Speed up of Fresnel transforms for Digital holography using pre-computation

We show how the common Fresnel reconstruction of digital holograms can be speeded up on ordinary computers by precomputing the two chirp factors for a given detector array size and then calling these values from memory during the reconstruction. The speedup in time is shown for various hologram sizes. We also run the same algorithm on a Nvidia GPU using Matlab

Removing the twin image in digital holography by segmented filtering of in-focus twin image

We propose and investigate a new digital method for the reduction of twin-image noise from digital Fresnel holograms. For the case of in-line Fresnel holography the unwanted twin is present as a highly corruptive noise when the object image is numerically reconstructed. We propose to firstly reconstruct the unwanted twin-image when it is in-focus and in this plane we calculate a segmentation mask that borders this in focus image. The twin-image is then segmented and removed by simple spatial filtering. The resulting digital wavefield is the inverse propagated to the desired object image plane. The image is free of the twin-image resulting in improved quality reconstructions. We demonstrate the segmentation and removal of the unwanted twin-image from in-line digital holograms containing real-world macroscopic objects. We offer suggestions for its rapid computational implementation

A Practical Guide to Digital Holography and Generalized Sampling

The theorems of Nyquist, Shannon and Whittaker have long held true for sampling optical signals. They showed that a signal (with finite bandwidth) should be sampled at a rate at least as fast as twice the maximum spatial frequency of the signal. They proceeded to show how the continuous signal could be reconstructed perfectly from its well sampled counterpart by convolving a Sinc function with the sampled signal. Recent years have seen the emergence of a new generalized sampling theorem of which Nyquist Shannon is a special case. This new theorem suggests that it is possible to sample and reconstruct certain signals at rates much slower than those predicted by Nyquist-Shannon. One application in which this new theorem is of considerable interest is Fresnel Holography. A number of papers have recently suggested that the sampling rate for the digital recording of Fresnel holograms can be relaxed considerably. This may allow the positioning of the object closer to the camera allowing for a greater numerical aperture and thus an improved range of 3D perspective. In this paper we: (i) Review generalized sampling for Fresnel propagated signals, (ii) Investigate the effect of the twin image, always present in recording, on the generalized sampling theorem and (iii) Discuss the effect of finite pixel size for the first time

Speed up of Fresnel transforms for Digital holography using pre-computation

We show how the common Fresnel reconstruction of digital holograms can be speeded up on ordinary computers by precomputing the two chirp factors for a given detector array size and then calling these values from memory during the reconstruction. The speedup in time is shown for various hologram sizes. We also run the same algorithm on a Nvidia GPU using Matlab

Reconstruction algorithms applied to in-line Gabor digital holographic microscopy

This paper investigates the application of Fresnel based numerical algorithms for the reconstruction of Gabor in-line holograms. We focus on the two most widely used Fresnel approximation algorithms, the direct method and the angular spectrum method. Both algorithms involve calculating a Fresnel integral, but they accomplish it in fundamentally different ways. The algorithms perform differently for different physical parameters such as distance, CCD pixel size, and so on. We investigate the constraints for the algorithms when applied to in-line Gabor digital holographic microscopy. We show why the algorithms fail in some instances and how to alter them in order to obtain useful images of the microscopic specimen. We verify the altered algorithms using an optically captured digital hologram

Multispectral lensless digital holographic microscope: imaging MCF-7 and MDA-MB-231 cancer cell cultures

Digital holography is the process where an object’s phase and amplitude information is retrieved from intensity images obtained using a digital camera (e.g. CCD or CMOS sensor). In-line digital holographic techniques offer full use of the recording device’s sampling bandwidth, unlike off-axis holography where object information is not modulated onto carrier fringes. Reconstructed images are obscured by the linear superposition of the unwanted, out of focus, twin images. In addition to this, speckle noise degrades overall quality of the reconstructed images. The speckle effect is a phenomenon of laser sources used in digital holographic systems. Minimizing the effects due to speckle noise, removal of the twin image and using the full sampling bandwidth of the capture device aids overall reconstructed image quality. Such improvements applied to digital holography can benefit applications such as holographic microscopy where the reconstructed images are obscured with twin image information. Overcoming such problems allows greater flexibility in current image processing techniques, which can be applied to segmenting biological cells (e.g. MCF-7 and MDA-MB- 231) to determine their overall cell density and viability. This could potentially be used to distinguish between apoptotic and necrotic cells in large scale mammalian cell processes, currently the system of choice, within the biopharmaceutical industry

