Automatic section thickness determination using an absolute gradient focus function.

Quantitative analysis of microstructures using computerized stereology systems is an essential tool in many disciplines of bioscience research. Section thickness determination in current nonautomated approaches requires manual location of upper and lower surfaces of tissue sections. In contrast to conventional autofocus functions that locate the optimally focused optical plane using the global maximum on a focus curve, this study identified by two sharp 'knees' on the focus curve as the transition from unfocused to focused optical planes. Analysis of 14 grey-scale focus functions showed, the thresholded absolute gradient function, was best for finding detectable bends that closely correspond to the bounding optical planes at the upper and lower tissue surfaces. Modifications to this function generated four novel functions that outperformed the original. The 'modified absolute gradient count' function outperformed all others with an average error of 0.56 µm on a test set of images similar to the training set; and, an average error of 0.39 µm on a test set comprised of images captured from a different case, that is, different staining methods on a different brain region from a different subject rat. We describe a novel algorithm that allows for automatic section thickness determination based on just out-of-focus planes, a prerequisite for fully automatic computerized stereology.

A generic knowledge-guided image segmentation and labeling system using fuzzy clustering algorithms.

Segmentation of an image into regions and the labeling of the regions is a challenging problem. In this paper, an approach that is applicable to any set of multifeature images of the same location is derived. Our approach applies to, for example, medical images of a region of the body; repeated camera images of the same area; and satellite images of a region. The segmentation and labeling approach described here uses a set of training images and domain knowledge to produce an image segmentation system that can be used without change on images of the same region collected over time. How to obtain training images, integrate domain knowledge, and utilize learning to segment and label images of the same region taken under any condition for which a training image exists is detailed. It is shown that clustering in conjunction with image processing techniques utilizing an iterative approach can effectively identify objects of interest in images. The segmentation and labeling approach described here is applied to color camera images and two other image domains are used to illustrate the applicability of the approach.

Automatic segmentation of non-enhancing brain tumors in magnetic resonance images.

Tumor segmentation from magnetic resonance (MR) images may aid in tumor treatment by tracking the progress of tumor growth and/or shrinkage. In this paper we present the first automatic segmentation method which separates non-enhancing brain tumors from healthy tissues in MR images to aid in the task of tracking tumor size over time. The MR feature images used for the segmentation consist of three weighted images (T1, T2 and proton density (PD)) for each axial slice through the head. An initial segmentation is computed using an unsupervised fuzzy clustering algorithm. Then, integrated domain knowledge and image processing techniques contribute to the final tumor segmentation. They are applied under the control of a knowledge-based system. The system knowledge was acquired by training on two patient volumes (14 images). Testing has shown successful tumor segmentations on four patient volumes (31 images). Our results show that we detected all six non-enhancing brain tumors, located tumor tissue in 35 of the 36 ground truth (radiologist labeled) slices containing tumor and successfully separated tumor regions from physically connected CSF regions in all the nine slices. Quantitative measurements are promising as correspondence ratios between ground truth and segmented tumor regions ranged between 0.368 and 0.871 per volume, with percent match ranging between 0.530 and 0.909 per volume.

Comparison of edge detection algorithms using a structure from motion task.

This paper presents an evaluation of edge detector performance. We use the task of structure from motion (SFM) as a "black box" through which to evaluate the performance of edge detection algorithms. Edge detector goodness is measured by how accurately the SFM could recover the known structure and motion from the edge detection of the image sequences. We use a variety of real image sequences with ground truth to evaluate eight different edge detectors from the literature. Our results suggest that ratings of edge detector performance based on pixel-level metrics and on the SFM are well correlated and that detectors such as the Canny detector and Heitger detector offer the best performance.

Fusion of physically-based registration and deformation modeling for nonrigid motion analysis.

In our previous work, we used finite element models to determine nonrigid motion parameters and recover unknown local properties of objects given correspondence data recovered with snakes or other tracking models. In this paper, we present a novel multiscale approach to recovery of nonrigid motion from sequences of registered intensity and range images. The main idea of our approach is that a finite element (FEM) model incorporating material properties of the object can naturally handle both registration and deformation modeling using a single model-driving strategy. The method includes a multiscale iterative algorithm based on analysis of the undirected Hausdorff distance to recover correspondences. The method is evaluated with respect to speed and accuracy. Noise sensitivity issues are addressed. Advantages of the proposed approach are demonstrated using man-made elastic materials and human skin motion. Experiments with regular grid features are used for performance comparison with a conventional approach (separate snakes and FEM models). It is shown, however, that the new method does not require a sampling/correspondence template and can adapt the model to available object features. Usefulness of the method is presented not only in the context of tracking and motion analysis, but also for a burn scar detection application.

Scar assessment: current problems and future solutions.

