Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against ...angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded light field can then be used to computationally reconstruct a full volume. In this paper, we present an optical model for light field microscopy based on wave optics, instead of previously reported ray optics models. We also present a 3-D deconvolution method for light field microscopy that is able to reconstruct volumes at higher spatial resolution, and with better optical sectioning, than previously reported. To accomplish this, we take advantage of the dense spatio-angular sampling provided by a microlens array at axial positions away from the native object plane. This dense sampling permits us to decode aliasing present in the light field to reconstruct high-frequency information. We formulate our method as an inverse problem for reconstructing the 3-D volume, which we solve using a GPU-accelerated iterative algorithm. Theoretical limits on the depth-dependent lateral resolution of the reconstructed volumes are derived. We show that these limits are in good agreement with experimental results on a standard USAF 1951 resolution target. Finally, we present 3-D reconstructions of pollen grains that demonstrate the improvements in fidelity made possible by our method.
Compared to DSLR cameras, smartphone cameras have smaller sensors, which limits their spatial resolution; smaller apertures, which limits their light gathering ability; and smaller pixels, which ...reduces their signal-to-noise ratio. The use of color filter arrays (CFAs) requires demosaicing, which further degrades resolution. In this paper, we supplant the use of traditional demosaicing in single-frame and burst photography pipelines with a multiframe super-resolution algorithm that creates a complete RGB image directly from a burst of CFA raw images. We harness natural hand tremor, typical in handheld photography, to acquire a burst of raw frames with small offsets. These frames are then aligned and merged to form a single image with red, green, and blue values at every pixel site. This approach, which includes no explicit demosaicing step, serves to both increase image resolution and boost signal to noise ratio. Our algorithm is robust to challenging scene conditions: local motion, occlusion, or scene changes. It runs at 100 milliseconds per 12-megapixel RAW input burst frame on mass-produced mobile phones. Specifically, the algorithm is the basis of the
Super-Res Zoom
feature, as well as the default merge method in
Night Sight
mode (whether zooming or not) on Google's flagship phone.
We present a system for interactively acquiring and rendering light fields using a hand‐held commodity camera. The main challenge we address is assisting a user in achieving good coverage of the 4D ...domain despite the challenges of hand‐held acquisition. We define coverage by bounding reprojection error between viewpoints, which accounts for all 4 dimensions of the light field. We use this criterion together with a recent Simultaneous Localization and Mapping technique to compute a coverage map on the space of viewpoints. We provide users with real‐time feedback and direct them toward under‐sampled parts of the light field. Our system is lightweight and has allowed us to capture hundreds of light fields. We further present a new rendering algorithm that is tailored to the unstructured yet dense data we capture. Our method can achieve piecewise‐bicubic reconstruction using a triangulation of the captured viewpoints and subdivision rules applied to reconstruction weights.
Cell phone cameras have small apertures, which limits the number of photons they can gather, leading to noisy images in low light. They also have small sensor pixels, which limits the number of ...electrons each pixel can store, leading to limited dynamic range. We describe a computational photography pipeline that captures, aligns, and merges a burst of frames to reduce noise and increase dynamic range. Our system has several key features that help make it robust and efficient. First, we do not use bracketed exposures. Instead, we capture frames of constant exposure, which makes alignment more robust, and we set this exposure low enough to avoid blowing out highlights. The resulting merged image has clean shadows and high bit depth, allowing us to apply standard HDR tone mapping methods. Second, we begin from Bayer raw frames rather than the demosaicked RGB (or YUV) frames produced by hardware Image Signal Processors (ISPs) common on mobile platforms. This gives us more bits per pixel and allows us to circumvent the ISP's unwanted tone mapping and spatial denoising. Third, we use a novel FFT-based alignment algorithm and a hybrid 2D/3D Wiener filter to denoise and merge the frames in a burst. Our implementation is built atop Android's Camera2 API, which provides per-frame camera control and access to raw imagery, and is written in the Halide domain-specific language (DSL). It runs in 4 seconds on device (for a 12 Mpix image), requires no user intervention, and ships on several mass-produced cell phones.
We propose a method for accelerating a broad class of non-linear filters that includes the bilateral, non-local means, and other related filters. These filters can all be expressed in a similar way: ...First, assign each value to be filtered a position in some vector space. Then, replace every value with a weighted linear combination of all values, with weights determined by a Gaussian function of distance between the positions. If the values are pixel colors and the positions are (
x, y
) coordinates, this describes a Gaussian blur. If the positions are instead (
x, y, r, g, b
) coordinates in a five-dimensional space-color volume, this describes a bilateral filter. If we instead set the positions to local patches of color around the associated pixel, this describes non-local means. We describe a Monte-Carlo kd-tree sampling algorithm that efficiently computes any filter that can be expressed in this way, along with a GPU implementation of this technique. We use this algorithm to implement an accelerated bilateral filter that respects full 3D color distance; accelerated non-local means on single images, volumes, and unaligned bursts of images for denoising; and a fast adaptation of non-local means to geometry. If we have
n
values to filter, and each is assigned a position in a
d
-dimensional space, then our space complexity is
O(dn
) and our time complexity is
O(dn
log
n
), whereas existing methods are typically either exponential in
d
or quadratic in
n
.
