Geometric Modeling and Recognition of Elongated Regions in Images.

The goal of this research is the recovery of elongated shapes from patterns of local features extracted from images. A generic geometric model-based approach is developed based on general concepts of 2-d form and structure. This is an intermediate-level analysis that is computed from groupings and decompositions of related low-level features. Axial representations are used to describe the shapes of image objects having the property of elongatedness. Curve-fitting is shown to compute axial sequences of the points in an elongated cluster. Script-clustering is performed about a parametric smooth curve to extract elongated partitions of the data incorporating constraints of point connectivity, curve alignment, and strip boundedness. A thresholded version of the Gabriel Graph (GG) is shown to offer most of the information needed from the Minimum Spanning Tree (MST) and Delauney Triangulation (DT), while being easily computable from finite neighborhood operations. An iterative curve-fitting method, that is placed in the general framework of Random Sample Consensus (RANSAC) model-fitting, is used to extract maximal partitions. The method is developed for general parametric curve-fitting over discrete point patterns. A complete structural analysis is presented for the recovery of elongated regions from multispectral classification. A region analysis is shown to be superior to an edge-based analysis in the early stages of recognition. First, the curve-fitting method is used to recover the linear components of complex object regions. The rough locations to start and end a region delineation are then detected by decomposing extracted linear shape clusters with a circular operator. Experimental results are shown for a variety of images, with the main result being an analysis of a high-resolution aerial image of a suburban road network. Analyses of printed circuit board patterns and a LANDSAT river image are also given. The generality of the curve-fitting approach is shown by these results and by its possible applications to other described image analysis problems

A survey of visual preprocessing and shape representation techniques

Many recent theories and methods proposed for visual preprocessing and shape representation are summarized. The survey brings together research from the fields of biology, psychology, computer science, electrical engineering, and most recently, neural networks. It was motivated by the need to preprocess images for a sparse distributed memory (SDM), but the techniques presented may also prove useful for applying other associative memories to visual pattern recognition. The material of this survey is divided into three sections: an overview of biological visual processing; methods of preprocessing (extracting parts of shape, texture, motion, and depth); and shape representation and recognition (form invariance, primitives and structural descriptions, and theories of attention)

GPIS: genetic programming based image segmentation with applications to biomedical object detection

Image segmentation plays a critical role in many image analysis applications. However, it is ill-defined in nature and remains one of the most intractable problems in image processing. In this thesis, we propose a genetic programming based algorithm for image segmentation (GPIS). Typically, genetic programming is a Darwinian-evolution inspired program discovery method and in the past it has been successfully used as an automatic programming tool. We make use of this property of GP to evolve efficient and accurate image segmentation programs from a pool of basic image analysis operators. In addition, we provide no a priori information about that nature of the images to the GP. The algorithm was tested on two separate medical image databases and results show the proposed GP's ability to adapt and produce short and accurate segmentation algorithms, irrespective of the database in use. We compared our results with a popular GA based image segmentation/classification system, GENIE Pro. We found that our proposed algorithm produced accurate image segmentations performed consistently on both databases and could possibly be extended to other image databases as a general-purpose image segmentation tool

Brain Tumor Detection and Segmentation in Multisequence MRI

Tato práce se zabývá detekcí a segmentací mozkového nádoru v multisekvenčních MR obrazech se zaměřením na gliomy vysokého a nízkého stupně malignity. Jsou zde pro tento účel navrženy tři metody. První metoda se zabývá detekcí prezence částí mozkového nádoru v axiálních a koronárních řezech. Jedná se o algoritmus založený na analýze symetrie při různých rozlišeních obrazu, který byl otestován na T1, T2, T1C a FLAIR obrazech. Druhá metoda se zabývá extrakcí oblasti celého mozkového nádoru, zahrnující oblast jádra tumoru a edému, ve FLAIR a T2 obrazech. Metoda je schopna extrahovat mozkový nádor z 2D i 3D obrazů. Je zde opět využita analýza symetrie, která je následována automatickým stanovením intenzitního prahu z nejvíce asymetrických částí. Třetí metoda je založena na predikci lokální struktury a je schopna segmentovat celou oblast nádoru, jeho jádro i jeho aktivní část. Metoda využívá faktu, že většina lékařských obrazů vykazuje vysokou podobnost intenzit sousedních pixelů a silnou korelaci mezi intenzitami v různých obrazových modalitách. Jedním ze způsobů, jak s touto korelací pracovat a používat ji, je využití lokálních obrazových polí. Podobná korelace existuje také mezi sousedními pixely v anotaci obrazu. Tento příznak byl využit v predikci lokální struktury při lokální anotaci polí. Jako klasifikační algoritmus je v této metodě použita konvoluční neuronová síť vzhledem k její známe schopnosti zacházet s korelací mezi příznaky. Všechny tři metody byly otestovány na veřejné databázi 254 multisekvenčních MR obrazech a byla dosáhnuta přesnost srovnatelná s nejmodernějšími metodami v mnohem kratším výpočetním čase (v řádu sekund při použitý CPU), což poskytuje možnost manuálních úprav při interaktivní segmetaci.This work deals with the brain tumor detection and segmentation in multisequence MR images with particular focus on high- and low-grade gliomas. Three methods are propose for this purpose. The first method deals with the presence detection of brain tumor structures in axial and coronal slices. This method is based on multi-resolution symmetry analysis and it was tested for T1, T2, T1C and FLAIR images. The second method deals with extraction of the whole brain tumor region, including tumor core and edema, in FLAIR and T2 images and is suitable to extract the whole brain tumor region from both 2D and 3D. It also uses the symmetry analysis approach which is followed by automatic determination of the intensity threshold from the most asymmetric parts. The third method is based on local structure prediction and it is able to segment the whole tumor region as well as tumor core and active tumor. This method takes the advantage of a fact that most medical images feature a high similarity in intensities of nearby pixels and a strong correlation of intensity profiles across different image modalities. One way of dealing with -- and even exploiting -- this correlation is the use of local image patches. In the same way, there is a high correlation between nearby labels in image annotation, a feature that has been used in the ``local structure prediction'' of local label patches. Convolutional neural network is chosen as a learning algorithm, as it is known to be suited for dealing with correlation between features. All three methods were evaluated on a public data set of 254 multisequence MR volumes being able to reach comparable results to state-of-the-art methods in much shorter computing time (order of seconds running on CPU) providing means, for example, to do online updates when aiming at an interactive segmentation.

