Monitoring mesenchymal stem cell cultures using image processing and pattern recognition techniques

Stem cells have attracted tremendous interest in recent times due to their promise in providing innovative new treatments for a great range of currently debilitating diseases. This is due to their potential ability to regenerate and repair damaged tissue, and hence restore lost body function, in a manner beyond the body's usual healing process. Bone marrow-derived mesenchymal stem cells or bone marrow stromal cells are one type of adult stem cells that are of particular interest. Since they are derived from a living human adult donor, they do not have the ethical issues associated with the use of human embryonic stem cells. They are also able to be taken from a patient or other donors with relative ease and then grown readily in the laboratory for clinical application. Despite the attractive properties of bone marrow stromal cells, there is presently no quick and easy way to determine the quality of a sample of such cells. Presently, a sample must be grown for weeks and subject to various time-consuming assays, under the direction of an expert cell biologist, to determine whether it will be useful. Hence there is a great need for innovative new ways to assess the quality of cell cultures for research and potential clinical application. The research presented in this thesis investigates the use of computerised image processing and pattern recognition techniques to provide a quicker and simpler method for the quality assessment of bone marrow stromal cell cultures. In particular, aim of this work is to find out whether it is possible, through the use of image processing and pattern recognition techniques, to predict the growth potential of a culture of human bone marrow stromal cells at early stages, before it is readily apparent to a human observer. With the above aim in mind, a computerised system was developed to classify the quality of bone marrow stromal cell cultures based on phase contrast microscopy images. Our system was trained and tested on mixed images of both healthy and unhealthy bone marrow stromal cell samples taken from three different patients. This system, when presented with 44 previously unseen bone marrow stromal cell culture images, outperformed human experts in the ability to correctly classify healthy and unhealthy cultures. The system correctly classified the health status of an image 88% of the time compared to an average of 72% of the time for human experts. Extensive training and testing of the system on a set of 139 normal sized images and 567 smaller image tiles showed an average performance of 86% and 85% correct classifications, respectively. The contributions of this thesis include demonstrating the applicability and potential of computerised image processing and pattern recognition techniques to the task of quality assessment of bone marrow stromal cell cultures. As part of this system, an image normalisation method has been suggested and a new segmentation algorithm has been developed for locating cell regions of irregularly shaped cells in phase contrast images. Importantly, we have validated the efficacy of both the normalisation and segmentation method, by demonstrating that both methods quantitatively improve the classification performance of subsequent pattern recognition algorithms, in discriminating between cell cultures of differing health status. We have shown that the quality of a cell culture of bone marrow stromal cells may be assessed without the need to either segment individual cells or to use time-lapse imaging. Finally, we have proposed a set of features, that when extracted from the cell regions of segmented input images, can be used to train current state of the art pattern recognition systems to predict the quality of bone marrow stromal cell cultures earlier and more consistently than human experts.

Designing for engagement towards healthier lifestyles through food image sharing : the case of I8DAT

This paper introduces the underlying design concepts of I8DAT, a food image sharing application that has been developed as part of a three-year research project – Eat, Cook, Grow: Ubiquitous Technology for Sustainable Food Culture in the City (http://www.urbaninformatics .net/projects/food) – exploring urban food practices to engage people in healthier, more environmentally and socially sustainable eating, cooking, and growing food in their everyday lives. The key aim of the project is to produce actionable knowledge, which is then applied to create and test several accessible, user-centred interactive design solutions that motivate user-engagement through playful and social means rather than authoritative information distribution. Through the design and implementation processes we envisage to integrate these design interventions to create a sustainable food network that is both technical and socio-cultural in nature (technosocial). Our primary research locale is Brisbane, Australia, with additional work carried out in three reference cities with divergent geographic, socio-cultural, and technological backgrounds: Seoul, South Korea, for its global leadership in ubiquitous technology, broadband access, and high population density; Lincoln, UK, for the regional and peri-urban dimension it provides, and Portland, Oregon, US, for its international standing as a hub of the sustainable food movement.

