Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

The structural connectivity of the brain is considered to encode species-wise and subject-wise patterns that will unlock large areas of understanding of the human brain. Currently, diffusion MRI of the living brain enables to map the microstructure of tissue, allowing to track the pathways of fiber bundles connecting the cortical regions across the brain. These bundles are summarized in a network representation called connectome that is analyzed using graph theory. The extraction of the connectome from diffusion MRI requires a large processing flow including image enhancement, reconstruction, segmentation, registration, diffusion tracking, etc. Although a concerted effort has been devoted to the definition of standard pipelines for the connectome extraction, it is still crucial to define quality assessment protocols of these workflows. The definition of quality control protocols is hindered by the complexity of the pipelines under test and the absolute lack of gold-standards for diffusion MRI data. Here we characterize the impact on structural connectivity workflows of the geometrical deformation typically shown by diffusion MRI data due to the inhomogeneity of magnetic susceptibility across the imaged object. We propose an evaluation framework to compare the existing methodologies to correct for these artifacts including whole-brain realistic phantoms. Additionally, we design and implement an image segmentation and registration method to avoid performing the correction task and to enable processing in the native space of diffusion data. We release PySDCev, an evaluation framework for the quality control of connectivity pipelines, specialized in the study of susceptibility-derived distortions. In this context, we propose Diffantom, a whole-brain phantom that provides a solution to the lack of gold-standard data. The three correction methodologies under comparison performed reasonably, and it is difficult to determine which method is more advisable. We demonstrate that susceptibility-derived correction is necessary to increase the sensitivity of connectivity pipelines, at the cost of specificity. Finally, with the registration and segmentation tool called regseg we demonstrate how the problem of susceptibility-derived distortion can be overcome allowing data to be used in their original coordinates. This is crucial to increase the sensitivity of the whole pipeline without any loss in specificity.

Human-computer interaction based on visual hand-gesture recognition using volumetric spatiograms of local binary patterns

A more natural, intuitive, user-friendly, and less intrusive Human–Computer interface for controlling an application by executing hand gestures is presented. For this purpose, a robust vision-based hand-gesture recognition system has been developed, and a new database has been created to test it. The system is divided into three stages: detection, tracking, and recognition. The detection stage searches in every frame of a video sequence potential hand poses using a binary Support Vector Machine classifier and Local Binary Patterns as feature vectors. These detections are employed as input of a tracker to generate a spatio-temporal trajectory of hand poses. Finally, the recognition stage segments a spatio-temporal volume of data using the obtained trajectories, and compute a video descriptor called Volumetric Spatiograms of Local Binary Patterns (VS-LBP), which is delivered to a bank of SVM classifiers to perform the gesture recognition. The VS-LBP is a novel video descriptor that constitutes one of the most important contributions of the paper, which is able to provide much richer spatio-temporal information than other existing approaches in the state of the art with a manageable computational cost. Excellent results have been obtained outperforming other approaches of the state of the art.

A Novel Prediction Method for Early Recognition of Global Human Behaviour in Image Sequences

Human behaviour recognition has been, and still remains, a challenging problem that involves different areas of computational intelligence. The automated understanding of people activities from video sequences is an open research topic in which the computer vision and pattern recognition areas have made big efforts. In this paper, the problem is studied from a prediction point of view. We propose a novel method able to early detect behaviour using a small portion of the input, in addition to the capabilities of it to predict behaviour from new inputs. Specifically, we propose a predictive method based on a simple representation of trajectories of a person in the scene which allows a high level understanding of the global human behaviour. The representation of the trajectory is used as a descriptor of the activity of the individual. The descriptors are used as a cue of a classification stage for pattern recognition purposes. Classifiers are trained using the trajectory representation of the complete sequence. However, partial sequences are processed to evaluate the early prediction capabilities having a specific observation time of the scene. The experiments have been carried out using the three different dataset of the CAVIAR database taken into account the behaviour of an individual. Additionally, different classic classifiers have been used for experimentation in order to evaluate the robustness of the proposal. Results confirm the high accuracy of the proposal on the early recognition of people behaviours.

Military Districts, England and Wales, United Kingdom, 1804 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: A complete representation of the coast of England, together with the interior, divided into counties and military districts : also the coast of France and Holland from the Texel to Brest ... to which is annexed eighteen plans of the ports of the enemy, the principal depôts of the flotilla intended for the invasion of England, by John Luffman, Geogr. It was published by J. Luffman in 1804. Scale [ca. 1:2,500,000]. The image inside the map neatline is georeferenced to the surface of the earth and fit to the 'British National Grid' coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, administrative and military district boundaries, shoreline features including distances between selected ports, and more. Includes insets of foreign military installations and index to the military districts. This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

