Gabor filters (GFs) play an important role in many application areas for the enhancement of various types of images and the extraction of Gabor features. For the purpose of enhancing curved structures in noisy images, we introduce curved GFs that locally adapt their shape to the direction of flow. These curved GFs enable the choice of filter parameters that increase the smoothing power without creating artifacts in the enhanced image. In this paper, curved GFs are applied to the curved ridge and valley structures of low-quality fingerprint images. First, we combine two orientation-field estimation methods in order to obtain a more robust estimation for very noisy images. Next, curved regions are constructed by following the respective local orientation. Subsequently, these curved regions are used for estimating the local ridge frequency. Finally, curved GFs are defined based on curved regions, and they apply the previously estimated orientations and ridge frequencies for the enhancement of low-quality fingerprint images. Experimental results on the FVC2004 databases show improvements of this approach in comparison with state-of-the-art enhancement methods.
In medical imaging, GFs are applied for the enhancement of structures like e.g. finger veins @cite_52 and muscle fibers in ultrasound images @cite_34 , for the detection of blood vessels in retinal images @cite_1 , as well as for many other tasks like e.g. analyzing event-related brain activity @cite_31 , assessing osteoporosis in radiographs @cite_59 and for modeling the behavior of simple cells in the mammalian visual cortex @cite_30 .
@cite_30 @cite_1 @cite_52 @cite_59 @cite_31 @cite_34
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A number of imaging techniques are being used for diagnosis and treatment of vascular pathologies like stenoses, aneurysms, embolisms, malformations and remodelings, which may affect a wide range of anatomical sites. For computer-aided detection and highlighting of potential sites of pathology or to improve visualization and segmentation, angiographic images are often enhanced by Hessian based filters. These filters aim to indicate elongated and or rounded structures by an enhancement function based on Hessian eigenvalues. However, established enhancement functions generally produce a response, which exhibits deficiencies such as poor and non-uniform response for vessels of different sizes and varying contrast, at bifurcations and aneurysms. This may compromise subsequent analysis of the enhanced images. This paper has three important contributions: i) reviews several established enhancement functions and elaborates their deficiencies, ii) proposes a novel enhancement function, which overcomes the deficiencies of the established functions, and iii) quantitatively evaluates and compares the novel and the established enhancement functions on clinical image datasets of the lung, cerebral and fundus vasculatures. The automatic extraction of blood vessels in non-fluorescein eye fundus images is a tough task in applications such as diabetic retinopathy screening. However, vessel shapes have complex variations, and accurate modeling of retinal vascular structures is challenging. We have therefore developed a new approach to accurately extract blood vessels in non-fluorescein fundus images using an orientation-aware detector (OAD). The detector was designed according to the intrinsic property of vessels being locally oriented and having linearly elongated structures. We employ the OAD to extract vessel shapes with no assumptions on parametric orientations of vessel shapes. The orientations of vessels can be efficiently modeled by the energy distribution of Fourier transformation. Accordingly, both wide and thin vessels can be extracted with two-scale segmentation in which line operators are applied in large scale and the Gabor filter bank is applied in small scale. A post-processing technique, based on the path opening operation, is applied to eliminate false responses to nonvascular areas, such as retinal structures (optic disc and macula) and pathologies (exudates, hemorrhages,and microaneurysms). This makes the detector robust and structure-aware. By achieving a competitive CAL measurement of 80.82 for the DRIVE database and 68.94 for the STARE, the experimental results demonstrated that the OAD approach outperforms existing segmentation methods. Furthermore, the proposed approach effectively works with non-fluorescein fundus images and proves highly accurate and robust in complicated regions such as the central reflex, close vessels, and crossover points, despite a high level of illumination noise in the original data. AbstractWe present a fast, efficient, and automatic method for extracting vessels from retinal images. The proposed method is based on the second local entropy and on the gray-level co-occurrence matrix (GLCM). The algorithm is designed to have flexibility in the definition of the blood vessel contours. Using information from the GLCM, a statistic feature is calculated to act as a threshold value. The performance of the proposed approach was evaluated in terms of its sensitivity, specificity, and accuracy. The results obtained for these metrics were 0.9648, 0.9480, and 0.9759, respectively. These results show the high performance and accuracy that the proposed method offers. Another aspect evaluated in this method is the elapsed time to carry out the segmentation. The average time required by the proposed method is 3 s for images of size 565 × 584 pixels. To assess the ability and speed of the proposed method, the experimental results are compared with those obtained using other existing methods.Graphical abstract[IMAGE] Abstract Biological collagenous tissues comprised of networks of collagen fibers are suitable for a broad spectrum of medical applications owing to their attractive mechanical properties. In this study, we developed a noninvasive approach to estimate collagenous tissue elastic properties directly from microscopy images using Machine Learning (ML) techniques. Glutaraldehyde-treated bovine pericardium (GLBP) tissue, widely used in the fabrication of bioprosthetic heart valves and vascular patches, was chosen to develop a representative application. A Deep Learning model was designed and trained to process second harmonic generation (SHG) images of collagen networks in GLBP tissue samples, and directly predict the tissue elastic mechanical properties. The trained model is capable of identifying the overall tissue stiffness with a classification accuracy of 84 , and predicting the nonlinear anisotropic stress-strain curves with average regression errors of 0.021 and 0.031. Thus, this study demonstrates the feasibility and great potential of using the Deep Learning approach for fast and noninvasive assessment of collagenous tissue elastic properties from microstructural images. Statement of Significance In this study, we developed, to our best knowledge, the first Deep Learning-based approach to estimate the elastic properties