Focus prediction in digital holographic microscopy using deep convolutional neural networks.

Deep artificial neural network learning is an emerging tool in image analysis. We demonstrate its potential in the field of digital holographic microscopy by addressing the challenging problem of determining the in-focus reconstruction depth of Madin-Darby canine kidney cell clusters encoded in digital holograms. A deep convolutional neural network learns the in-focus depths from half a million hologram amplitude images.

Space-variant video compression and processing in digital holographic microscopy sensor networks with application to potable water monitoring.

Water-related diseases affect societies in all parts of the world. Online sensors are considered a solution to the problems associated with laboratory testing in potable water. One of the most active research areas of such online sensors has been within optics.

Enhancement of three-dimensional perception of numerical hologram reconstructions of real-world objects by motion and stereo.

We investigated the question of how the perception of three-dimensional information reconstructed numerically from digital holograms of real-world objects, and presented on conventional displays, depends on motion and stereoscopic presentation. Perceived depth in an adjustable random pattern stereogram was matched to the depth in hologram reconstructions. The objects in holograms were a microscopic biological cell and a macroscopic metal coil.

Calculating depth maps from digital holograms using stereo disparity.

Depth extraction is an important aspect of three-dimensional (3D) image processing with digital holograms and an essential step in extended focus imaging and metrology. All available depth extraction techniques with macroscopic objects are based on variance; however, the effectiveness of this is object dependent. We propose to use disparity between corresponding points in intensity reconstructions to determine depth.

Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system.

We present a multi-heuristic evolutionary task allocation algorithm to dynamically map tasks to processors in a heterogeneous distributed system. It utilizes a genetic algorithm, combined with eight common heuristics, in an effort to minimize the total execution time. It operates on batches of unmapped tasks and can preemptively remap tasks to processors.

Synthesis and display of dynamic holographic 3D scenes with real-world objects.

A 3D scene is synthesized combining multiple optically recorded digital holograms of different objects. The novel idea consists of compositing moving 3D objects in a dynamic 3D scene using a process that is analogous to stop-motion video. However in this case the movie has the exciting attribute that it can be displayed and observed in 3D.

Statistical investigation of the double random phase encoding technique.

The amplitude-encoding case of the double random phase encoding technique is examined by defining a cost function as a metric to compare an attempted decryption against the corresponding original input image. For the case when a cipher-text pair has been obtained and the correct decryption key is unknown, an iterative attack technique can be employed to ascertain the key. During such an attack the noise in the output field for an attempted decryption can be used as a measure of a possible decryption key's correctness.

Three dimensional digital holographic profiling of micro-fibers.

A method to measure the size, orientation, and location of opaque micro-fibers using digital holography is presented. The method involves the recording of a digital hologram followed by reconstruction at different depths. A novel combination of automated image analysis and statistical techniques, applied on the intensity of reconstructed digital holograms is used to accurately determine the characteristics of the micro-fibers.

Introducing secure modes of operation for optical encryption.

We analyze optical encryption systems using the techniques of conventional cryptography. All conventional block encryption algorithms are vulnerable to attack, and often they employ secure modes of operation as one way to increase security. We introduce the concept of conventional secure modes to optical encryption and analyze the results in the context of known conventional and optical attacks.

Role of phase key in the double random phase encoding technique: an error analysis.

We perform a numerical analysis of the double random phase encryption-decryption technique to determine how, in the case of both amplitude and phase encoding, the two decryption keys (the image- and Fourier-plane keys) affect the output gray-scale image when they are in error. We perform perfect encryption and imperfect decryption. We introduce errors into the decrypting keys that correspond to the use of random distributions of incorrect pixel values.

Extended focused imaging for digital holograms of macroscopic three-dimensional objects.

When a digital hologram is reconstructed, only points located at the reconstruction distance are in focus. We have developed a novel technique for creating an in-focus image of the macroscopic objects encoded in a digital hologram. This extended focused image is created by combining numerical reconstructions with depth information extracted by using our depth-from-focus algorithm.

Low memory distributed reconstruction of large digital holograms.

We present a parallel implementation of the Fresnel transform suitable for reconstructing large digital holograms. Our method has a small memory footprint and utilizes the spare resources of a distributed set of desktop PCs connected by a network. We show how we parallelize the Fresnel transform and discuss how it is constrained by computer and communication resources.

Noninterferometric phase retrieval using a fractional Fourier system.