New Techniques in Deep Representation Learning

Thesis (Ph.D.)--University of Washington, 2016-06

Multigradient field-active contour model for multilayer boundary detection of ultrasound rectal wall image

Extraction and reconstruction of rectal wall structures from an ultrasound image is helpful for surgeons in rectal clinical diagnosis and 3-D reconstruction of rectal structures from ultrasound images. The primary task is to extract the boundary of the muscular layers on the rectal wall. However, due to the low SNR from ultrasound imaging and the thin muscular layer structure of the rectum, this boundary detection task remains a challenge. An active contour model is an effective high-level model, which has been used successfully to aid the tasks of object representation and recognition in many image-processing applications. We present a novel multigradient field active contour algorithm with an extended ability for multiple-object detection, which overcomes some limitations of ordinary active contour models—"snakes." The core part in the algorithm is the proposal of multigradient vector fields, which are used to replace image forces in kinetic function for alternative constraints on the deformation of active contour, thereby partially solving the initialization limitation of active contour for rectal wall boundary detection. An adaptive expanding force is also added to the model to help the active contour go through the homogenous region in the image. The efficacy of the model is explained and tested on the boundary detection of a ring-shaped image, a synthetic image, and an ultrasound image. The experimental results show that the proposed multigradient field-active contour is feasible for multilayer boundary detection of rectal wall

Disrupted cortical proprioceptive representation evokes symptoms of peculiarity, foreignness and swelling, but not pain

Objectives. It has been proposed that disruption of the internal proprioceptive representation, via incongruent sensory input, may underpin pathological pain states, but experimental evidence relies on conflicting visual input, which is not clinically relevant. We aimed to determine the symptomatic effect of incongruent proprioceptive input, imparted by vibration of the wrist tendons, which evokes the illusion of perpetual wrist flexion and disrupts cortical proprioceptive representation. Methods. Twenty-nine healthy and naive volunteers reported symptoms during five conditions: control, active and passive wrist flexion, extensor carpi radialis tendon vibration to evoke illusion of perpetual wrist flexion, and ulnar styloid (sham) vibration. No advice was given about possible illusions. Results. Twenty-one subjects reported the illusion of perpetual wrist flexion during tendon vibration. There was no effect of condition or of whether or not subjects reported an illusion on discomfort/pain (P > 0.28). Peculiarity, swelling and foreignness were greater during tendon vibration than during the other conditions, and greater during tendon vibration in those who reported an illusion of wrist flexion than in those who did not (P < 0.05 for all). Symptoms were reported by at least two subjects in each condition and four subjects reported systemic symptoms (e.g. nausea). Conclusions. In healthy volunteers, incongruent proprioceptive input does not cause discomfort or pain but does evoke feelings of peculiarity, swelling and foreignness in the limb.

Representation and parameterisation issues in genetic algorithms

A multi-chromosome GA (Multi-GA) was developed, based upon concepts from the natural world, allowing improved flexibility in a number of areas including representation, genetic operators, their parameter rates and real world multi-dimensional applications. A series of experiments were conducted, comparing the performance of the Multi-GA to a traditional GA on a number of recognised and increasingly complex test optimisation surfaces, with promising results. Further experiments demonstrated the Multi-GA's flexibility through the use of non-binary chromosome representations and its applicability to dynamic parameterisation. A number of alternative and new methods of dynamic parameterisation were investigated, in addition to a new non-binary 'Quotient crossover' mechanism. Finally, the Multi-GA was applied to two real world problems, demonstrating its ability to handle mixed type chromosomes within an individual, the limited use of a chromosome level fitness function, the introduction of new genetic operators for structural self-adaptation and its viability as a serious real world analysis tool. The first problem involved optimum placement of computers within a building, allowing the Multi-GA to use multiple chromosomes with different type representations and different operators in a single individual. The second problem, commonly associated with Geographical Information Systems (GIS), required a spatial analysis location of the optimum number and distribution of retail sites over two different population grids. In applying the Multi-GA, two new genetic operators (addition and deletion) were developed and explored, resulting in the definition of a mechanism for self-modification of genetic material within the Multi-GA structure and a study of this behaviour.

Digital image watermarking

In recent years, interest in digital watermarking has grown significantly. Indeed, the use of digital watermarking techniques is seen as a promising mean to protect intellectual property rights of digital data and to ensure the authentication of digital data. Thus, a significant research effort has been devoted to the study of practical watermarking systems, in particular for digital images. In this thesis, a practical and principled approach to the problem is adopted. Several aspects of practical watermarking schemes are investigated. First, a power constaint formulation of the problem is presented. Then, a new analysis of quantisation effects on the information rate of digital watermarking scheme is proposed and compared to other approaches suggested in the literature. Subsequently, a new information embedding technique, based on quantisation, is put forward and its performance evaluated. Finally, the influence of image data representation on the performance of practical scheme is studied along with a new representation based on independent component analysis.

