Multiresolution Segmentation of Natural Images: From linear to Non-Linear Scale-Space Representations

In this paper, we introduce a framework that merges classical ideas borrowed from scale-space and multi-resolution segmentation with non-linear partial differential equations. A non-linear scale-space stack is constructed by means of an appropriate diffusion equation. This stack is analyzed and a tree of coherent segments is constructed based on relationships between different scale layers. Pruning this tree proves to be a very efficient tool for unsupervised segmentation of different classes of images (e.g. natural, medical ...). This technique is light on the computational point of view and can be extended to non-scalar data in a straightforward manner

Generalizable automated pixel-level structural segmentation of medical and biological data

Over the years, the rapid expansion in imaging techniques and equipments has driven the demand for more automation in handling large medical and biological data sets. A wealth of approaches have been suggested as optimal solutions for their respective imaging types. These solutions span various image resolutions, modalities and contrast (staining) mechanisms. Few approaches generalise well across multiple image types, contrasts or resolution. This thesis proposes an automated pixel-level framework that addresses 2D, 2D+t and 3D structural segmentation in a more generalizable manner, yet has enough adaptability to address a number of specific image modalities, spanning retinal funduscopy, sequential fluorescein angiography and two-photon microscopy. The pixel-level segmentation scheme involves: i ) constructing a phase-invariant orientation field of the local spatial neighbourhood; ii ) combining local feature maps with intensity-based measures in a structural patch context; iii ) using a complex supervised learning process to interpret the combination of all the elements in the patch in order to reach a classification decision. This has the advantage of transferability from retinal blood vessels in 2D to neural structures in 3D. To process the temporal components in non-standard 2D+t retinal angiography sequences, we first introduce a co-registration procedure: at the pairwise level, we combine projective RANSAC with a quadratic homography transformation to map the coordinate systems between any two frames. At the joint level, we construct a hierarchical approach in order for each individual frame to be registered to the global reference intra- and inter- sequence(s). We then take a non-training approach that searches in both the spatial neighbourhood of each pixel and the filter output across varying scales to locate and link microvascular centrelines to (sub-) pixel accuracy. In essence, this \link while extract" piece-wise segmentation approach combines the local phase-invariant orientation field information with additional local phase estimates to obtain a soft classification of the centreline (sub-) pixel locations. Unlike retinal segmentation problems where vasculature is the main focus, 3D neural segmentation requires additional exibility, allowing a variety of structures of anatomical importance yet with different geometric properties to be differentiated both from the background and against other structures. Notably, cellular structures, such as Purkinje cells, neural dendrites and interneurons, all display certain elongation along their medial axes, yet each class has a characteristic shape captured by an orientation field that distinguishes it from other structures. To take this into consideration, we introduce a 5D orientation mapping to capture these orientation properties. This mapping is incorporated into the local feature map description prior to a learning machine. Extensive performance evaluations and validation of each of the techniques presented in this thesis is carried out. For retinal fundus images, we compute Receiver Operating Characteristic (ROC) curves on existing public databases (DRIVE & STARE) to assess and compare our algorithms with other benchmark methods. For 2D+t retinal angiography sequences, we compute the error metrics ("Centreline Error") of our scheme with other benchmark methods. For microscopic cortical data stacks, we present segmentation results on both surrogate data with known ground-truth and experimental rat cerebellar cortex two-photon microscopic tissue stacks.Open Acces

Segmentation of Natural Images Using Scale-Space Representation with Multi-Scale Edge Supervised Hierarchical Linking

In general purpose computer vision systems, non-supervised image analysis is mandatory in order to achieve an automatic operation. In this paper a different approach to image segmentation for natural scenes is presented. Scale-Space representation is used to extract the structure from meaningful objects in the image. A hierarchical decomposition of the image is performed from the iso-intensity paths. The Scale-Space stack is generated using isotropic diffusion on the basis of linear Scale-Space theory. From that, the independence of the algorithm from the image content and particular characteristics is ensured. In the framework of this work, it is also introduced the use of additional information to improve the robustness in the structure extraction. In addition to the set of several diffused versions of the image, a representation of edges through scale is included as a feature in order to supervise the generation of the hierarchical tree that represents the image

Bridging Nano and Micro-scale X-ray Tomography for Battery Research by Leveraging Artificial Intelligence

