Assessment of sparse-based inpainting for retinal vessel removal

[EN] Some important eye diseases, like macular degeneration or diabetic retinopathy, can induce changes visible on the retina, for example as lesions. Segmentation of lesions or extraction of textural features from the fundus images are possible steps towards automatic detection of such diseases which could facilitate screening as well as provide support for clinicians. For the task of detecting significant features, retinal blood vessels are considered as being interference on the retinal images. If these blood vessel structures could be suppressed, it might lead to a more accurate segmentation of retinal lesions as well as a better extraction of textural features to be used for pathology detection. This work proposes the use of sparse representations and dictionary learning techniques for retinal vessel inpainting. The performance of the algorithm is tested for greyscale and RGB images from the DRIVE and STARE public databases, employing different neighbourhoods and sparseness factors. Moreover, a comparison with the most common inpainting family, diffusion-based methods, is carried out. For this purpose, two different ways of assessing the quality of the inpainting are presented and used to evaluate the results of the non-artificial inpainting, i.e. where a reference image does not exist. The results suggest that the use of sparse-based inpainting performs very well for retinal blood vessels removal which will be useful for the future detection and classification of eye diseases. (C) 2017 Elsevier B.V. All rights reserved.This work was supported by NILS Science and Sustainability Programme (014-ABEL-IM-2013) and by the Ministerio de Economia y Competitividad of Spain, Project ACRIMA (TIN2013-46751-R). The work of Adrian Colomer has been supported by the Spanish Government under the FPI Grant BES-2014-067889.Colomer, A.; Naranjo Ornedo, V.; Engan, K.; Skretting, K. (2017). Assessment of sparse-based inpainting for retinal vessel removal. Signal Processing: Image Communication. 59:73-82. https://doi.org/10.1016/j.image.2017.03.018S73825

Retinal vessel segmentation using textons

Segmenting vessels from retinal images, like segmentation in many other medical image domains, is a challenging task, as there is no unified way that can be adopted to extract the vessels accurately. However, it is the most critical stage in automatic assessment of various forms of diseases (e.g. Glaucoma, Age-related macular degeneration, diabetic retinopathy and cardiovascular diseases etc.). Our research aims to investigate retinal image segmentation approaches based on textons as they provide a compact description of texture that can be learnt from a training set. This thesis presents a brief review of those diseases and also includes their current situations, future trends and techniques used for their automatic diagnosis in routine clinical applications. The importance of retinal vessel segmentation is particularly emphasized in such applications. An extensive review of previous work on retinal vessel segmentation and salient texture analysis methods is presented. Five automatic retinal vessel segmentation methods are proposed in this thesis. The first method focuses on addressing the problem of removing pathological anomalies (Drusen, exudates) for retinal vessel segmentation, which have been identified by other researchers as a problem and a common source of error. The results show that the modified method shows some improvement compared to a previously published method. The second novel supervised segmentation method employs textons. We propose a new filter bank (MR11) that includes bar detectors for vascular feature extraction and other kernels to detect edges and photometric variations in the image. The k-means clustering algorithm is adopted for texton generation based on the vessel and non-vessel elements which are identified by ground truth. The third improved supervised method is developed based on the second one, in which textons are generated by k-means clustering and texton maps representing vessels are derived by back projecting pixel clusters onto hand labelled ground truth. A further step is implemented to ensure that the best combinations of textons are represented in the map and subsequently used to identify vessels in the test set. The experimental results on two benchmark datasets show that our proposed method performs well compared to other published work and the results of human experts. A further test of our system on an independent set of optical fundus images verified its consistent performance. The statistical analysis on experimental results also reveals that it is possible to train unified textons for retinal vessel segmentation. In the fourth method a novel scheme using Gabor filter bank for vessel feature extraction is proposed. The ii method is inspired by the human visual system. Machine learning is used to optimize the Gabor filter parameters. The experimental results demonstrate that our method significantly enhances the true positive rate while maintaining a level of specificity that is comparable with other approaches. Finally, we proposed a new unsupervised texton based retinal vessel segmentation method using derivative of SIFT and multi-scale Gabor filers. The lack of sufficient quantities of hand labelled ground truth and the high level of variability in ground truth labels amongst experts provides the motivation for this approach. The evaluation results reveal that our unsupervised segmentation method is comparable with the best other supervised methods and other best state of the art methods