Multi-Scale Vector-Ridge-Detection for Perceptual Organization Without Edges

We present a novel ridge detector that finds ridges on vector fields. It is designed to automatically find the right scale of a ridge even in the presence of noise, multiple steps and narrow valleys. One of the key features of such ridge detector is that it has a zero response at discontinuities. The ridge detector can be applied to scalar and vector quantities such as color. We also present a parallel perceptual organization scheme based on such ridge detector that works without edges; in addition to perceptual groups, the scheme computes potential focus of attention points at which to direct future processing. The relation to human perception and several theoretical findings supporting the scheme are presented. We also show results of a Connection Machine implementation of the scheme for perceptual organization (without edges) using color

Taking aim at moving targets in computational cell migration

Cell migration is central to the development and maintenance of multicellular organisms. Fundamental understanding of cell migration can, for example, direct novel therapeutic strategies to control invasive tumor cells. However, the study of cell migration yields an overabundance of experimental data that require demanding processing and analysis for results extraction. Computational methods and tools have therefore become essential in the quantification and modeling of cell migration data. We review computational approaches for the key tasks in the quantification of in vitro cell migration: image pre-processing, motion estimation and feature extraction. Moreover, we summarize the current state-of-the-art for in silico modeling of cell migration. Finally, we provide a list of available software tools for cell migration to assist researchers in choosing the most appropriate solution for their needs

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

SEEKING A COMMON THEME: A STUDY OF CERAMIC EFFIGY ARTIFACTS IN THE PRE-HISPANIC AMERICAN SOUTHWEST AND NORTHERN MEXICO USING COMPUTER IMAGE PATTERN RECOGNITION AND PHYLOGENETIC ANALYSIS

Effigy artifacts are found throughout the Pre-Hispanic American Southwest and Northern Mexico (PHASNM), as well as in other cultures around the world, with many sharing the same forms and design features. The earliest figurines within the PHASNM were partial anthropomorphic figurines made from fired clay, dating to between A.D. 287 and A.D. 312 (Morss 1954:27). They were found in a pit house village of Bluff Ruin in the Forestdale Valley of eastern Arizona, and they appeared to be associated with the Mogollon culture. The temporal range of the samples examined in this study is from approximately 200 A.D. to 1650 A.D., and the geographical range includes the Southwestern United States (Arizona, New Mexico, Texas, Colorado, and Utah) and the northcentral section of Mexico (Casas Grandes and the surrounding area). This research looks at the similarities among the markings of ceramic effigy artifacts from the PHASNM, using computer image pattern recognition, design analysis, and phylogenetics, to determine whether their ceramic traditions share a common theme and whether the specific method of social learning responsible for the transmission of information relating to ceramic effigy decoration can be identified. Transmission is possible in one of three ways: vertical transmission, where parents/teachers distribute information by encouraging imitation and sharing learned traditions with children/students (Richerson and Boyd 2005; Shennan 2002); horizontal transmission, where information is transmitted among peers, either from within the individual’s group or from interaction with peers from neighboring populations (Borgerhoff Mulder et al. 2006), and where the individual comes into contact with a wide range of attributes related to the item of interest and then adopts those that allow for the fastest, most economical methods of production and distribution (Eerkens et al 2006; Rogers 1983); and oblique transmission, where information is transmitted by adults, masters, or institutions of elite or higher social status, either internally or externally to the adopting cultural Type (Jensen 2016; Jordan 2014), and where particular traits are adopted or left out in disproportionate ways, creating patterns in localized traditions that can be empirically identified. Horizontal transmission can be broken into two types: unlimited, where contact is not confined to a particular group; and limited, where contact is restricted to a particular set of contacts. Using criteria for each of the categories as set forth by the New Mexico Office of Archaeological Studies Pottery Typology Project, the samples were classified in terms of cultural area (culture), branch, tradition, ware, and type. The research v group consisted of 360 photographic samples represented by 868 images that were resized to a 640x640 pixel format. The images were then examined through computer image pattern recognition (using YOLOv5) and through manual observation. This study resulted in a database representing 230 traits. These traits were assembled into groups by cultural area, branch, tradition, ware, and type, and phylogenetic analysis was applied to show how the different entities transfer information among each other