Petrographic image analysis and understanding

This study considers the application of image analysis in petrography and investigates the possibilities for advancing existing techniques by introducing feature extraction and analysis capabilities of a higher level than those currently employed. The aim is to construct relevant, useful descriptions of crystal form and inter-crystal relations in polycrystalline igneous rock sections. Such descriptions cannot be derived until the `ownership' of boundaries between adjacent crystals has been established: this is the fundamental problem of crystal boundary assignment. An analysis of this problem establishes key image features which reveal boundary ownership; a set of explicit analysis rules is presented. A petrographic image analysis scheme based on these principles is outlined and the implementation of key components of the scheme considered. An algorithm for the extraction and symbolic representation of image structural information is developed. A new multiscale analysis algorithm which produces a hierarchical description of the linear and near-linear structure on a contour is presented in detail. Novel techniques for symmetry analysis are developed. The analyses considered contribute both to the solution of the boundary assignment problem and to the construction of geologically useful descriptions of crystal form. The analysis scheme which is developed employs grouping principles such as collinearity, parallelism, symmetry and continuity, so providing a link between this study and more general work in perceptual grouping and intermediate level computer vision. Consequently, the techniques developed in this study may be expected to find wider application beyond the petrographic domain.

Exploring the effectiveness of similarity-based visualisations for colour-based image retrieval

In April 2009, Google Images added a filter for narrowing search results by colour. Several other systems for searching image databases by colour were also released around this time. These colour-based image retrieval systems enable users to search image databases either by selecting colours from a graphical palette (i.e., query-by-colour), by drawing a representation of the colour layout sought (i.e., query-by-sketch), or both. It was comments left by readers of online articles describing these colour-based image retrieval systems that provided us with the inspiration for this research. We were surprised to learn that the underlying query-based technology used in colour-based image retrieval systems today remains remarkably similar to that of systems developed nearly two decades ago. Discovering this ageing retrieval approach, as well as uncovering a large user demographic requiring image search by colour, made us eager to research more effective approaches for colour-based image retrieval. In this thesis, we detail two user studies designed to compare the effectiveness of systems adopting similarity-based visualisations, query-based approaches, or a combination of both, for colour-based image retrieval. In contrast to query-based approaches, similarity-based visualisations display and arrange database images so that images with similar content are located closer together on screen than images with dissimilar content. This removes the need for queries, as users can instead visually explore the database using interactive navigation tools to retrieve images from the database. As we found existing evaluation approaches to be unreliable, we describe how we assessed and compared systems adopting similarity-based visualisations, query-based approaches, or both, meaningfully and systematically using our Mosaic Test - a user-based evaluation approach in which evaluation study participants complete an image mosaic of a predetermined target image using the colour-based image retrieval system under evaluation.

Three-dimensional capture, representation, and manipulation of Cuneiform tablets

This paper presents the digital imaging results of a collaborative research project working toward the generation of an on-line interactive digital image database of signs from ancient cuneiform tablets. An important aim of this project is the application of forensic analysis to the cuneiform symbols to identify scribal hands. Cuneiform tablets are amongst the earliest records of written communication, and could be considered as one of the original information technologies; an accessible, portable and robust medium for communication across distance and time. The earliest examples are up to 5,000 years old, and the writing technique remained in use for some 3,000 years. Unfortunately, only a small fraction of these tablets can be made available for display in museums and much important academic work has yet to be performed on the very large numbers of tablets to which there is necessarily restricted access. Our paper will describe the challenges encountered in the 2D image capture of a sample set of tablets held in the British Museum, explaining the motivation for attempting 3D imaging and the results of initial experiments scanning the smaller, more densely inscribed cuneiform tablets. We will also discuss the tractability of 3D digital capture, representation and manipulation, and investigate the requirements for scaleable data compression and transmission methods. Additional information can be found on the project website: www.cuneiform.net

Hausdorff Distances for Searching in Binary Text Images

This work has been partially supported by Grant No. DO 02-275, 16.12.2008, Bulgarian NSF, Ministry of Education and Science.

Multiplierless DCT Algorithm for Image Compression Applications

This paper presents a novel error-free (infinite-precision) architecture for the fast implementation of 8x8 2-D Discrete Cosine Transform. The architecture uses a new algebraic integer encoding of a 1-D radix-8 DCT that allows the separable computation of a 2-D 8x8 DCT without any intermediate number representation conversions. This is a considerable improvement on previously introduced algebraic integer encoding techniques to compute both DCT and IDCT which eliminates the requirements to approximate the transformation matrix ele- ments by obtaining their exact representations and hence mapping the transcendental functions without any errors. Apart from the multiplication-free nature, this new mapping scheme fits to this algorithm, eliminating any computational or quantization errors and resulting short-word-length and high-speed-design.