Kristina Monakhova

Kristina Monakhova, Stephan R. Richter, Laura Waller et al.

Imaging in low light is extremely challenging due to low photon counts. Using sensitive CMOS cameras, it is currently possible to take videos at night under moonlight (0.05-0.3 lux illumination). In this paper, we demonstrate photorealistic video under starlight (no moon present, $<$0.001 lux) for the first time. To enable this, we develop a GAN-tuned physics-based noise model to more accurately represent camera noise at the lowest light levels. Using this noise model, we train a video denoiser using a combination of simulated noisy video clips and real noisy still images. We capture a 5-10 fps video dataset with significant motion at approximately 0.6-0.7 millilux with no active illumination. Comparing against alternative methods, we achieve improved video quality at the lowest light levels, demonstrating photorealistic video denoising in starlight for the first time.

Cassandra Tong Ye, Jiashu Han, Kunzan Liu et al.

Scanning microscopy systems, such as confocal and multiphoton microscopy, are powerful imaging tools for probing deep into biological tissue. However, scanning systems have an inherent trade-off between acquisition time, field of view, phototoxicity, and image quality, often resulting in noisy measurements when fast, large field of view, and/or gentle imaging is needed. Deep learning could be used to denoise noisy microscopy measurements, but these algorithms can be prone to hallucination, which can be disastrous for medical and scientific applications. We propose a method to simultaneously denoise and predict pixel-wise uncertainty for scanning microscopy systems, improving algorithm trustworthiness and providing statistical guarantees for deep learning predictions. Furthermore, we propose to leverage this learned, pixel-wise uncertainty to drive an adaptive acquisition technique that rescans only the most uncertain regions of a sample, saving time and reducing the total light dose to the sample. We demonstrate our method on experimental confocal and multiphoton microscopy systems, showing that our uncertainty maps can pinpoint hallucinations in the deep learned predictions. Finally, with our adaptive acquisition technique, we demonstrate up to 16X reduction in acquisition time and total light dose while successfully recovering fine features in the sample and reducing hallucinations. We are the first to demonstrate distribution-free uncertainty quantification for a denoising task with real experimental data and the first to propose adaptive acquisition based on reconstruction uncertainty.

Cassandra Tong Ye, Shamus Li, Tyler King et al.

Deep learning models often hallucinate, producing realistic artifacts that are not truly present in the sample. This can have dire consequences for scientific and medical inverse problems, such as MRI and microscopy denoising, where accuracy is more important than perceptual quality. Uncertainty quantification techniques, such as conformal prediction, can pinpoint outliers and provide guarantees for image regression tasks, improving reliability. However, existing methods utilize a linear constant scaling factor to calibrate uncertainty bounds, resulting in larger, less informative bounds. We propose QUTCC, a quantile uncertainty training and calibration technique that enables nonlinear, non-uniform scaling of quantile predictions to enable tighter uncertainty estimates. Using a U-Net architecture with a quantile embedding, QUTCC enables the prediction of the full conditional distribution of quantiles for the imaging task. During calibration, QUTCC generates uncertainty bounds by iteratively querying the network for upper and lower quantiles, progressively refining the bounds to obtain a tighter interval that captures the desired coverage. We evaluate our method on several denoising tasks as well as compressive MRI reconstruction. Our method successfully pinpoints hallucinations in image estimates and consistently achieves tighter uncertainty intervals than prior methods while maintaining the same statistical coverage.

Xiang Dai, Kyrollos Yanny, Kristina Monakhova et al.

High-dynamic-range (HDR) imaging is an essential technique for overcoming the dynamic range limits of image sensors. The classic method relies on multiple exposures, which slows capture time, resulting in motion artifacts when imaging dynamic scenes. Single-shot HDR imaging alleviates this issue by encoding HDR data into a single exposure, then computationally recovering it. Many established methods use strong image priors to recover improperly exposed image detail. These approaches struggle with extended highlight regions. We utilize the global reset release (GRR) shutter mode of an off-the-shelf sensor. GRR shutter mode applies a longer exposure time to rows closer to the bottom of the sensor. We use optics that relay a randomly permuted (shuffled) image onto the sensor, effectively creating spatially randomized exposures across the scene. The exposure diversity allows us to recover HDR data by solving an optimization problem with a simple total variation image prior. In simulation, we demonstrate that our method outperforms other single-shot methods when many sensor pixels are saturated (10% or more), and is competitive at a modest saturation (1%). Finally, we demonstrate a physical lab prototype that uses an off-the-shelf random fiber bundle for the optical shuffling. The fiber bundle is coupled to a low-cost commercial sensor operating in GRR shutter mode. Our prototype achieves a dynamic range of up to 73dB using an 8-bit sensor with 48dB dynamic range.

Kristina Monakhova, Vi Tran, Grace Kuo et al.

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.

Kyrollos Yanny, Nick Antipa, William Liberti et al.

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.

Kristina Monakhova, Kyrollos Yanny, Neerja Aggarwal et al.

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.

Kristina Monakhova, Joshua Yurtsever, Grace Kuo et al.

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.