Dual Consistency Enabled Weakly and Semi-Supervised Optic Disc and Cup Segmentation with Dual Adaptive Graph Convolutional Networks.

Glaucoma is a progressive eye disease that results in permanent vision loss, and the vertical cup to disc ratio (vCDR) in colour fundus images is essential in glaucoma screening and assessment. Previous fully supervised convolution neural networks segment the optic disc (OD) and optic cup (OC) from color fundus images and then calculate the vCDR offline. However, they rely on a large set of labeled masks for training, which is expensive and time-consuming to acquire. To address this, we propose a weakly and semi-supervised graph-based network that investigates geometric associations and domain knowledge between segmentation probability maps (PM), modified signed distance function representations (mSDF), and boundary region of interest characteristics (B-ROI) in three aspects. Firstly, we propose a novel Dual Adaptive Graph Convolutional Network (DAGCN) to reason the long-range features of the PM and the mSDF w.r.t. the regional uniformity. Secondly, we propose a dual consistency regularization-based semi-supervised learning paradigm. The regional consistency between the PM and the mSDF, and the marginal consistency between the derived B-ROI from each of them boost the proposed model's performance due to the inherent geometric associations. Thirdly, we exploit the task-specific domain knowledge via the oval shapes of OD & OC, where a differentiable vCDR estimating layer is proposed. Furthermore, without additional annotations, the supervision on vCDR serves as weakly-supervisions for segmentation tasks. Experiments on six large-scale datasets demonstrate our model's superior performance on OD & OC segmentation and vCDR estimation. The implementation code has been made available 1

Upper airways segmentation using principal curvatures

Esta tesis propone una nueva técnica para segmentar las vías aéreas superiores. Esta propuesta permite la extracción de estructuras curvilíneas usando curvaturas principales. La propuesta permite la extracción de éstas estructuras en imágenes 2D y 3D. Entre las principales novedades se encuentra la propuesta de un nuevo criterio de parada en la propagación del algoritmo de realce de contraste (operador multi-escala de tipo sombrero alto). De la misma forma, el criterio de parada propuesto es usado para detener los algoritmos de difusión anisotrópica. Además, un nuevo criterio es propuesto para seleccionar las curvaturas principales que conforman las estructuras curvilíneas, que se basa en los criterios propuestos por Steger, Deng et. al. y Armande et. al. Además, se propone un nuevo algoritmo para realizar la supresión de nomáximos que permite reducir la presencia de discontinuidades en el borde de las estructuras curvilíneas. Para extraer los bordes de las estructuras curvilíneas, se utiliza un algoritmo de enlace que incluye un nuevo criterio de distancia para reducir la aparición de agujeros en la estructura final. Finalmente, con base en los resultados obtenidos, se utiliza un algoritmo morfológico para cerrar los agujeros y se aplica un algoritmo de crecimiento de regiones para obtener la segmentación final de las vías respiratorias superiores.This dissertation proposes a new approach to segment the upper airways. This proposal allows the extraction of curvilinear structures based on the principal curvatures. The proposal allows extracting these structures from 2D and 3D images. Among the main novelties is the proposal of a new stopping criterion to stop the propagation of the contrast enhancement algorithm (multiscale top-hat morphological operator). In the same way, the proposed stopping criterion is used to stop the anisotropic diffusion algorithms. In addition, a new criterion is proposed to select the principal curvatures that make up the curvilinear structures, which is based on the criteria proposed by Steger, Deng et. al. and Armande et. al. Furthermore, a new algorithm to perform the non-maximum suppression that allows reducing the presence of discontinuities in the border of curvilinear structures is proposed. To extract the edges of the curvilinear structures, a linking algorithm is used that includes a new distance criterion to reduce the appearance of gaps in the final structure. Finally, based on the obtained results, a morphological algorithm is used to close the gaps and a region growing algorithm to obtain the final upper airways segmentation is applied.Doctor en IngenieríaDoctorad