BiPMAP: a toolbox for predicting perceived motion artifacts on modern displays.

Viewers of digital displays often experience motion artifacts (e.g., flicker, judder, edge banding, motion blur, color breakup, depth distortion) when presented with dynamic scenes. We developed an interactive software tool for display designers that predicts how a viewer perceives motion artifacts for a variety of stimulus, display, and viewing parameters: the Binocular Perceived Motion Artifact Predictor (BiPMAP). The tool enables the user to specify numerous stimulus, display, and viewing parameters. It implements a model of human spatiotemporal contrast sensitivity in order to determine which artifacts will be seen by a viewer and which will not. The tool visualizes the perceptual effects of discrete space-time sampling on the display by presenting side by side the expected perception when the stimulus is continuous compared to when the same stimulus is presented with the spatial and temporal parameters of a prototype display.

Fast non-iterative algorithm for 3D point-cloud holography.

Recently developed iterative and deep learning-based approaches to computer-generated holography (CGH) have been shown to achieve high-quality photorealistic 3D images with spatial light modulators. However, such approaches remain overly cumbersome for patterning sparse collections of target points across a photoresponsive volume in applications including biological microscopy and material processing. Specifically, in addition to requiring heavy computation that cannot accommodate real-time operation in mobile or hardware-light settings, existing sampling-dependent 3D CGH methods preclude the ability to place target points with arbitrary precision, limiting accessible depths to a handful of planes. Accordingly, we present a non-iterative point cloud holography algorithm that employs fast deterministic calculations in order to efficiently allocate patches of SLM pixels to different target points in the 3D volume and spread the patterning of all points across multiple time frames. Compared to a matched-performance implementation of the iterative Gerchberg-Saxton algorithm, our algorithm's relative computation speed advantage was found to increase with SLM pixel count, reaching >100,000x at 512 × 512 array format.

Quantitative differential phase contrast imaging in an LED array microscope: errata.

This errata corrects typos found in the derived transfer functions in [Opt. Express23, 11394 (2015)10.1364/OE.23.011394].

Roadmap on Deep Learning for Microscopy.

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

DiffuserSpec: spectroscopy with Scotch tape.

Computational spectroscopy breaks the inherent one-to-one spatial-to-spectral pixel mapping of traditional spectrometers by multiplexing spectral data over a given sensor region. Most computational spectrometers require components that are complex to design, fabricate, or both. DiffuserSpec is a simple computational spectrometer that uses the inherent spectral dispersion of commercially available diffusers to generate speckle patterns that are unique to each wavelength. Using Scotch tape as a diffuser, we demonstrate narrowband and broadband spectral reconstructions with 2-nm spectral resolution over an 85-nm bandwidth in the near-infrared, limited only by the bandwidth of the calibration dataset. We also investigate the effect of spatial sub-sampling of the 2D speckle pattern on resolution performance.

Data-driven modeling and control of an X-ray bimorph adaptive mirror.

Adaptive X-ray mirrors are being adopted on high-coherent-flux synchrotron and X-ray free-electron laser beamlines where dynamic phase control and aberration compensation are necessary to preserve wavefront quality from source to sample, yet challenging to achieve. Additional difficulties arise from the inability to continuously probe the wavefront in this context, which demands methods of control that require little to no feedback. In this work, a data-driven approach to the control of adaptive X-ray optics with piezo-bimorph actuators is demonstrated. This approach approximates the non-linear system dynamics with a discrete-time model using random mirror shapes and interferometric measurements as training data. For mirrors of this type, prior states and voltage inputs affect the shape-change trajectory, and therefore must be included in the model. Without the need for assumed physical models of the mirror's behavior, the generality of the neural network structure accommodates drift, creep and hysteresis, and enables a control algorithm that achieves shape control and stability below 2 nm RMS. Using a prototype mirror and ex situ metrology, it is shown that the accuracy of our trained model enables open-loop shape control across a diverse set of states and that the control algorithm achieves shape error magnitudes that fall within diffraction-limited performance.

Recent Advances in Lensless Imaging.

Lensless imaging provides opportunities to design imaging systems free from the constraints imposed by traditional camera architectures. Thanks to advances in imaging hardware, fabrication techniques, and new algorithms, researchers have recently developed lensless imaging systems that are extremely compact, lightweight or able to image higher-dimensional quantities. Here we review these recent advances and describe the design principles and their effects that one should consider when developing and using lensless imaging systems.

Ion complexation waves emerge at the curved interfaces of layered minerals.

Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation.

Self-calibrated 3D differential phase contrast microscopy with optimized illumination.

3D phase imaging recovers an object's volumetric refractive index from intensity and/or holographic measurements. Partially coherent methods, such as illumination-based differential phase contrast (DPC), are particularly simple to implement in a commercial brightfield microscope. 3D DPC acquires images at multiple focus positions and with different illumination source patterns in order to reconstruct 3D refractive index. Here, we present a practical extension of the 3D DPC method that does not require a precise motion stage for scanning the focus and uses optimized illumination patterns for improved performance. The user scans the focus by hand, using the microscope's focus knob, and the algorithm self-calibrates the axial position to solve for the 3D refractive index of the sample through a computational inverse problem. We further show that the illumination patterns can be optimized by an end-to-end learning procedure. Combining these two, we demonstrate improved 3D DPC with a commercial microscope whose only hardware modification is LED array illumination.

Relationship Between CT Head Findings and Long-term Recovery in Children with Complicated Mild Traumatic Brain Injury.

