Antonio Foncubierta-Rodríguez

Three-dimensional solid texture analysis in biomedical imaging: review and opportunities.

Three-dimensional computerized characterization of biomedical solid textures is key to large-scale and high-throughput screening of imaging data. Such data increasingly become available in the clinical and research environments with an ever increasing spatial resolution. In this text we exhaustively analyze the state-of-the-art in 3-D biomedical texture analysis to identify the specific needs of the application domains and extract promising trends in image processing algorithms. The geometrical properties of biomedical textures are studied both in their natural space and on digitized lattices. It is found that most of the tissue types have strong multi-scale directional properties, that are well captured by imaging protocols with high resolutions and spherical spatial transfer functions. The information modeled by the various image processing techniques is analyzed and visualized by displaying their 3-D texture primitives. We demonstrate that non-convolutional approaches are expected to provide best results when the size of structures are inferior to five voxels. For larger structures, it is shown that only multi-scale directional convolutional approaches that are non-separable allow for an unbiased modeling of 3-D biomedical textures. With the increase of high-resolution isotropic imaging protocols in clinical routine and research, these models are expected to best leverage the wealth of 3-D biomedical texture analysis in the future. Future research directions and opportunities are proposed to efficiently model personalized image-based phenotypes of normal biomedical tissue and its alterations. The integration of the clinical and genomic context is expected to better explain the intra class variation of healthy biomedical textures. Using texture synthesis, this provides the exciting opportunity to simulate and visualize texture atlases of normal ageing process and disease progression for enhanced treatment planning and clinical care management.

Rotation–Covariant Texture Learning Using Steerable Riesz Wavelets

We propose a texture learning approach that exploits local organizations of scales and directions. First, linear combinations of Riesz wavelets are learned using kernel support vector machines. The resulting texture signatures are modeling optimal class-wise discriminatory properties. The visualization of the obtained signatures allows verifying the visual relevance of the learned concepts. Second, the local orientations of the signatures are optimized to maximize their responses, which is carried out analytically and can still be expressed as a linear combination of the initial steerable Riesz templates. The global process is iteratively repeated to obtain final rotation-covariant texture signatures. Rapid convergence of class-wise signatures is observed, which demonstrates that the instances are projected into a feature space that leverages the local organizations of scales and directions. Experimental evaluation reveals average classification accuracies in the range of 97% to 98% for the Outex_TC_00010, the Outex_TC_00012, and the Contrib_TC_00000 suites for even orders of the Riesz transform, and suggests high robustness to changes in images orientation and illumination. The proposed framework requires no arbitrary choices of scales and directions and is expected to perform well in a large range of computer vision applications.

Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks

Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.

Using multiscale visual words for lung texture classification and retrieval

Interstitial lung diseases (ILDs) are regrouping over 150 heterogeneous disorders of the lung parenchyma. High---Resolution Computed Tomography (HRCT) plays an important role in diagnosis, as standard chest x---rays are often non---specific for ILDs. Assessment of ILDs is considerd hard for clinicians because the diseases are rare, patterns often look visually similar and various clinical data need to be integrated. An image retrieval system to support interpretation of HRCT images by retrieving similar images is presented in this paper. The system uses a wavelet transform based on Difference of Gaussians (DoG) in order to extract texture descriptors from a set of 90 image series containing 1679 manually annotated regions corresponding to various ILDs. Visual words are used for feature aggregation and to describe tissue patterns. The optimal scale---progression scheme, number of visual words, as well as distance measure for clustering to generate visual words are investigated. A sufficiently high number of visual words is required to accurately describe patterns with high intra---class variations such as healthy tissue. Scale progression has less influence and the Euclidean distance performs better than other distances. The results show that the system is able to learn the wide intra---class variations of healthy tissue and the characteristics of abnormal lung tissue to provide reliable assistance to clinicians.

Overview of the VISCERAL Retrieval Benchmark 2015

The results of the VISCERAL 3D case retrieval benchmark were presented during the Multimodal Retrieval in the Medical Domain MRMD 2015 workshop in Vienna, Austria on March 29, 2015. The main task for the participanta was to find and rank similar medical cases from a large multimodal semantic RadLex terms extracted from text and visual 3D data data set using a query case as input. The approaches that integrated information from both the RadLex terms and the 3D volumes provided in the benchmark obtained the best results based on 5 standard evaluation metrics. The benchmark set up, data set description and result analysis from the benchmark are presented for all the submitted methods.

