arXiv subjects

Laura Waller

Publications and source records attributed to Laura Waller.

At least 55 records · Page 3Linked to original sources

arXiv2021

Exceeding the limits of algorithmic self-calibration in super-resolution imaging

Fourier ptychographic microscopy is a computational imaging technique that provides quantitative phase information and high resolution over a large field-of-view. Although the technique presents numerous advantages over conventional microscopy, model mismatch due to unknown optical aberrations can significantly limit reconstruction quality. Many attempts to address this issue rely on embedding pupil recovery into the reconstruction algorithm. In this paper we demonstrate the limitations of a purely algorithmic approach and evaluate the merits of implementing a simple, dedicated calibration procedure. In simulations, we find that for a target sample reconstruction error, we can image without any aberration corrections up to a maximum aberration magnitude of $λ$/40. When we use algorithmic self-calibration, we can increase the aberration magnitude up to $λ$/10, and with our in situ speckle calibration technique, this working range is extended further to a maximum aberration magnitude of $λ$/3. Hence, one can trade-off complexity for accuracy by using a separate calibration process, which is particularly useful for larger aberrations.

physics.optics↗

arXiv2021

Untrained networks for compressive lensless photography

Compressive lensless imagers enable novel applications in an extremely compact device, requiring only a phase or amplitude mask placed close to the sensor. They have been demonstrated for 2D and 3D microscopy, single-shot video, and single-shot hyperspectral imaging; in each of these cases, a compressive-sensing-based inverse problem is solved in order to recover a 3D data-cube from a 2D measurement. Typically, this is accomplished using convex optimization and hand-picked priors. Alternatively, deep learning-based reconstruction methods offer the promise of better priors, but require many thousands of ground truth training pairs, which can be difficult or impossible to acquire. In this work, we propose the use of untrained networks for compressive image recovery. Our approach does not require any labeled training data, but instead uses the measurement itself to update the network weights. We demonstrate our untrained approach on lensless compressive 2D imaging as well as single-shot high-speed video recovery using the camera's rolling shutter, and single-shot hyperspectral imaging. We provide simulation and experimental verification, showing that our method results in improved image quality over existing methods.

eess.IV↗

arXiv2020

Dynamic clay microstructures emerge via ion complexation waves

Clays control carbon, water and nutrient transport in the lithosphere, promote cloud formation5 and lubricate fault slip through interactions among hydrated mineral interfaces. Clay mineral properties are difficult to model because their structures are disordered, curved and dynamic. Consequently, interactions at the clay mineral-aqueous interface have been approximated using electric double layer models based on single crystals of mica and atomistic simulations. We discover that waves of complexation dipoles at dynamically curving interfaces create an emergent long-range force that drives exfoliation and restacking over time- and length-scales that are not captured in existing models. Curvature delocalizes electrostatic interactions in ways that fundamentally differ from planar surfaces, altering the ratio of ions bound to the convex and concave sides of a layer. Multiple-scattering reconstruction of low-dose energy-filtered cryo electron tomography enabled direct imaging of ion complexes and electrolyte distributions at hydrated and curved mineral interfaces with ångstrom resolution over micron length scales. Layers exfoliate and restack abruptly and repeatedly over timescales that depend strongly on the counterion identity, demonstrating that the strong coupling between elastic, electrostatic and hydration forces in clays promote collective reorganization previously thought to be a feature only of active matter.

cond-mat.soft↗

arXiv2020

Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

Miniature fluorescence microscopes are a standard tool in systems biology. However, widefield miniature microscopes capture only 2D information, and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth range. Here, we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective's aperture stop. Placing the phase mask at the aperture stop significantly reduces the size of the device, and varying the focal lengths enables a uniform resolution across a wide depth range. The phase mask encodes the 3D fluorescence intensity into a single 2D measurement, and the 3D volume is recovered by solving a sparsity-constrained inverse problem. We provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the field-varying aberrations in miniature objectives. We demonstrate a prototype that is 17 mm tall and weighs 2.5 grams, achieving 2.76 $μ$m lateral, and 15 $μ$m axial resolution across most of the 900x700x390 $μm^3$ volume at 40 volumes per second. The performance is validated experimentally on resolution targets, dynamic biological samples, and mouse brain tissue. Compared with existing miniature single-shot volume-capture implementations, our system is smaller and lighter and achieves a more than 2x better lateral and axial resolution throughout a 10x larger usable depth range. Our microscope design provides single-shot 3D imaging for applications where a compact platform matters, such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.

