex speckle pattern with wavelength-limited spatial features is effortless and can be implemented via a simple random diffuser. With this observation and inspired by the concept of near-field ptychography, we report a new imaging modality, termed near-field Fourier ptychography, for tackling high-resolution imaging challenges in both microscopic and macroscopic imaging settings. The meaning of 'near-field' is referred to placing the object at a short defocus distance with a large Fresnel number. In our implementations, we project a speckle pattern with fine spatial features on the object instead of directly resolving the spatial features via a high-resolution lens. We then translate the object (or speckle) to different positions and acquire the corresponding images using a low-resolution lens. A ptychographic phase retrieval process is used to recover the complex object, the unknown speckle pattern, and the coherent transfer function at the same time. In a microscopic imaging setup, we use a 0.12 numerical aperture (NA) lens to achieve a NA of 0.85 in the reconstruction process. In a macroscale photographic imaging setup, we achieve ~7-fold resolution gain using a photographic lens. The final achievable resolution is not determined by the collection optics. Instead, it is determined by the feature size of the speckle pattern. The reported imaging modality can be employed in light, coherent X-ray, and transmission electron imaging systems to increase resolution and provide quantitative absorption and phase contrast of the object.

physics.optics↗

arXiv2018

Axially-shifted pattern illumination for macroscale turbidity suppression and virtual volumetric confocal imaging without axial scanning

Structured illumination has been widely used for optical sectioning and 3D surface recovery. In a typical implementation, multiple images under non-uniform pattern illumination are used to recover a single object section. Axial scanning of the sample or the objective lens is needed for acquiring the 3D volumetric data. Here we demonstrate the use of axially-shifted pattern illumination (asPI) for virtual volumetric confocal imaging without axial scanning. In the reported approach, we project illumination patterns at a tilted angle with respect to the detection optics. As such, the illumination patterns shift laterally at different z sections and the sample information at different z-sections can be recovered based on the captured 2D images. We demonstrate the reported approach for virtual confocal imaging through a diffusing layer and underwater 3D imaging through diluted milk. We show that we can acquire the entire confocal volume in ~1s with a throughput of 420 megapixels per second. Our approach may provide new insights for developing confocal light ranging and detection systems in degraded visual environments.

cs.CV↗

arXiv2018

Solving Fourier ptychographic imaging problems via neural network modeling and TensorFlow

Fourier ptychography is a recently developed imaging approach for large field-of-view and high-resolution microscopy. Here we model the Fourier ptychographic forward imaging process using a convolution neural network (CNN) and recover the complex object information in the network training process. In this approach, the input of the network is the point spread function in the spatial domain or the coherent transfer function in the Fourier domain. The object is treated as 2D learnable weights of a convolution or a multiplication layer. The output of the network is modeled as the loss function we aim to minimize. The batch size of the network corresponds to the number of captured low-resolution images in one forward / backward pass. We use a popular open-source machine learning library, TensorFlow, for setting up the network and conducting the optimization process. We analyze the performance of different learning rates, different solvers, and different batch sizes. It is shown that a large batch size with the Adam optimizer achieves the best performance in general. To accelerate the phase retrieval process, we also discuss a strategy to implement Fourier-magnitude projection using a multiplication neural network model. Since convolution and multiplication are the two most-common operations in imaging modeling, the reported approach may provide a new perspective to examine many coherent and incoherent systems. As a demonstration, we discuss the extensions of the reported networks for modeling single-pixel imaging and structured illumination microscopy (SIM). 4-frame resolution doubling is demonstrated using a neural network for SIM. We have made our implementation code open-source for the broad research community.

cs.CV↗

arXiv2017

Dual-LED-based multichannel microscopy for whole-slide multiplane, multispectral, and phase imaging

We report the development of a multichannel microscopy for whole-slide multiplane, multispectral, and phase imaging. We use trinocular heads to split the beam path into 6 independent channels and employ a camera array for parallel data acquisition, achieving a maximum data throughput of ~1 gigapixel per second. To perform single-frame rapid autofocusing, we place two near-infrared LEDs at the back focal plane of the condenser lens to illuminate the sample from two different incident angles. A hot mirror is used to direct the near-infrared light to an autofocusing camera. For multiplane whole slide imaging (WSI), we acquire 6 different focal planes of a thick specimen simultaneously. For multispectral WSI, we relay the 6 independent image planes to the same focal position and simultaneously acquire information at 6 spectral bands. For whole-slide phase imaging, we acquire images at 3 focal positions simultaneously and use the transport-of-intensity equation to recover the phase information. We also provide an open-source design to further increase the number of channels from 6 to 15. The reported platform provides a simple solution for multiplexed fluorescence imaging and multimodal WSI. Acquiring an instant focal stack without z-scanning may also enable fast 3D dynamic tracking of various biological samples.

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