Current problems in the assessment of scars are discussed. The concept of subjective and objective aspects of scar assessment is introduced. The patient's own view of the scar (the subjective component) can currently be assessed and may be very influential in determining the patient's quality of life, irrespective of the actual physical characteristics of the scar. The objective aspects of the scar, including size, shape, texture, and pliability, are currently difficult to measure. Although the Vancouver Scar Scale has been used as the standard for objective measurements, there are problems with both the validity and reliability of this instrument. Various imaging techniques may permit more reliable and accurate methods for measuring the quantitative aspects of scars.

A vision-based technique for objective assessment of burn scars.

In this paper a method for the objective assessment of burn scars is proposed. The quantitative measures developed in this research provide an objective way to calculate elastic properties of burn scars relative to the surrounding areas. The approach combines range data and the mechanics and motion dynamics of human tissues. Active contours are employed to locate regions of interest and to find displacements of feature points using automatically established correspondences. Changes in strain distribution over time are evaluated. Given images at two time instances and their corresponding features, the finite element method is used to synthesize strain distributions of the underlying tissues. This results in a physically based framework for motion and strain analysis. Relative elasticity of the burn scar is then recovered using iterative descent search for the best nonlinear finite element model that approximates stretching behavior of the region containing the burn scar. The results from the skin elasticity experiments illustrate the ability to objectively detect differences in elasticity between normal and abnormal tissue. These estimated differences in elasticity are correlated against the subjective judgments of physicians that are presently the practice.

Automatic tumor segmentation using knowledge-based techniques.

A system that automatically segments and labels glioblastoma-multiforme tumors in magnetic resonance images (MRI's) of the human brain is presented. The MRI's consist of T1-weighted, proton density, and T2-weighted feature images and are processed by a system which integrates knowledge-based (KB) techniques with multispectral analysis. Initial segmentation is performed by an unsupervised clustering algorithm. The segmented image, along with cluster centers for each class are provided to a rule-based expert system which extracts the intracranial region. Multispectral histogram analysis separates suspected tumor from the rest of the intracranial region, with region analysis used in performing the final tumor labeling. This system has been trained on three volume data sets and tested on thirteen unseen volume data sets acquired from a single MRI system. The KB tumor segmentation was compared with supervised, radiologist-labeled "ground truth" tumor volumes and supervised k-nearest neighbors tumor segmentations. The results of this system generally correspond well to ground truth, both on a per slice basis and more importantly in tracking total tumor volume during treatment over time.

Medical image analysis with fuzzy models.

This paper updates several recent surveys on the use of fuzzy models for segmentation and edge detection in medical image data. Our survey is divided into methods based on supervised and unsupervised learning (that is, on whether there are or are not labelled data available for supervising the computations), and is organized first and foremost by groups (that we know of!) that are active in this area. Our review is aimed more towards 'who is doing it' rather than 'how good it is'. This is partially dictated by the fact that direct comparisons of supervised and unsupervised methods is somewhat akin to comparing apples and oranges. There is a further subdivision into methods for two- and three-dimensional data and/or problems. We do not cover methods based on neural-like networks or fuzzy reasoning systems. These topics are covered in a recently published companion survey by keller et al.

Left ventricular boundary detection from spatio-temporal volumetric computed tomography images.

This paper presents a new automatic technique for left ventricle boundary detection from a set of three-dimensional (3D) computed tomography (CT) volumetric cardiac images. The goals of this paper are to incorporate the temporal information into LV boundary detection, to link the shape modeling and LV boundary detection together, and to provide a compact representation of recovered LV boundaries to cardiac imaging. The proposed technique introduces spatio-temporal boundary detection and iterative model-based boundary refinement to left ventricular boundary extraction. The proposed technique has been applied to two sets of four-dimensional (4D) computed tomography images. Experimental results are compared with the manually edited images.

Knowledge-based classification and tissue labeling of MR images of human brain.

Presents a knowledge-based approach to automatic classification and tissue labeling of 2D magnetic resonance (MR) images of the human brain. The system consists of 2 components: an unsupervised clustering algorithm and an expert system. MR brain data is initially segmented by the unsupervised algorithm, then the expert system locates a landmark tissue or cluster and analyzes it by matching it with a model or searching in it for an expected feature. The landmark tissue location and its analysis are repeated until a tumor is found or all tissues are labeled. The knowledge base contains information on cluster distribution in feature space and tissue models. Since tissue shapes are irregular, their models and matching are specially designed: 1) qualitative tissue models are defined for brain tissues such as white matter; 2) default reasoning is used to match a model with an MR image; that is, if there is no mismatch between a model and an image, they are taken as matched. The system has been tested with 53 slices of MR images acquired at different times by 2 different scanners. It accurately identifies abnormal slices and provides a partial labeling of the tissues. It provides an accurate complete labeling of all normal tissues in the absence of large amounts of data nonuniformity, as verified by radiologists. Thus the system can be used to provide automatic screening of slices for abnormality. It also provides a first step toward the complete description of abnormal images for use in automatic tumor volume determination.