Resolution limits in practical digital holographic systems

We examine some fundamental theoretical limits on the ability of practical digital holography DH systems to resolve detail in an image. Unlike conventional diffraction-limited imaging systems, where a projected image of the limiting aperture is used to define the system performance, there are at least three major effects that determine the performance of a DH system: i The spacing between adjacent pixels on the CCD, ii an averaging effect introduced by the finite size of these pixels, and iii the finite extent of the camera face itself. Using a theoretical model, we define a single expression that accounts for all these physical effects. With this model, we explore several different DH recording techniques: off-axis and inline, considering both the dc terms, as well as the real and twin images that are features of the holographic recording process. Our analysis shows that the imaging operation is shift variant and we demonstrate this using a simple example. We examine how our theoretical model can be used to optimize CCD design for lensless DH capture. We present a series of experimental results to confirm the validity of our theoretical model, demonstrating recovery of super- Nyquist frequencies for the first time

Resolution limits in practical digital holographic systems

We examine some fundamental theoretical limits on the ability of practical digital holography DH systems to resolve detail in an image. Unlike conventional diffraction-limited imaging systems, where a projected image of the limiting aperture is used to define the system performance, there are at least three major effects that determine the performance of a DH system: i The spacing between adjacent pixels on the CCD, ii an averaging effect introduced by the finite size of these pixels, and iii the finite extent of the camera face itself. Using a theoretical model, we define a single expression that accounts for all these physical effects. With this model, we explore several different DH recording techniques: off-axis and inline, considering both the dc terms, as well as the real and twin images that are features of the holographic recording process. Our analysis shows that the imaging operation is shift variant and we demonstrate this using a simple example. We examine how our theoretical model can be used to optimize CCD design for lensless DH capture. We present a series of experimental results to confirm the validity of our theoretical model, demonstrating recovery of super- Nyquist frequencies for the first time

Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung

Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people with cystic fibrosis (CF), adapts for survival in the CF lung through both mutation and gene expression changes. Frequent clonal strains such as the Australian Epidemic Strain-1 (AES-1), have increased ability to establish infection in the CF lung and to superimpose and replace infrequent clonal strains. Little is known about the factors underpinning these properties. Analysis has been hampered by lack of expression array templates containing CF-strain specific genes. We sequenced the genome of an acute infection AES-1 isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes, including 338 not found in the other seven genomes. The PANarray contained 12,543 gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326 quality-control probes and 70 probes for non-P. aeruginosa genes, including phage and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same patient 10.5 years later and not eradicated in the intervening period, in our validated artificial sputum medium (ASMDM) and used the PANarray to compare gene expression of both in duplicate. 675 genes were differentially expressed between the isogenic pairs, including upregulation of alginate, biofilm, persistence genes and virulence-related genes such as dihydroorotase, uridylate kinase and cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and numerous phage genes. Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients. © 2011 Naughton et al

Systematic errors of an optical encryption system due to the discrete values of a spatial light modulator

An optical implementation of the amplitude encoded double random phase encryption/decryption technique is implemented, and both numerical and experimental results are presented. In particular, we examine the effect of quantization in the decryption process due to the discrete values and quantized levels, which a spatial light modulator (SLM) can physically display. To do this, we characterize a transmissive SLM using Jones matrices and then map a complex image to the physically achievable levels of the SLM using the pseudorandom encoding technique. We present both numerical and experimental results that quantify the performance of the system