eess.IV↗

arXiv2020

A micromirror array with annular partitioning for high-speed random-access axial focusing

Dynamic axial focusing functionality has recently experienced widespread incorporation in microscopy, augmented/virtual reality (AR/VR), adaptive optics, and material processing. However, the limitations of existing varifocal tools continue to beset the performance capabilities and operating overhead of the optical systems that mobilize such functionality. The varifocal tools that are the least burdensome to drive (ex: liquid crystal, elastomeric or optofluidic lenses) suffer from low (~ 100 Hz) refresh rates. Conversely, the fastest devices sacrifice either critical capabilities such as their dwelling capacity (ex: acoustic gradient lenses or monolithic micromechanical mirrors) or low operating overhead (e.g., deformable mirrors). Here, we present a general-purpose random-access axial focusing device that bridges these previously conflicting features of high speed, dwelling capacity and lightweight drive by employing low-rigidity micromirrors that exploit the robustness of defocusing phase profiles. Geometrically, the device consists of an 8.2 mm diameter array of piston-motion and 48 um-pitch micromirror pixels that provide 2pi phase shifting for wavelengths shorter than 1 100 nm with 10-90 % settling in 64.8 us (i.e., 15.44 kHz refresh rate). The pixels are electrically partitioned into 32 rings for a driving scheme that enables phase-wrapped operation with circular symmetry and requires less than 30 V per channel. Optical experiments demonstrated the array's wide focusing range with a measured ability to target 29 distinct, resolvable depth planes. Overall, the features of the proposed array offer the potential for compact, straightforward methods of tackling bottlenecked applications including high-throughput single-cell targeting in neurobiology and the delivery of dense 3D visual information in AR/VR.

physics.optics↗

arXiv2020

Spectral DiffuserCam: lensless snapshot hyperspectral imaging with a spectral filter array

Hyperspectral imaging is useful for applications ranging from medical diagnostics to agricultural crop monitoring; however, traditional scanning hyperspectral imagers are prohibitively slow and expensive for widespread adoption. Snapshot techniques exist but are often confined to bulky benchtop setups or have low spatio-spectral resolution. In this paper, we propose a novel, compact, and inexpensive computational camera for snapshot hyperspectral imaging. Our system consists of a tiled spectral filter array placed directly on the image sensor and a diffuser placed close to the sensor. Each point in the world maps to a unique pseudorandom pattern on the spectral filter array, which encodes multiplexed spatio-spectral information. By solving a sparsity-constrained inverse problem, we recover the hyperspectral volume with sub-super-pixel resolution. Our hyperspectral imaging framework is flexible and can be designed with contiguous or non-contiguous spectral filters that can be chosen for a given application. We provide theory for system design, demonstrate a prototype device, and present experimental results with high spatio-spectral resolution.

eess.IV↗

arXiv2020

Fourier DiffuserScope: Single-shot 3D Fourier light field microscopy with a diffuser

Light field microscopy (LFM) uses a microlens array (MLA) near the sensor plane of a microscope to achieve single-shot 3D imaging of a sample without any moving parts. Unfortunately, the 3D capability of LFM comes with a significant loss of lateral resolution at the focal plane. Placing the MLA near the pupil plane of the microscope, instead of the image plane, can mitigate the artifacts and provide an efficient forward model, at the expense of field-of-view (FOV). Here, we demonstrate improved resolution across a large volume with Fourier DiffuserScope, which uses a diffuser in the pupil plane to encode 3D information, then computationally reconstructs the volume by solving a sparsity-constrained inverse problem. Our diffuser consists of randomly placed microlenses with varying focal lengths; the random positions provide a larger FOV compared to a conventional MLA, and the diverse focal lengths improve the axial depth range. To predict system performance based on diffuser parameters, we for the first time establish a theoretical framework and design guidelines, which are verified by numerical simulations, then build an experimental system that achieves $< 3$ um lateral and $4$ um axial resolution over a $1000 \times 1000 \times 280$ um$^3$ volume. Our diffuser design outperforms the MLA used in LFM, providing more uniform resolution over a larger volume, both laterally and axially.

eess.IV↗

arXiv2020

Pycro-manager: open-source software for integrated microscopy hardware control and image processing