PRIMARY OBJECTIVE: Complicated mild traumatic brain injury (C-mTBI) refers to CT positive patients with clinically mild TBI. This study investigates the association between CT head findings at time of injury and recovery of paediatric patients with C-mTBI. RESEARCH DESIGN: Retrospective survey and chart review. METHODS: For paediatric patients with C-mTBI (N = 77), CT findings associated with corresponding degree and lengths of recovery from C-mTBI using logistic regression analysis. RESULTS: There was a trend that the odds of incomplete recovery at the time of survey was higher for older children than for younger children (OR = 1.14, 95% CI = 0.98-1.32, p = 0.072). There was a trend that the odds of incomplete recovery (OR = 6.26, 95% CI = 0.97-40.57, p = 0.054) and longer duration for recovery (OR = 8.14, 95% CI = 0.78-84.46, p = 0.079) was higher for children with multiple haemorrhagic contusions than those with single haemorrhagic contusion. No other imaging patterns predicted degree or length of recovery with statistical significance (p > 0.05). CONCLUSIONS: Other than the presence of multiple haemorrhagic contusions, no other pattern of imaging abnormality in paediatric C-mTBI appears to be associated with degree or length of recovery. Further studies with larger cohorts are encouraged.

Three-dimensional multi-site random access photostimulation (3D-MAP).

Optical control of neural ensemble activity is crucial for understanding brain function and disease, yet no technology can achieve optogenetic control of very large numbers of neurons at an extremely fast rate over a large volume. State-of-the-art multiphoton holographic optogenetics requires high-power illumination that only addresses relatively small populations of neurons in parallel. Conversely, one-photon holographic techniques can stimulate more neurons with two to three orders lower power, but with limited resolution or addressable volume. Perhaps most problematically, two-photon holographic optogenetic systems are extremely expensive and sophisticated which has precluded their broader adoption in the neuroscience community. To address this technical gap, we introduce a new one-photon light sculpting technique, three-dimensional multi-site random access photostimulation (3D-MAP), that overcomes these limitations by modulating light dynamically, both in the spatial and in the angular domain at multi-kHz rates. We use 3D-MAP to interrogate neural circuits in 3D and demonstrate simultaneous photostimulation and imaging of dozens of user-selected neurons in the intact mouse brain in vivo with high spatio-temporal resolution. 3D-MAP can be broadly adopted for high-throughput all-optical interrogation of brain circuits owing to its powerful combination of scale, speed, simplicity, and cost.

Three-dimensional bi-functional refractive index and fluorescence microscopy (BRIEF).

Fluorescence microscopy is a powerful tool for imaging biological samples with molecular specificity. In contrast, phase microscopy provides label-free measurement of the sample's refractive index (RI), which is an intrinsic optical property that quantitatively relates to cell morphology, mass, and stiffness. Conventional imaging techniques measure either the labeled fluorescence (functional) information or the label-free RI (structural) information, though it may be valuable to have both. For example, biological tissues have heterogeneous RI distributions, causing sample-induced scattering that degrades the fluorescence image quality. When both fluorescence and 3D RI are measured, one can use the RI information to digitally correct multiple-scattering effects in the fluorescence image. Here, we develop a new computational multi-modal imaging method based on epi-mode microscopy that reconstructs both 3D fluorescence and 3D RI from a single dataset. We acquire dozens of fluorescence images, each 'illuminated' by a single fluorophore, then solve an inverse problem with a multiple-scattering forward model. We experimentally demonstrate our method for epi-mode 3D RI imaging and digital correction of multiple-scattering effects in fluorescence images.

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 case, 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 an unsupervised approach based on 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, 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.

Learned adaptive multiphoton illumination microscopy for large-scale immune response imaging.

Multiphoton microscopy is a powerful technique for deep in vivo imaging in scattering samples. However, it requires precise, sample-dependent increases in excitation power with depth in order to generate contrast in scattering tissue, while minimizing photobleaching and phototoxicity. We show here how adaptive imaging can optimize illumination power at each point in a 3D volume as a function of the sample's shape, without the need for specialized fluorescent labeling. Our method relies on training a physics-based machine learning model using cells with identical fluorescent labels imaged in situ. We use this technique for in vivo imaging of immune responses in mouse lymph nodes following vaccination. We achieve visualization of physiologically realistic numbers of antigen-specific T cells (~2 orders of magnitude lower than previous studies), and demonstrate changes in the global organization and motility of dendritic cell networks during the early stages of the immune response. We provide a step-by-step tutorial for implementing this technique using exclusively open-source hardware and software.

Nondestructive, high-resolution, chemically specific 3D nanostructure characterization using phase-sensitive EUV imaging reflectometry.

Next-generation nano- and quantum devices have increasingly complex 3D structure. As the dimensions of these devices shrink to the nanoscale, their performance is often governed by interface quality or precise chemical or dopant composition. Here, we present the first phase-sensitive extreme ultraviolet imaging reflectometer. It combines the excellent phase stability of coherent high-harmonic sources, the unique chemical sensitivity of extreme ultraviolet reflectometry, and state-of-the-art ptychography imaging algorithms. This tabletop microscope can nondestructively probe surface topography, layer thicknesses, and interface quality, as well as dopant concentrations and profiles. High-fidelity imaging was achieved by implementing variable-angle ptychographic imaging, by using total variation regularization to mitigate noise and artifacts in the reconstructed image, and by using a high-brightness, high-harmonic source with excellent intensity and wavefront stability. We validate our measurements through multiscale, multimodal imaging to show that this technique has unique advantages compared with other techniques based on electron and scanning probe microscopies.

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 operate (e.g. 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 (e.g. 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-µm-pitch micromirror pixels that provide 2π phase shifting for wavelengths shorter than 1100 nm with 10-90% settling in 64.8 µs (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 <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.

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 µm lateral, and 15 µm axial resolution across most of the 900 × 700 × 390 µm3 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 2× better lateral and axial resolution throughout a 10× 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.