643 research outputs found
A robust framework for medical image segmentation through adaptable class-specific representation
Medical image segmentation is an increasingly important component in virtual pathology, diagnostic imaging and computer-assisted surgery. Better hardware for image acquisition and a variety of advanced visualisation methods have paved the way for the development of computer based tools for medical image analysis and interpretation. The routine use of medical imaging scans of multiple modalities has been growing over the last decades and data sets such as the Visible Human Project have introduced a new modality in the form of colour cryo section data. These developments have given rise to an increasing need for better automatic and semiautomatic segmentation methods. The work presented in this thesis concerns the development of a new framework for robust semi-automatic segmentation of medical imaging data of multiple modalities. Following the specification of a set of conceptual and technical requirements, the framework known as ACSR (Adaptable Class-Specific Representation) is developed in the first case for 2D colour cryo section
segmentation. This is achieved through the development of a novel algorithm for adaptable class-specific sampling of point neighbourhoods, known as the PGA (Path Growing Algorithm), combined with Learning Vector Quantization. The framework is extended to accommodate 3D volume segmentation of cryo section data and subsequently segmentation of single and multi-channel greyscale MRl data. For the latter the issues of inhomogeneity and noise are specifically addressed. Evaluation is based on comparison with previously published results on standard simulated and real data sets, using visual presentation, ground truth comparison and human observer experiments. ACSR provides the user with a simple and intuitive visual initialisation process followed by a fully automatic segmentation. Results on both cryo section and MRI data compare favourably to existing methods, demonstrating robustness both to common artefacts and multiple user initialisations. Further developments into specific clinical applications are discussed in the future work section
Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors
Segmentation of biomedical images is essential for studying and
characterizing anatomical structures, detection and evaluation of pathological
tissues. Segmentation has been further shown to enhance the reconstruction
performance in many tomographic imaging modalities by accounting for
heterogeneities of the excitation field and tissue properties in the imaged
region. This is particularly relevant in optoacoustic tomography, where
discontinuities in the optical and acoustic tissue properties, if not properly
accounted for, may result in deterioration of the imaging performance.
Efficient segmentation of optoacoustic images is often hampered by the
relatively low intrinsic contrast of large anatomical structures, which is
further impaired by the limited angular coverage of some commonly employed
tomographic imaging configurations. Herein, we analyze the performance of
active contour models for boundary segmentation in cross-sectional optoacoustic
tomography. The segmented mask is employed to construct a two compartment model
for the acoustic and optical parameters of the imaged tissues, which is
subsequently used to improve accuracy of the image reconstruction routines. The
performance of the suggested segmentation and modeling approach are showcased
in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin
Generalized fuzzy clustering for segmentation of multi-spectral magnetic resonance images.
An integrated approach for multi-spectral segmentation of MR images is presented. This method is based on the fuzzy c-means (FCM) and includes bias field correction and contextual constraints over spatial intensity distribution and accounts for the non-spherical cluster\u27s shape in the feature space. The bias field is modeled as a linear combination of smooth polynomial basis functions for fast computation in the clustering iterations. Regularization terms for the neighborhood continuity of intensity are added into the FCM cost functions. To reduce the computational complexity, the contextual regularizations are separated from the clustering iterations. Since the feature space is not isotropic, distance measure adopted in Gustafson-Kessel (G-K) algorithm is used instead of the Euclidean distance, to account for the non-spherical shape of the clusters in the feature space. These algorithms are quantitatively evaluated on MR brain images using the similarity measures
Markov Random Field Segmentation of Brain MR Images
We describe a fully-automatic 3D-segmentation technique for brain MR images.
Using Markov random fields the segmentation algorithm captures three important
MR features, i.e. non-parametric distributions of tissue intensities,
neighborhood correlations and signal inhomogeneities. Detailed simulations and
real MR images demonstrate the performance of the segmentation algorithm. The
impact of noise, inhomogeneity, smoothing and structure thickness is analyzed
quantitatively. Even single echo MR images are well classified into gray
matter, white matter, cerebrospinal fluid, scalp-bone and background. A
simulated annealing and an iterated conditional modes implementation are
presented.
Keywords: Magnetic Resonance Imaging, Segmentation, Markov Random FieldsComment: 34 pages, 10 figures; the paper (published in 1997) has introduced
the concept of Markov random field to the segmentation of medical MR images.