Prolonged behavioral challenges can cause animals to switch from active to passive coping strategies to manage effort-expenditure during stress; such normally adaptive behavioral state transitions ...can become maladaptive in psychiatric disorders such as depression. The underlying neuronal dynamics and brainwide interactions important for passive coping have remained unclear. Here, we develop a paradigm to study these behavioral state transitions at cellular-resolution across the entire vertebrate brain. Using brainwide imaging in zebrafish, we observed that the transition to passive coping is manifested by progressive activation of neurons in the ventral (lateral) habenula. Activation of these ventral-habenula neurons suppressed downstream neurons in the serotonergic raphe nucleus and caused behavioral passivity, whereas inhibition of these neurons prevented passivity. Data-driven recurrent neural network modeling pointed to altered intra-habenula interactions as a contributory mechanism. These results demonstrate ongoing encoding of experience features in the habenula, which guides recruitment of downstream networks and imposes a passive coping behavioral strategy.
Display omitted
•Passive coping in response to behavioral challenge is conserved in larval zebrafish•Brainwide cellular-resolution activity screen shows unique role for habenula in passivity•Habenular neurons encode stress by progressive recruitment into active ensembles•Optogenetics and network modeling reveal causal contributions of habenulo-raphe circuitry
Brainwide imaging in zebrafish and network modeling reveal that switching from active to passive coping state arises from progressive activation of habenular neurons in response to behavioral challenge.
Light field microscopy Levoy, Marc; Ng, Ren; Adams, Andrew ...
ACM transactions on graphics,
07/2006, Letnik:
25, Številka:
3
Journal Article
Recenzirano
By inserting a microlens array into the optical train of a conventional microscope, one can capture light fields of biological specimens in a single photograph. Although diffraction places a limit on ...the product of spatial and angular resolution in these light fields, we can nevertheless produce useful perspective views and focal stacks from them. Since microscopes are inherently orthographic devices, perspective views represent a new way to look at microscopic specimens. The ability to create focal stacks from a single photograph allows moving or light-sensitive specimens to be recorded. Applying 3D deconvolution to these focal stacks, we can produce a set of cross sections, which can be visualized using volume rendering. In this paper, we demonstrate a prototype light field microscope (LFM), analyze its optical performance, and show perspective views, focal stacks, and reconstructed volumes for a variety of biological specimens. We also show that synthetic focusing followed by 3D deconvolution is equivalent to applying limited-angle tomography directly to the 4D light field.
Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. ...Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.
Using existing programming tools, writing high-performance image processing code requires sacrificing readability, portability, and modularity. We argue that this is a consequence of conflating what ...computations define the
algorithm
, with decisions about
storage
and the
order
of computation. We refer to these latter two concerns as the
schedule
, including choices of tiling, fusion, recomputation vs. storage, vectorization, and parallelism.
We propose a representation for feed-forward imaging pipelines that separates the algorithm from its schedule, enabling high-performance without sacrificing code clarity. This decoupling simplifies the algorithm specification: images and intermediate buffers become functions over an infinite integer domain, with no explicit storage or boundary conditions. Imaging pipelines are compositions of functions. Programmers separately specify scheduling strategies for the various functions composing the algorithm, which allows them to efficiently explore different optimizations without changing the algorithmic code.
We demonstrate the power of this representation by expressing a range of recent image processing applications in an embedded domain specific language called Halide, and compiling them for ARM, x86, and GPUs. Our compiler targets SIMD units, multiple cores, and complex memory hierarchies. We demonstrate that it can handle algorithms such as a camera raw pipeline, the bilateral grid, fast local Laplacian filtering, and image segmentation. The algorithms expressed in our language are both shorter and faster than state-of-the-art implementations.
The advent of inexpensive digital image sensors and the ability to create photographs that combine information from a number of sensed images are changing the way we think about photography. In this ...paper, we describe a unique array of 100 custom video cameras that we have built, and we summarize our experiences using this array in a range of imaging applications. Our goal was to explore the capabilities of a system that would be inexpensive to produce in the future. With this in mind, we used simple cameras, lenses, and mountings, and we assumed that processing large numbers of images would eventually be easy and cheap. The applications we have explored include approximating a conventional single center of projection video camera with high performance along one or more axes, such as resolution, dynamic range, frame rate, and/or large aperture, and using multiple cameras to approximate a video camera with a large synthetic aperture. This permits us to capture a video light field, to which we can apply spatiotemporal view interpolation algorithms in order to digitally simulate time dilation and camera motion. It also permits us to create video sequences using custom non-uniform synthetic apertures.
PDF