The signal extraction method based on intensity measurements in two close fractional Fourier domains is examined by using the phase space formalism. The fractional order separation has a lower bound and an upper bound that depend on the signal at hand and the noise in the optical system used for measurement. On the basis of a theoretical analysis, it is shown that for a given optical system a judicious choice of fractional order separation requires some a priori knowledge of the signal bandwidth.

Key-space analysis of double random phase encryption technique.

We perform a numerical analysis on the double random phase encryption/decryption technique. The key-space of an encryption technique is the set of possible keys that can be used to encode data using that technique. In the case of a strong encryption scheme, many keys must be tried in any brute-force attack on that technique.

Resistance of the double random phase encryption against various attacks.

Several attacks are proposed against the double random phase encryption scheme. These attacks are demonstrated on computer-generated ciphered images. The scheme is shown to be resistant against brute force attacks but susceptible to chosen and known plaintext attacks.

Compression defects in different reconstructions from phase-shifting digital holographic data.

Three principal strategies for the compression of phase-shifting digital holograms (interferogram domain-, hologram domain-, and reconstruction domain-based strategies) are reviewed and their effects in the reconstruction domain are investigated. Images of the reconstructions are provided to visually compare the performances of the methods. In addition to single reconstructions the compression effects on different depth reconstructions and reconstructions corresponding to different viewing angles are investigated so that a range of the 3D aspects of the holograms may be considered.

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods.

Histogram approaches for lossy compression of digital holograms of three-dimensional objects.

We present a novel nonuniform quantization compression technique-histogram quantization-for digital holograms of 3-D real-world objects. We exploit a priori knowledge of the distribution of the values in our data. We compare this technique to another histogram based approach: a modified version of Max's algorithm that has been adapted in a straight-forward manner to complex-valued 2-D signals.

Reduction of speckle in digital holography by discrete Fourier filtering.

We present a digital signal processing technique that reduces the speckle content in reconstructed digital holograms. The method is based on sequential sampling of the discrete Fourier transform of the reconstructed image field. Speckle reduction is achieved at the expense of a reduced intensity and resolution, but this trade-off is shown to be greatly superior to that imposed by the traditional mean and median filtering techniques.

Depth-independent segmentation of macroscopic three-dimensional objects encoded in single perspectives of digital holograms.

We present a technique for performing segmentation of macroscopic three-dimensional objects recorded using in-line digital holography. We numerically reconstruct a single perspective of each object at a range of depths. At each point in the digital wavefront we calculate variance about a neighborhood.

Polarization encoding and multiplexing of two-dimensional signals: application to image encryption.

We discuss an optical system that encodes an input signal to a polarization state, using a spatial light modulator (SLM). Using two SLMs the optical system multiplexes two 2D signals in the polarization domain, and we demonstrate the multiplexing of two binary images. The encryption and decryption of two binary images using an XOR operation is also presented.

A companding approach for nonuniform quantization of digital holograms of three-dimensional objects.

We apply two novel nonuniform quantization techniques to digital holograms of three-dimensional real-world objects. Our companding approach, combines the efficiency of uniform quantization with the improved performance of nonuniform quantization. We show that the performance of companding techniques can be comparable with k-means clustering and a competitive neural network, while only requiring a single-pass processing step.

Reconstruction of partially occluded objects encoded in three-dimensional scenes by using digital holograms.

We propose a task-specific digital holographic capture system for three-dimensional scenes, which can reduce the amount of data sent from the camera system to the receiver and can effectively reconstruct partially occluded objects. The system requires knowledge of the object of interest, but it does not require a priori knowledge of either the occlusion or the distance the object is from the camera. Subwindows of the camera-plane Fresnel field are digitally propagated to reveal different perspectives of the scene, and these are combined to overcome the unknown foreground occlusions.

A known-plaintext heuristic attack on the Fourier plane encryption algorithm.

The Fourier plane encryption algorithm is subjected to a known-plaintext attack. The simulated annealing heuristic algorithm is used to estimate the key, using a known plaintext-ciphertext pair, which decrypts the ciphertext with arbitrarily low error. The strength of the algorithm is tested by using this estimated key to decrypt a different ciphertext which was also encrypted using the same original key.

Compression of digital holograms of three-dimensional objects using wavelets.

We present the results of what we believe is the first application of wavelet analysis to the compression of complex-valued digital holograms of three-dimensional real-world objects. We achieve compression through thresholding and quantization of the wavelet coefficients, followed by lossless encoding of the quantized data.