μManager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely coupled. This is because μManager libraries are written in C++ and Java, whereas image processing is increasingly carried out with data science and machine learning tools most easily accessible through the Python programming language. We present Pycro-Manager, a tool that enables rapid development of such experiments, while also providing access to the wealth of existing tools within μManager through Python.

q-bio.QM↗

arXiv2020

How to do Physics-based Learning

The goal of this tutorial is to explain step-by-step how to implement physics-based learning for the rapid prototyping of a computational imaging system. We provide a basic overview of physics-based learning, the construction of a physics-based network, and its reduction to practice. Specifically, we advocate exploiting the auto-differentiation functionality twice, once to build a physics-based network and again to perform physics-based learning. Thus, the user need only implement the forward model process for their system, speeding up prototyping time. We provide an open-source Pytorch implementation of a physics-based network and training procedure for a generic sparse recovery problem

eess.IV↗

arXiv2020

Memory-efficient Learning for Large-scale Computational Imaging -- NeurIPS deep inverse workshop

Computational imaging systems jointly design computation and hardware to retrieve information which is not traditionally accessible with standard imaging systems. Recently, critical aspects such as experimental design and image priors are optimized through deep neural networks formed by the unrolled iterations of classical physics-based reconstructions (termed physics-based networks). However, for real-world large-scale systems, computing gradients via backpropagation restricts learning due to memory limitations of graphical processing units. In this work, we propose a memory-efficient learning procedure that exploits the reversibility of the network's layers to enable data-driven design for large-scale computational imaging. We demonstrate our methods practicality on two large-scale systems: super-resolution optical microscopy and multi-channel magnetic resonance imaging.

eess.IV↗

arXiv2020

Memory-efficient Learning for Large-scale Computational Imaging

Critical aspects of computational imaging systems, such as experimental design and image priors, can be optimized through deep networks formed by the unrolled iterations of classical model-based reconstructions (termed physics-based networks). However, for real-world large-scale inverse problems, computing gradients via backpropagation is infeasible due to memory limitations of graphics processing units. In this work, we propose a memory-efficient learning procedure that exploits the reversibility of the network's layers to enable data-driven design for large-scale computational imaging systems. We demonstrate our method on a small-scale compressed sensing example, as well as two large-scale real-world systems: multi-channel magnetic resonance imaging and super-resolution optical microscopy.

cs.CV↗

arXiv2020

Deep Phase Decoder: Self-calibrating phase microscopy with an untrained deep neural network

Deep neural networks have emerged as effective tools for computational imaging including quantitative phase microscopy of transparent samples. To reconstruct phase from intensity, current approaches rely on supervised learning with training examples; consequently, their performance is sensitive to a match of training and imaging settings. Here we propose a new approach to phase microscopy by using an untrained deep neural network for measurement formation, encapsulating the image prior and imaging physics. Our approach does not require any training data and simultaneously reconstructs the sought phase and pupil-plane aberrations by fitting the weights of the network to the captured images. To demonstrate experimentally, we reconstruct quantitative phase from through-focus images blindly (i.e. no explicit knowledge of the aberrations).

eess.IV↗

arXiv2019

High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images

Optical diffraction tomography (ODT) reconstructs a samples volumetric refractive index (RI) to create high-contrast, quantitative 3D visualizations of biological samples. However, standard implementations of ODT use interferometric systems, and so are sensitive to phase instabilities, complex mechanical design, and coherent noise. Furthermore, their reconstruction framework is typically limited to weakly-scattering samples, and thus excludes a whole class of multiple-scattering samples. Here, we implement a new 3D RI microscopy technique that utilizes a computational multi-slice beam propagation method to invert the optical scattering process and reconstruct high-resolution (NA>1.0) 3D RI distributions of multiple-scattering samples. The method acquires intensity-only measurements from different illumination angles, and then solves a non-linear optimization problem to recover the sample 3D RI distribution. We experimentally demonstrate reconstruction of samples with varying amounts of multiple scattering: a 3T3 fibroblast cell, a cluster of C. elegans embryos, and a whole C. elegans worm, with lateral and axial resolutions of 250 nm and 900 nm, respectively.