For the published version see http://dx.doi.org/10.1109/42.65088
Unsupervised Multi Class Segmentation of 3D Images with Intensity Inhomogeneities
Intensity inhomogeneities in images constitute a considerable challenge in
image segmentation. In this paper we propose a novel biconvex variational model
to tackle this task. We combine a total variation approach for multi class
segmentation with a multiplicative model to handle the inhomogeneities. Our
method assumes that the image intensity is the product of a smoothly varying
part and a component which resembles important image structures such as edges.
Therefore, we penalize in addition to the total variation of the label
assignment matrix a quadratic difference term to cope with the smoothly varying
factor. A critical point of our biconvex functional is computed by a modified
proximal alternating linearized minimization method (PALM). We show that the
assumptions for the convergence of the algorithm are fulfilled by our model.
Various numerical examples demonstrate the very good performance of our method.
Particular attention is paid to the segmentation of 3D FIB tomographical images
which was indeed the motivation of our work
Simultaneous MAP estimation of inhomogeneity and segmentation of brain tissues from MR images
Intrascan and interscan intensity inhomogeneities have been identified as a common source of making many advanced segmentation techniques fail to produce satisfactory results in separating brains tissues from multi-spectral magnetic resonance (MR) images. A common solution is to correct the inhomogeneity before applying the segmentation techniques. This paper presents a method that is able to achieve simultaneous semi-supervised MAP (maximum a-posterior probability) estimation of the inhomogeneity field and segmentation of brain tissues, where the inhomogeneity is parameterized. Our method can incorporate any available incomplete training data and their contribution can be controlled in a flexible manner and therefore the segmentation of the brain tissues can be optimised. Experiments on both simulated and real MR images have demonstrated that the proposed method estimated the inhomogeneity field accurately and improved the segmentation
Method for bias field correction of brain T1-weighted magnetic resonance images minimizing segmentation error
This work presents a new algorithm (nonuniform intensity correction; NIC) for correction of intensity inhomogeneities in T1-weighted magnetic resonance (MR) images. The bias field and a bias-free image are obtained through an iterative process that uses brain tissue segmentation. The algorithm was validated by means of realistic phantom images and a set of 24 real images. The first evaluation phase was based on a public domain phantom dataset, used previously to assess bias field correction algorithms. NIC performed similar to previously described methods in removing the bias field from phantom images, without introduction of degradation in the absence of intensity inhomogeneity. The real image dataset was used to compare the performance of this new algorithm to that of other widely used methods (N3, SPM'99, and SPM2). This dataset included both low and high bias field images from two different MR scanners of low (0.5 T) and medium (1.5 T) static fields. Using standard quality criteria for determining the goodness of the different methods, NIC achieved the best results, correcting the images of the real MR dataset, enabling its systematic use in images from both low and medium static field MR scanners. A limitation of our method is that it might fail if the bias field is so high that the initial histogram does not show bimodal distribution for white and gray matterPublicad
Illumination Correction on Biomedical Images
RF-Inhomogeneity Correction (aka bias) artifact is an important research field in Magnetic Resonance Imaging (MRI). Bias corrupts MR images altering their illumination even though they are acquired with the most recent scanners. Homomorphic Unsharp Masking (HUM) is a filtering technique aimed at correcting illumination inhomogeneity, but it produces a halo around the edges as a side effect. In this paper a novel correction scheme based on HUM is proposed to correct the artifact mentioned above without introducing the halo. A wide experimentation has been performed on MR images. The method has been tuned and evaluated using the simulated Brainweb image database. In this framework, the approach has been compared successfully against the Guillemaud filter and the SPM2 method. Moreover, the method has been successfully applied on several real MR images of the brain (0.18 T, 1.5 T and 7 T). The description of the overall technique is reported along with the experimental results that show its effectiveness in different anatomical regions and its ability to compensate both underexposed and overexposed areas. Our approach is also effective on non-radiological images, like retinal ones
A Review on MR Image Intensity Inhomogeneity Correction
Intensity inhomogeneity (IIH) is often encountered in MR imaging,
and a number of techniques have been devised to correct this
artifact. This paper attempts to review some of the recent
developments in the mathematical modeling of IIH field.
Low-frequency models are widely used, but they tend to corrupt the
low-frequency components of the tissue. Hypersurface models and
statistical models can be adaptive to the image and generally more
stable, but they are also generally more complex and consume more
computer memory and CPU time. They are often formulated together
with image segmentation within one framework and the overall
performance is highly dependent on the segmentation process.
Beside these three popular models, this paper also summarizes
other techniques based on different principles. In addition, the
issue of quantitative evaluation and comparative study are
discussed
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