Facial expression recognition using facial movement features

Facial expression is an important channel for human communication and can be applied in many real applications. One critical step for facial expression recognition (FER) is to accurately extract emotional features. Current approaches on FER in static images have not fully considered and utilized the features of facial element and muscle movements, which represent static and dynamic, as well as geometric and appearance characteristics of facial expressions. This paper proposes an approach to solve this limitation using ‘salient’ distance features, which are obtained by extracting patch-based 3D Gabor features, selecting the ‘salient’ patches, and performing patch matching operations. The experimental results demonstrate high correct recognition rate (CRR), significant performance improvements due to the consideration of facial element and muscle movements, promising results under face registration errors, and fast processing time. The comparison with the state-of-the-art performance confirms that the proposed approach achieves the highest CRR on the JAFFE database and is among the top performers on the Cohn-Kanade (CK) database.

Improving the performance of facial expression recognition using dynamic, subtle and regional features

Human facial expression is a complex process characterized of dynamic, subtle and regional emotional features. State-of-the-art approaches on facial expression recognition (FER) have not fully utilized this kind of features to improve the recognition performance. This paper proposes an approach to overcome this limitation using patch-based ‘salient’ Gabor features. A set of 3D patches are extracted to represent the subtle and regional features, and then inputted into patch matching operations for capturing the dynamic features. Experimental results show a significant performance improvement of the proposed approach due to the use of the dynamic features. Performance comparison with pervious work also confirms that the proposed approach achieves the highest CRR reported to date on the JAFFE database and a top-level performance on the Cohn-Kanade (CK) database.

Geometry vs appearance for discriminating between posed and spontaneous emotions

Spontaneous facial expressions differ from posed ones in appearance, timing and accompanying head movements. Still images cannot provide timing or head movement information directly. However, indirectly the distances between key points on a face extracted from a still image using active shape models can capture some movement and pose changes. This information is superposed on information about non-rigid facial movement that is also part of the expression. Does geometric information improve the discrimination between spontaneous and posed facial expressions arising from discrete emotions? We investigate the performance of a machine vision system for discrimination between posed and spontaneous versions of six basic emotions that uses SIFT appearance based features and FAP geometric features. Experimental results on the NVIE database demonstrate that fusion of geometric information leads only to marginal improvement over appearance features. Using fusion features, surprise is the easiest emotion (83.4% accuracy) to be distinguished, while disgust is the most difficult (76.1%). Our results find different important facial regions between discriminating posed versus spontaneous version of one emotion and classifying the same emotion versus other emotions. The distribution of the selected SIFT features shows that mouth is more important for sadness, while nose is more important for surprise, however, both the nose and mouth are important for disgust, fear, and happiness. Eyebrows, eyes, nose and mouth are important for anger.

Evaluation of texture and geometry for dimensional facial expression recognition

Facial expression recognition (FER) algorithms mainly focus on classification into a small discrete set of emotions or representation of emotions using facial action units (AUs). Dimensional representation of emotions as continuous values in an arousal-valence space is relatively less investigated. It is not fully known whether fusion of geometric and texture features will result in better dimensional representation of spontaneous emotions. Moreover, the performance of many previously proposed approaches to dimensional representation has not been evaluated thoroughly on publicly available databases. To address these limitations, this paper presents an evaluation framework for dimensional representation of spontaneous facial expressions using texture and geometric features. SIFT, Gabor and LBP features are extracted around facial fiducial points and fused with FAP distance features. The CFS algorithm is adopted for discriminative texture feature selection. Experimental results evaluated on the publicly accessible NVIE database demonstrate that fusion of texture and geometry does not lead to a much better performance than using texture alone, but does result in a significant performance improvement over geometry alone. LBP features perform the best when fused with geometric features. Distributions of arousal and valence for different emotions obtained via the feature extraction process are compared with those obtained from subjective ground truth values assigned by viewers. Predicted valence is found to have a more similar distribution to ground truth than arousal in terms of covariance or Bhattacharya distance, but it shows a greater distance between the means.