eess.IV↗

arXiv2019

Learned reconstructions for practical mask-based lensless imaging

Mask-based lensless imagers are smaller and lighter than traditional lensed cameras. In these imagers, the sensor does not directly record an image of the scene; rather, a computational algorithm reconstructs it. Typically, mask-based lensless imagers use a model-based reconstruction approach that suffers from long compute times and a heavy reliance on both system calibration and heuristically chosen denoisers. In this work, we address these limitations using a bounded-compute, trainable neural network to reconstruct the image. We leverage our knowledge of the physical system by unrolling a traditional model-based optimization algorithm, whose parameters we optimize using experimentally gathered ground-truth data. Optionally, images produced by the unrolled network are then fed into a jointly-trained denoiser. As compared to traditional methods, our architecture achieves better perceptual image quality and runs 20x faster, enabling interactive previewing of the scene. We explore a spectrum between model-based and deep learning methods, showing the benefits of using an intermediate approach. Finally, we test our network on images taken in the wild with a prototype mask-based camera, demonstrating that our network generalizes to natural images.

eess.IV↗

arXiv2019

Video from Stills: Lensless Imaging with Rolling Shutter

Because image sensor chips have a finite bandwidth with which to read out pixels, recording video typically requires a trade-off between frame rate and pixel count. Compressed sensing techniques can circumvent this trade-off by assuming that the image is compressible. Here, we propose using multiplexing optics to spatially compress the scene, enabling information about the whole scene to be sampled from a row of sensor pixels, which can be read off quickly via a rolling shutter CMOS sensor. Conveniently, such multiplexing can be achieved with a simple lensless, diffuser-based imaging system. Using sparse recovery methods, we are able to recover 140 video frames at over 4,500 frames per second, all from a single captured image with a rolling shutter sensor. Our proof-of-concept system uses easily-fabricated diffusers paired with an off-the-shelf sensor. The resulting prototype enables compressive encoding of high frame rate video into a single rolling shutter exposure, and exceeds the sampling-limited performance of an equivalent global shutter system for sufficiently sparse objects.

eess.IV↗

arXiv2019

Data-Driven Design for Fourier Ptychographic Microscopy

Fourier Ptychographic Microscopy (FPM) is a computational imaging method that is able to super-resolve features beyond the diffraction-limit set by the objective lens of a traditional microscope. This is accomplished by using synthetic aperture and phase retrieval algorithms to combine many measurements captured by an LED array microscope with programmable source patterns. FPM provides simultaneous large field-of-view and high resolution imaging, but at the cost of reduced temporal resolution, thereby limiting live cell applications. In this work, we learn LED source pattern designs that compress the many required measurements into only a few, with negligible loss in reconstruction quality or resolution. This is accomplished by recasting the super-resolution reconstruction as a Physics-based Neural Network and learning the experimental design to optimize the network's overall performance. Specifically, we learn LED patterns for different applications (e.g. amplitude contrast and quantitative phase imaging) and show that the designs we learn through simulation generalize well in the experimental setting. Further, we discuss a context-specific loss function, practical memory limitations, and interpretability of our learned designs.

eess.SP↗

arXiv2019

Computational structured illumination for high-content fluorescent and phase microscopy

High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample's super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4x the objective's diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 um QP resolution, across a FOV of 2x2.7 mm^2, giving a space-bandwidth product (SBP) of 60 megapixels.

eess.IV↗

arXiv2019

Physics-based Learned Design: Optimized Coded-Illumination for Quantitative Phase Imaging

Coded-illumination can enable quantitative phase microscopy of transparent samples with minimal hardware requirements. Intensity images are captured with different source patterns and a non-linear phase retrieval optimization reconstructs the image. The non-linear nature of the processing makes optimizing the illumination pattern designs complicated. Traditional techniques for experimental design (e.g. condition number optimization, spectral analysis) consider only linear measurement formation models and linear reconstructions. Deep neural networks (DNNs) can efficiently represent the non-linear process and can be optimized over via training in an end-to-end framework. However, DNNs typically require a large amount of training examples and parameters to properly learn the phase retrieval process, without making use of the known physical models. Here, we aim to use both our knowledge of the physics and the power of machine learning together. We develop a new data-driven approach to optimizing coded-illumination patterns for a LED array microscope for a given phase reconstruction algorithm. Our method incorporates both the physics of the measurement scheme and the non-linearity of the reconstruction algorithm into the design problem. This enables efficient parameterization, which allows us to use only a small number of training examples to learn designs that generalize well in the experimental setting without retraining. We show experimental results for both a well-characterized phase target and mouse fibroblast cells using coded-illumination patterns optimized for a sparsity-based phase reconstruction algorithm. Our learned design results using 2 measurements demonstrate similar accuracy to Fourier Ptychography with 69 measurements.

eess.SP↗