Rotation-covariant texture analysis of 4D dual-energy CT as an indicator of local pulmonary perfusion

We propose rotation-covariant texture analysis of 4D dual- energy computed tomography (DECT) as a diagnosis aid tool for acute pulmonary embolism in emergency radiology. The cornerstone of the proposed approach is to align 3D Riesz directional filters along bronchovascular structures to enable rotation-covariant comparisons of the parenchymal texture. The latter is enabled using the steerability property of Riesz filterbanks. Blockwise classification of the parenchyma from all pulmonary lobes allowed a mean area under the receiver operating characteristic (ROC) curve of 0.85, which suggests that the proposed approach can be successfully used to assist radiologists in DECT data interpretation.

Medical image retrieval using bag of meaningful visual words: unsupervised visual vocabulary pruning with PLSA

Content--based medical image retrieval has been proposed as a technique that allows not only for easy access to images from the relevant literature and electronic health records but also for training physicians, for research and clinical decision support. The bag-of-visual-words approach is a widely used technique that tries to shorten the semantic gap by learning meaningful features from the dataset and describing documents and images in terms of the histogram of these features. Visual vocabularies are often redundant, over--complete and noisy. Larger than required vocabularies lead to high--dimensional feature spaces, which present important disadvantages with the curse of dimensionality and computational cost being the most obvious ones. In this work a visual vocabulary pruning technique is presented. It enormously reduces the amount of required words to describe a medical image dataset with no significant effect on the accuracy. Results show that a reduction of up to 90% can be achieved without impact on the system performance. Obtaining a more compact representation of a document enables multimodal description as well as using classifiers requiring low--dimensional representations.

Region-based volumetric medical image retrieval

Volumetric medical images contain an enormous amount of visual information that can discourage the exhaustive use of local descriptors for image analysis, comparison and retrieval. Distinctive features and patterns that need to be analyzed for finding diseases are most often local or regional, often in only very small parts of the image. Separating the large amount of image data that might contain little important information is an important task as it could reduce the current information overload of physicians and make clinical work more efficient. In this paper a novel method for detecting key-regions is introduced as a way of extending the concept of keypoints often used in 2D image analysis. In this way also computation is reduced as important visual features are only extracted from the detected key regions. The region detection method is integrated into a platform-independent, web-based graphical interface for medical image visualization and retrieval in three dimensions. This web-based interface makes it easy to deploy on existing infrastructures in both small and large-scale clinical environments. By including the region detection method into the interface, manual annotation is reduced and time is saved, making it possible to integrate the presented interface and methods into clinical routine and workflows, analyzing image data at a large scale.

Benefits of texture analysis of dual energy CT for Computer-Aided pulmonary embolism detection

Pulmonary embolism is an avoidable cause of death if treated immediately but delays in diagnosis and treatment lead to an increased risk. Computer-assisted image analysis of both unenhanced and contrast-enhanced computed tomography (CT) have proven useful for diagnosis of pulmonary embolism. Dual energy CT provides additional information over the standard single energy scan by generating four-dimensional (4D) data, in our case with 11 energy levels in 3D. In this paper a 4D texture analysis method capable of detecting pulmonary embolism in dual energy CT is presented. The method uses wavelet-based visual words together with an automatic geodesic-based region of interest detection algorithm to characterize the texture properties of each lung lobe. Results show an increase in performance with respect to the single energy CT analysis, as well as an accuracy gain compared to preliminary work on a small dataset.

Retrieval of 4d dual energy CT for pulmonary embolism diagnosis

Pulmonary embolism is a common condition with high short---term morbidity. Pulmonary embolism can be treated successfully but diagnosis remains difficult due to the large variability of symptoms, which are often non---specific including breath shortness, chest pain and cough. Dual energy CT produces 4---dimensional data by acquiring variation of attenuation with respect to spatial coordinates and also with respect to the energy level. This additional information opens the possibility of discriminating tissue with specific material content, such as bone and adjacent contrast. Despite having already been available for clinical use for a while, there are few applications where Dual energy CT is currently showing a clear clinical advantage. In this article we propose to use the additional energy---level data in a 4D dataset to quantify texture changes in lung parenchyma as a way of finding parenchyma perfusion deficits characteristic of pulmonary embolism.