Improved image quality for x-ray CT imaging of gel dosimeters

Purpose: This study provides a simple method for improving precision of x-ray computed tomography (CT) scans of irradiated polymer gel dosimetry. The noise affecting CT scans of irradiated gels has been an impediment to the use of clinical CT scanners for gel dosimetry studies. Method: In this study, it is shown that multiple scans of a single PAGAT gel dosimeter can be used to extrapolate a ‘zero-scan’ image which displays a similar level of precision to an image obtained by averaging multiple CT images, without the compromised dose measurement resulting from the exposure of the gel to radiation from the CT scanner. Results: When extrapolating the zero-scan image, it is shown that exponential and simple linear fits to the relationship between Hounsfield unit and scan number, for each pixel in the image, provides an accurate indication of gel density. Conclusions: It is expected that this work will be utilised in the analysis of three-dimensional gel volumes irradiated using complex radiotherapy treatments.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

Pattern recognition using invariants defined from higher order spectra : 2-D image inputs

A new algorithm for extracting features from images for object recognition is described. The algorithm uses higher order spectra to provide desirable invariance properties, to provide noise immunity, and to incorporate nonlinearity into the feature extraction procedure thereby allowing the use of simple classifiers. An image can be reduced to a set of 1D functions via the Radon transform, or alternatively, the Fourier transform of each 1D projection can be obtained from a radial slice of the 2D Fourier transform of the image according to the Fourier slice theorem. A triple product of Fourier coefficients, referred to as the deterministic bispectrum, is computed for each 1D function and is integrated along radial lines in bifrequency space. Phases of the integrated bispectra are shown to be translation- and scale-invariant. Rotation invariance is achieved by a regrouping of these invariants at a constant radius followed by a second stage of invariant extraction. Rotation invariance is thus converted to translation invariance in the second step. Results using synthetic and actual images show that isolated, compact clusters are formed in feature space. These clusters are linearly separable, indicating that the nonlinearity required in the mapping from the input space to the classification space is incorporated well into the feature extraction stage. The use of higher order spectra results in good noise immunity, as verified with synthetic and real images. Classification of images using the higher order spectra-based algorithm compares favorably to classification using the method of moment invariants

Face recognition using fractal codes

In this paper we propose a new method for face recognition using fractal codes. Fractal codes represent local contractive, affine transformations which when iteratively applied to range-domain pairs in an arbitrary initial image result in a fixed point close to a given image. The transformation parameters such as brightness offset, contrast factor, orientation and the address of the corresponding domain for each range are used directly as features in our method. Features of an unknown face image are compared with those pre-computed for images in a database. There is no need to iterate, use fractal neighbor distances or fractal dimensions for comparison in the proposed method. This method is robust to scale change, frame size change and rotations as well as to some noise, facial expressions and blur distortion in the image

Machine recognition of hand-drawn circuit diagrams

An application of image processing techniques to recognition of hand-drawn circuit diagrams is presented. The scanned image of a diagram is pre-processed to remove noise and converted to bilevel. Morphological operations are applied to obtain a clean, connected representation using thinned lines. The diagram comprises of nodes, connections and components. Nodes and components are segmented using appropriate thresholds on a spatially varying object pixel density. Connection paths are traced using a pixel-stack. Nodes are classified using syntactic analysis. Components are classified using a combination of invariant moments, scalar pixel-distribution features, and vector relationships between straight lines in polygonal representations. A node recognition accuracy of 82% and a component recognition accuracy of 86% was achieved on a database comprising 107 nodes and 449 components. This recogniser can be used for layout “beautification” or to generate input code for circuit analysis and simulation packages