Segmentation of phase contrast microscopy images based on multi-scale local Basic Image Features histograms

Phase contrast microscopy (PCM) is routinely used for the inspection of adherent cell cultures in all fields of biology and biomedicine. Key decisions for experimental protocols are often taken by an operator based on typically qualitative observations. However, automated processing and analysis of PCM images remain challenging due to the low contrast between foreground objects (cells) and background as well as various imaging artefacts. We propose a trainable pixel-wise segmentation approach whereby image structures and symmetries are encoded in the form of multi-scale Basic Image Features local histograms, and classification of them is learned by random decision trees. This approach was validated for segmentation of cell versus background, and discrimination between two different cell types. Performance close to that of state-of-the-art specialised algorithms was achieved despite the general nature of the method. The low processing time ( < 4 s per 1280 × 960 pixel images) is suitable for batch processing of experimental data as well as for interactive segmentation applications

Detection of concealed cars in complex cargo X-ray imagery using Deep Learning

BACKGROUND: Non-intrusive inspection systems based on X-ray radiography techniques are routinely used at transport hubs to ensure the conformity of cargo content with the supplied shipping manifest. As trade volumes increase and regulations become more stringent, manual inspection by trained operators is less and less viable due to low throughput. Machine vision techniques can assist operators in their task by automating parts of the inspection workflow. Since cars are routinely involved in trafficking, export fraud, and tax evasion schemes, they represent an attractive target for automated detection and flagging for subsequent inspection by operators. OBJECTIVE: Development and evaluation of a novel method for the automated detection of cars in complex X-ray cargo imagery. METHODS: X-ray cargo images from a stream-of-commerce dataset were classified using a window-based scheme. The limited number of car images was addressed by using an oversampling scheme. Different Convolutional Neural Network (CNN) architectures were compared with well-established bag of words approaches. In addition, robustness to concealment was evaluated by projection of objects into car images. RESULTS: CNN approaches outperformed all other methods evaluated, achieving 100% car image classification rate for a false positive rate of 1-in-454. Cars that were partially or completely obscured by other goods, a modus operandi frequently adopted by criminals, were correctly detected. CONCLUSIONS: We believe that this level of performance suggests that the method is suitable for deployment in the field. It is expected that the generic object detection workflow described can be extended to other object classes given the availability of suitable training data

Tackling the X-ray cargo inspection challenge using machine learning

The current infrastructure for non-intrusive inspection of cargo containers cannot accommodate exploding com-merce volumes and increasingly stringent regulations. There is a pressing need to develop methods to automate parts of the inspection workflow, enabling expert operators to focus on a manageable number of high-risk images. To tackle this challenge, we developed a modular framework for automated X-ray cargo image inspection. Employing state-of-the-art machine learning approaches, including deep learning, we demonstrate high performance for empty container verification and specific threat detection. This work constitutes a significant step towards the partial automation of X-ray cargo image inspection

Development of an image processing method for automated, non-invasive and scale-independent monitoring of adherent cell cultures

Adherent cell culture is a key experimental method for biological investigations in diverse areas such as developmental biology, drug discovery and biotechnology. Light microscopy-based methods, for example phase contrast microscopy (PCM), are routinely used for visual inspection of adherent cells cultured in transparent polymeric vessels. However, the outcome of such inspections is qualitative and highly subjective. Analytical methods that produce quantitative results can be used but often at the expense of culture integrity or viability. In this work, an imaging-based strategy to adherent cell cultures monitoring was investigated. Automated image processing and analysis of PCM images enabled quantitative measurements of key cell culture characteristics. Two types of segmentation algorithms for the detection of cellular objects on PCM images were evaluated. The first one, based on contrast filters and dynamic programming was quick (<1s per 1280×960 image) and performed well for different cell lines, over a wide range of imaging conditions. The second approach, termed ‘trainable segmentation’, was based on machine learning using a variety of image features such as local structures and symmetries. It accommodated complex segmentation tasks while maintaining low processing times (<5s per 1280×960 image). Based on the output from these segmentation algorithms, imaging-based monitoring of a large palette of cell responses was demonstrated, including proliferation, growth arrest, differentiation, and cell death. This approach is non-invasive and applicable to any transparent culture vessel, including microfabricated culture devices where a lack of suitable analytical methods often limits their applicability. This work was a significant contribution towards the establishment of robust, standardised, and affordable monitoring methods for adherent cell cultures. Finally, automated image processing was combined with computer-controlled cultures in small-scale devices. This provided a first demonstration of how adaptive culture protocols could be established; i.e. culture protocols which are based on cellular response instead of arbitrary time points

Automated X-ray image analysis for cargo security: Critical review and future promise