X-ray Computed Tomography (X-ray CT) is a well-known non-destructive imaging technique where contrast originates from the materials' absorption coefficients. Novel battery characterization studies on increasingly challenging samples have been enabled by the rapid development of both synchrotron and laboratory-scale imaging systems as well as innovative analysis techniques. Furthermore, the recent development of laboratory nano-scale CT (NanoCT) systems has pushed the limits of battery material imaging towards voxel sizes previously achievable only using synchrotron facilities. Such systems are now able to reach spatial resolutions down to 50 nm. Given the non-destructive nature of CT, in-situ and operando studies have emerged as powerful methods to quantify morphological parameters, such as tortuosity factor, porosity, surface area, and volume expansion during battery operation or cycling. Combined with powerful Artificial Intelligence (AI)/Machine Learning (ML) analysis techniques, extracted 3D tomograms and battery-specific morphological parameters enable the development of predictive physics-based models that can provide valuable insights for battery engineering. These models can predict the impact of the electrode microstructure on cell performances or analyze the influence of material heterogeneities on electrochemical responses. In this work, we review the increasing role of X-ray CT experimentation in the battery field, discuss the incorporation of AI/ML in analysis, and provide a perspective on how the combination of multi-scale CT imaging techniques can expand the development of predictive multiscale battery behavioral models.Comment: 33 pages, 5 figure

Segmentation of Natural Images Using Scale-Space Representations: A Linear and a Non-Linear Approach

In general purpose computer vision systems, unsupervised image analysis is mandatory in order to achieve an automatic operation. In this paper a different approach to image segmentation for natural scenes is presented. Scale-Space representation is used to extract the structure from meaningful objects in the image. Two different scale-spaces are analysed in the paper. On one hand Isotropic Diffusion (linear scale-space) is presented as the basis for an uncommitted front end, not relying on any special feature of the image. On the other hand the Total Variation Diffusion (non-linear scale-space) which makes a special emphasis on edges is also analysed. A hierarchical decomposition of the image is performed on the basis of the special characteristics of each scale-space. Iso-intensity paths will be tracked in the case of linear scale-space, whereas in the case of non-linear scale-space the evolution of level sets through scale will be tracked. In the framework of linear scale-space, the use of additional information to improve the robustness in the structure extraction is introduced. Appart from the set of several diffused versions of the image, a representation of edges through scale is included to supervise the generation of the hierarchical tree that represents the image

Multi-scale active shape description in medical imaging

Shape description in medical imaging has become an increasingly important research field in recent years. Fast and high-resolution image acquisition methods like Magnetic Resonance (MR) imaging produce very detailed cross-sectional images of the human body - shape description is then a post-processing operation which abstracts quantitative descriptions of anatomically relevant object shapes. This task is usually performed by clinicians and other experts by first segmenting the shapes of interest, and then making volumetric and other quantitative measurements. High demand on expert time and inter- and intra-observer variability impose a clinical need of automating this process. Furthermore, recent studies in clinical neurology on the correspondence between disease status and degree of shape deformations necessitate the use of more sophisticated, higher-level shape description techniques. In this work a new hierarchical tool for shape description has been developed, combining two recently developed and powerful techniques in image processing: differential invariants in scale-space, and active contour models. This tool enables quantitative and qualitative shape studies at multiple levels of image detail, exploring the extra image scale degree of freedom. Using scale-space continuity, the global object shape can be detected at a coarse level of image detail, and finer shape characteristics can be found at higher levels of detail or scales. New methods for active shape evolution and focusing have been developed for the extraction of shapes at a large set of scales using an active contour model whose energy function is regularized with respect to scale and geometric differential image invariants. The resulting set of shapes is formulated as a multiscale shape stack which is analysed and described for each scale level with a large set of shape descriptors to obtain and analyse shape changes across scales. This shape stack leads naturally to several questions in regard to variable sampling and appropriate levels of detail to investigate an image. The relationship between active contour sampling precision and scale-space is addressed. After a thorough review of modem shape description, multi-scale image processing and active contour model techniques, the novel framework for multi-scale active shape description is presented and tested on synthetic images and medical images. An interesting result is the recovery of the fractal dimension of a known fractal boundary using this framework. Medical applications addressed are grey-matter deformations occurring for patients with epilepsy, spinal cord atrophy for patients with Multiple Sclerosis, and cortical impairment for neonates. Extensions to non-linear scale-spaces, comparisons to binary curve and curvature evolution schemes as well as other hierarchical shape descriptors are discussed