An automated workflow for parallel processing of large multiview SPIM recordings

Multiview light sheet fluorescence microscopy (LSFM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance cluster (HPC). Here we introduce an automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse LSFM data on a single workstation or in parallel on a HPC. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing LSFM data in a fraction of the time required to collect it.Comment: 13 pages with supplement, LATEX; 1 table, 1 figure, 2 supplementary figures, 2 supplementary lists, 2 supplementary tables; corrected error in results table, results unchange

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.Web of Science9art. no. e5254

Learning to Find Eye Region Landmarks for Remote Gaze Estimation in Unconstrained Settings

Conventional feature-based and model-based gaze estimation methods have proven to perform well in settings with controlled illumination and specialized cameras. In unconstrained real-world settings, however, such methods are surpassed by recent appearance-based methods due to difficulties in modeling factors such as illumination changes and other visual artifacts. We present a novel learning-based method for eye region landmark localization that enables conventional methods to be competitive to latest appearance-based methods. Despite having been trained exclusively on synthetic data, our method exceeds the state of the art for iris localization and eye shape registration on real-world imagery. We then use the detected landmarks as input to iterative model-fitting and lightweight learning-based gaze estimation methods. Our approach outperforms existing model-fitting and appearance-based methods in the context of person-independent and personalized gaze estimation

PlaceRaider: Virtual Theft in Physical Spaces with Smartphones

As smartphones become more pervasive, they are increasingly targeted by malware. At the same time, each new generation of smartphone features increasingly powerful onboard sensor suites. A new strain of sensor malware has been developing that leverages these sensors to steal information from the physical environment (e.g., researchers have recently demonstrated how malware can listen for spoken credit card numbers through the microphone, or feel keystroke vibrations using the accelerometer). Yet the possibilities of what malware can see through a camera have been understudied. This paper introduces a novel visual malware called PlaceRaider, which allows remote attackers to engage in remote reconnaissance and what we call virtual theft. Through completely opportunistic use of the camera on the phone and other sensors, PlaceRaider constructs rich, three dimensional models of indoor environments. Remote burglars can thus download the physical space, study the environment carefully, and steal virtual objects from the environment (such as financial documents, information on computer monitors, and personally identifiable information). Through two human subject studies we demonstrate the effectiveness of using mobile devices as powerful surveillance and virtual theft platforms, and we suggest several possible defenses against visual malware

ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Human behavior understanding for worker-centered intelligent manufacturing

“In a worker-centered intelligent manufacturing system, sensing and understanding of the worker’s behavior are the primary tasks, which are essential for automatic performance evaluation & optimization, intelligent training & assistance, and human-robot collaboration. In this study, a worker-centered training & assistant system is proposed for intelligent manufacturing, which is featured with self-awareness and active-guidance. To understand the hand behavior, a method is proposed for complex hand gesture recognition using Convolutional Neural Networks (CNN) with multiview augmentation and inference fusion, from depth images captured by Microsoft Kinect. To sense and understand the worker in a more comprehensive way, a multi-modal approach is proposed for worker activity recognition using Inertial Measurement Unit (IMU) signals obtained from a Myo armband and videos from a visual camera. To automatically learn the importance of different sensors, a novel attention-based approach is proposed to human activity recognition using multiple IMU sensors worn at different body locations. To deploy the developed algorithms to the factory floor, a real-time assembly operation recognition system is proposed with fog computing and transfer learning. The proposed worker-centered training & assistant system has been validated and demonstrated the feasibility and great potential for applying to the manufacturing industry for frontline workers. Our developed approaches have been evaluated: 1) the multi-view approach outperforms the state-of-the-arts on two public benchmark datasets, 2) the multi-modal approach achieves an accuracy of 97% on a worker activity dataset including 6 activities and achieves the best performance on a public dataset, 3) the attention-based method outperforms the state-of-the-art methods on five publicly available datasets, and 4) the developed transfer learning model achieves a real-time recognition accuracy of 95% on a dataset including 10 worker operations”--Abstract, page iv

Holoscopic 3D imaging and display technology: Camera/ processing/ display

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonHoloscopic 3D imaging “Integral imaging” was first proposed by Lippmann in 1908. It has become an attractive technique for creating full colour 3D scene that exists in space. It promotes a single camera aperture for recording spatial information of a real scene and it uses a regularly spaced microlens arrays to simulate the principle of Fly’s eye technique, which creates physical duplicates of light field “true 3D-imaging technique”. While stereoscopic and multiview 3D imaging systems which simulate human eye technique are widely available in the commercial market, holoscopic 3D imaging technology is still in the research phase. The aim of this research is to investigate spatial resolution of holoscopic 3D imaging and display technology, which includes holoscopic 3D camera, processing and display. Smart microlens array architecture is proposed that doubles spatial resolution of holoscopic 3D camera horizontally by trading horizontal and vertical resolutions. In particular, it overcomes unbalanced pixel aspect ratio of unidirectional holoscopic 3D images. In addition, omnidirectional holoscopic 3D computer graphics rendering techniques are proposed that simplify the rendering complexity and facilitate holoscopic 3D content generation. Holoscopic 3D image stitching algorithm is proposed that widens overall viewing angle of holoscopic 3D camera aperture and pre-processing of holoscopic 3D image filters are proposed for spatial data alignment and 3D image data processing. In addition, Dynamic hyperlinker tool is developed that offers interactive holoscopic 3D video content search-ability and browse-ability. Novel pixel mapping techniques are proposed that improves spatial resolution and visual definition in space. For instance, 4D-DSPM enhances 3D pixels per inch from 44 3D-PPIs to 176 3D-PPIs horizontally and achieves spatial resolution of 1365 × 384 3D-Pixels whereas the traditional spatial resolution is 341 × 1536 3D-Pixels. In addition distributed pixel mapping is proposed that improves quality of holoscopic 3D scene in space by creating RGB-colour channel elemental images

Generating collaborative systems for digital libraries: A model-driven approach

This is an open access article shared under a Creative Commons Attribution 3.0 Licence (http://creativecommons.org/licenses/by/3.0/). Copyright @ 2010 The Authors.The design and development of a digital library involves different stakeholders, such as: information architects, librarians, and domain experts, who need to agree on a common language to describe, discuss, and negotiate the services the library has to offer. To this end, high-level, language-neutral models have to be devised. Metamodeling techniques favor the definition of domainspecific visual languages through which stakeholders can share their views and directly manipulate representations of the domain entities. This paper describes CRADLE (Cooperative-Relational Approach to Digital Library Environments), a metamodel-based framework and visual language for the definition of notions and services related to the development of digital libraries. A collection of tools allows the automatic generation of several services, defined with the CRADLE visual language, and of the graphical user interfaces providing access to them for the final user. The effectiveness of the approach is illustrated by presenting digital libraries generated with CRADLE, while the CRADLE environment has been evaluated by using the cognitive dimensions framework