We review the relatively immature field of automated image analysis for X-ray cargo imagery. There is increasing demand for automated analysis methods that can assist in the inspection and selection of containers, due to the ever-growing volumes of traded cargo and the increasing concerns that customs- and security-related threats are being smuggled across borders by organised crime and terrorist networks. We split the field into the classical pipeline of image preprocessing and image understanding. Preprocessing includes: image manipulation; quality improvement; Threat Image Projection (TIP); and material discrimination and segmentation. Image understanding includes: Automated Threat Detection (ATD); and Automated Contents Verification (ACV). We identify several gaps in the literature that need to be addressed and propose ideas for future research. Where the current literature is sparse we borrow from the single-view, multi-view, and CT X-ray baggage domains, which have some characteristics in common with X-ray cargo

High-pressure transport properties of CeRu_2Ge_2

The pressure-induced changes in the temperature-dependent thermopower S(T) and electrical resistivity \rho(T) of CeRu_2Ge_2 are described within the single-site Anderson model. The Ce-ions are treated as impurities and the coherent scattering on different Ce-sites is neglected. Changing the hybridisation \Gamma between the 4f-states and the conduction band accounts for the pressure effect. The transport coefficients are calculated in the non-crossing approximation above the phase boundary line. The theoretical S(T) and \rho(T) curves show many features of the experimental data. The seemingly complicated temperature dependence of S(T) and \rho(T), and their evolution as a function of pressure, is related to the crossovers between various fixed points of the model.Comment: 9 pages, 10 figure

Threat Image Projection (TIP) into X-ray images of cargo containers for training humans and machines

We propose a framework for Threat Image Projection (TIP) in cargo transmission X-ray imagery. The method exploits the approximately multiplicative nature of X-ray imagery to extract a library of threat items. These items can then be projected into real cargo. We show using experimental data that there is no significant qualitative or quantitative difference between real threat images and TIP images. We also describe methods for adding realistic variation to TIP images in order to robustify Machine Learning (ML) based algorithms trained on TIP. These variations are derived from cargo X-ray image formation, and include: (i) translations; (ii) magnification; (iii) rotations; (iv) noise; (v) illumination; (vi) volume and density; and (vii) obscuration. These methods are particularly relevant for representation learning, since it allows the system to learn features that are invariant to these variations. The framework also allows efficient addition of new or emerging threats to a detection system, which is important if time is critical. We have applied the framework to training ML-based cargo algorithms for (i) detection of loads (empty verification), (ii) detection of concealed cars (ii) detection of Small Metallic Threats (SMTs). TIP also enables algorithm testing under controlled conditions, allowing one to gain a deeper understanding of performance. Whilst we have focused on robustifying ML-based threat detectors, our TIP method can also be used to train and robustify human threat detectors as is done in cabin baggage screening

Real-time monitoring of specific oxygen uptake rates of embryonic stem cells in a microfluidic cell culture device

Oxygen plays a key role in stem cell biology as a signaling molecule and as an indicator of cell energy metabolism. Quantification of cellular oxygen kinetics, i.e. the determination of specific oxygen uptake rates (sOURs), is routinely used to understand metabolic shifts. However current methods to determine sOUR in adherent cell cultures rely on cell sampling, which impacts on cellular phenotype. We present real-time monitoring of cell growth from phase contrast microscopy images, and of respiration using optical sensors for dissolved oxygen. Time-course data for bulk and peri-cellular oxygen concentrations obtained for Chinese hamster ovary (CHO) and mouse embryonic stem cell (mESCs) cultures successfully demonstrated this non-invasive and label-free approach. Additionally, we confirmed non-invasive detection of cellular responses to rapidly changing culture conditions by exposing the cells to mitochondrial inhibiting and uncoupling agents. For the CHO and mESCs, sOUR values between 8 and 60 amol cell(-1) s(-1) , and 5 and 35 amol cell(-1) s(-1) were obtained, respectively. These values compare favorably with literature data. The capability to monitor oxygen tensions, cell growth, and sOUR, of adherent stem cell cultures, non-invasively and in real time, will be of significant benefit for future studies in stem cell biology and stem cell-based therapies

Optical and transport properties of heavy fermions: theory compared to experiment

Employing a local moment approach to the periodic Anderson model within the framework of dynamical mean-field theory, direct comparison is made between theory and experiment for the dc transport and optical conductivities of paramagnetic heavy fermion and intermediate valence metals. Four materials, exhibiting a diverse range of behaviour in their transport/optics, are analysed in detail: CeB6, YbAl3, CeAl3 and CeCoIn5. Good agreement between theory and experiment is in general found, even quantitatively, and a mutually consistent picture of transport and optics results.Comment: 21 pages, 10 figures; Replacement with minor style changes made to avoid postscript file error