Grid computing for the numerical reconstruction of digital holograms

Digital holography has the potential to greatly extend holography's applications and move it from the lab into the field: a single CCD or other solid-state sensor can capture any number of holograms while numerical reconstruction within a computer eliminates the need for chemical processing and readily allows further processing and visualisation of the holographic image. The steady increase in sensor pixel count and resolution leads to the possibilities of larger sample volumes and of higher spatial resolution sampling, enabling the practical use of digital off-axis holography. However this increase in pixel count also drives a corresponding expansion of the computational effort needed to numerically reconstruct such holograms to an extent where the reconstruction process for a single depth slice takes significantly longer than the capture process for each single hologram. Grid computing - a recent innovation in largescale distributed processing -provides a convenient means of harnessing significant computing resources in an ad-hoc fashion that might match the field deployment of a holographic instrument. In this paper we consider the computational needs of digital holography and discuss the deployment of numericals reconstruction software over an existing Grid testbed. The analysis of marine organisms is used as an exemplar for work flow and job execution of in-line digital holography

leave a trace - A People Tracking System Meets Anomaly Detection

Video surveillance always had a negative connotation, among others because of the loss of privacy and because it may not automatically increase public safety. If it was able to detect atypical (i.e. dangerous) situations in real time, autonomously and anonymously, this could change. A prerequisite for this is a reliable automatic detection of possibly dangerous situations from video data. This is done classically by object extraction and tracking. From the derived trajectories, we then want to determine dangerous situations by detecting atypical trajectories. However, due to ethical considerations it is better to develop such a system on data without people being threatened or even harmed, plus with having them know that there is such a tracking system installed. Another important point is that these situations do not occur very often in real, public CCTV areas and may be captured properly even less. In the artistic project leave a trace the tracked objects, people in an atrium of a institutional building, become actor and thus part of the installation. Visualisation in real-time allows interaction by these actors, which in turn creates many atypical interaction situations on which we can develop our situation detection. The data set has evolved over three years and hence, is huge. In this article we describe the tracking system and several approaches for the detection of atypical trajectories

Low-Cost Motility Tracking System (LOCOMOTIS) for time-lapse microscopy applications and cell visualisation

This article has been made available through the Brunel Open Access Publishing Fund.Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6x. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8x). In preliminary cell culture experiments using our system, velocities (mean mm/min ± SE) of 0.81±0.01 (Biomphalaria glabrata hemocytes on uncoated plates), 1.17±0.004 (MDA-MB-231 breast cancer cells), 1.24±0.006 (SC5 mouse Sertoli cells) and 2.21±0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates), were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers. © 2014 Lynch et al

GEANT4 : a simulation toolkit

Abstract Geant4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics. PACS: 07.05.Tp; 13; 2

Decomposition of Optical Flow on the Sphere

We propose a number of variational regularisation methods for the estimation and decomposition of motion fields on the $2$-sphere. While motion estimation is based on the optical flow equation, the presented decomposition models are motivated by recent trends in image analysis. In particular we treat $u+v$ decomposition as well as hierarchical decomposition. Helmholtz decomposition of motion fields is obtained as a natural by-product of the chosen numerical method based on vector spherical harmonics. All models are tested on time-lapse microscopy data depicting fluorescently labelled endodermal cells of a zebrafish embryo.Comment: The final publication is available at link.springer.co

A multi-modal stereo microscope based on a spatial light modulator

Spatial Light Modulators (SLMs) can emulate the classic microscopy techniques, including differential interference (DIC) contrast and (spiral) phase contrast. Their programmability entails the benefit of flexibility or the option to multiplex images, for single-shot quantitative imaging or for simultaneous multi-plane imaging (depth-of-field multiplexing). We report the development of a microscope sharing many of the previously demonstrated capabilities, within a holographic implementation of a stereo microscope. Furthermore, we use the SLM to combine stereo microscopy with a refocusing filter and with a darkfield filter. The instrument is built around a custom inverted microscope and equipped with an SLM which gives various imaging modes laterally displaced on the same camera chip. In addition, there is a wide angle camera for visualisation of a larger region of the sample

BDSIM: An Accelerator Tracking Code with Particle-Matter Interactions

Beam Delivery Simulation (BDSIM) is a program that simulates the passage of particles in a particle accelerator. It uses a suite of standard high energy physics codes (Geant4, ROOT and CLHEP) to create a computational model of a particle accelerator that combines accurate accelerator tracking routines with all of the physics processes of particles in Geant4. This unique combination permits radiation and detector background simulations in accelerators where both accurate tracking of all particles is required over long range or over many revolutions of a circular machine, as well as interaction with the material of the accelerator.Comment: 20 pages, 17 figures. Accepted for publication 28th Jan 202