Visual analysis and synthesis with physically grounded constraints

The past decade has witnessed remarkable progress in image-based, data-driven vision and graphics. However, existing approaches often treat the images as pure 2D signals and not as a 2D projection of the physical 3D world. As a result, a lot of training examples are required to cover sufficiently diverse appearances and inevitably suffer from limited generalization capability. In this thesis, I propose "inference-by-composition" approaches to overcome these limitations by modeling and interpreting visual signals in terms of physical surface, object, and scene. I show how we can incorporate physically grounded constraints such as scene-specific geometry in a non-parametric optimization framework for (1) revealing the missing parts of an image due to removal of a foreground or background element, (2) recovering high spatial frequency details that are not resolvable in low-resolution observations. I then extend the framework from 2D images to handle spatio-temporal visual data (videos). I demonstrate that we can convincingly fill spatio-temporal holes in a temporally coherent fashion by jointly reconstructing the appearance and motion. Compared to existing approaches, our technique can synthesize physically plausible contents even in challenging videos. For visual analysis, I apply stereo camera constraints for discovering multiple approximately linear structures in extremely noisy videos with an ecological application to bird migration monitoring at night. The resulting algorithms are simple and intuitive while achieving state-of-the-art performance without the need of training on an exhaustive set of visual examples

Robust density modelling using the student's t-distribution for human action recognition

The extraction of human features from videos is often inaccurate and prone to outliers. Such outliers can severely affect density modelling when the Gaussian distribution is used as the model since it is highly sensitive to outliers. The Gaussian distribution is also often used as base component of graphical models for recognising human actions in the videos (hidden Markov model and others) and the presence of outliers can significantly affect the recognition accuracy. In contrast, the Student's t-distribution is more robust to outliers and can be exploited to improve the recognition rate in the presence of abnormal data. In this paper, we present an HMM which uses mixtures of t-distributions as observation probabilities and show how experiments over two well-known datasets (Weizmann, MuHAVi) reported a remarkable improvement in classification accuracy. © 2011 IEEE

Applications of Physically Accurate Deep Learning for Processing Digital Rock Images

Digital rock analysis aims to improve our understanding of the fluid flow properties of reservoir rocks, which are important for enhanced oil recovery, hydrogen storage, carbonate dioxide storage, and groundwater management. X-ray microcomputed tomography (micro-CT) is the primary approach to capturing the structure of porous rock samples for digital rock analysis. Initially, the obtained micro-CT images are processed using image-based techniques, such as registration, denoising, and segmentation depending on various requirements. Numerical simulations are then conducted on the digital models for petrophysical prediction. The accuracy of the numerical simulation highly depends on the quality of the micro-CT images. Therefore, image processing is a critical step for digital rock analysis. Recent advances in deep learning have surpassed conventional methods for image processing. Herein, the utility of convolutional neural networks (CNN) and generative adversarial networks (GAN) are assessed in regard to various applications in digital rock image processing, such as segmentation, super-resolution, and denoising. To obtain training data, different sandstone and carbonate samples were scanned using various micro-CT facilities. After that, validation images previously unseen by the trained neural networks are utilised to evaluate the performance and robustness of the proposed deep learning techniques. Various threshold scenarios are applied to segment the reconstructed digital rock images for sensitivity analyses. Then, quantitative petrophysical analyses, such as porosity, absolute/relative permeability, and pore size distribution, are implemented to estimate the physical accuracy of the digital rock data with the corresponding ground truth data. The results show that both CNN and GAN deep learning methods can provide physically accurate digital rock images with less user bias than traditional approaches. These results unlock new pathways for various applications related to the reservoir characterisation of porous reservoir rocks