of collagenous tissues directly from noninvasive second harmonic generation images. The success of this study holds promise for the use of Machine Learning techniques to noninvasively and efficiently estimate the mechanical properties of many structure-based biological materials, and it also enables many potential applications such as serving as a quality control tool to select tissue for the manufacturing of medical devices (e.g. bioprosthetic heart valves). Automated tissue characterization is one of the most crucial components of a computer aided diagnosis (CAD) system for interstitial lung diseases (ILDs). Although much research has been conducted in this field, the problem remains challenging. Deep learning techniques have recently achieved impressive results in a variety of computer vision problems, raising expectations that they might be applied in other domains, such as medical image analysis. In this paper, we propose and evaluate a convolutional neural network (CNN), designed for the classification of ILD patterns. The proposed network consists of 5 convolutional layers with 2 @math 2 kernels and LeakyReLU activations, followed by average pooling with size equal to the size of the final feature maps and three dense layers. The last dense layer has 7 outputs, equivalent to the classes considered: healthy, ground glass opacity (GGO), micronodules, consolidation, reticulation, honeycombing and a combination of GGO reticulation. To train and evaluate the CNN, we used a dataset of 14696 image patches, derived by 120 CT scans from different scanners and hospitals. To the best of our knowledge, this is the first deep CNN designed for the specific problem. A comparative analysis proved the effectiveness of the proposed CNN against previous methods in a challenging dataset. The classification performance ( @math ) demonstrated the potential of CNNs in analyzing lung patterns. Future work includes, extending the CNN to three-dimensional data provided by CT volume scans and integrating the proposed method into a CAD system that aims to provide differential diagnosis for ILDs as a supportive tool for radiologists. Abstract Automatic segmentation of retinal vessels in fundus images plays an important role in the diagnosis of some diseases such as diabetes and hypertension. In this paper, we propose Deformable U-Net (DUNet), which exploits the retinal vessels’ local features with a U-shape architecture, in an end to end manner for retinal vessel segmentation. Inspired by the recently introduced deformable convolutional networks, we integrate the deformable convolution into the proposed network. The DUNet, with upsampling operators to increase the output resolution, is designed to extract context information and enable precise localization by combining low-level features with high-level ones. Furthermore, DUNet captures the retinal vessels at various shapes and scales by adaptively adjusting the receptive fields according to vessels’ scales and shapes. Public datasets: DRIVE, STARE, CHASE_DB1 and HRF are used to test our models. Detailed comparisons between the proposed network and the deformable neural network, U-Net are provided in our study. Results show that more detailed vessels can be extracted by DUNet and it exhibits state-of-the-art performance for retinal vessel segmentation with a global accuracy of 0.9566 0.9641 0.9610 0.9651 and AUC of 0.9802 0.9832 0.9804 0.9831 on DRIVE, STARE, CHASE_DB1 and HRF respectively. Moreover, to show the generalization ability of the DUNet, we use another two retinal vessel data sets, i.e., WIDE and SYNTHE, to qualitatively and quantitatively analyze and compare with other methods. Extensive cross-training evaluations are used to further assess the extendibility of DUNet. The proposed method has the potential to be applied to the early diagnosis of diseases. Abstract Since the retinal blood vessel has been acknowledged as an indispensable element in both ophthalmological and cardiovascular disease diagnosis, the accurate segmentation of the retinal vessel tree has become the prerequisite step for automated or computer-aided diagnosis systems. In this paper, a supervised method is presented based on a pre-trained fully convolutional network through transfer learning. This proposed method has simplified the typical retinal vessel segmentation problem from full-size image segmentation to regional vessel element recognition and result merging. Meanwhile, additional unsupervised image post-processing techniques are applied to this proposed method so as to refine the final result. Extensive experiments have been conducted on DRIVE, STARE, CHASE_DB1 and HRF databases, and the accuracy of the cross-database test on these four databases is state-of-the-art, which also presents the high robustness of the proposed approach. This successful result has not only contributed to the area of automated retinal blood vessel segmentation but also supports the effectiveness of transfer learning when applying deep learning technique to medical imaging. We present three-dimensional Fourier transform-second-harmonic generation (3D FT-SHG) imaging, a generalization of the previously reported two-dimensional FT-SHG, to quantify collagen fiber organization from 3D image stacks of biological tissues. The current implementation calculates 3D preferred orientation of a region of interest, and classifies regions of interest based on orientation anisotropy and average voxel intensity. Presented are some example applications of the technique which reveal the layered structure of collagen fibers in porcine sclera, and estimates the cut angle of porcine tendon tissues. This technique shows promising potential for studying biological tissues that contain fibrillar structures in 3D. Describes an automated method to locate and outline blood vessels in images of the ocular fundus. Such a tool should prove useful to eye care specialists for purposes of patient screening, treatment evaluation, and clinical study. The authors' method differs from previously known methods in that it uses local and global vessel features cooperatively to segment the vessel network. The authors evaluate their method using hand-labeled ground truth segmentations of 20 images. A plot of the operating characteristic shows that the authors' method reduces false positives by as much as 15 times over basic thresholding of a matched filter response (MFR), at up to a 75 true positive rate. For a baseline, they also compared the ground truth against a second hand-labeling, yielding a 90 true positive and a 4 false positive detection rate, on average. These numbers suggest there is still room for a 15 true positive rate improvement, with the same false positive rate, over the authors' method. They are making all their images and hand labelings publicly available for interested researchers to use in evaluating related methods. Projection images, such as those routinely acquired in radiological practice, are difficult to analyze because multiple 3-D structures superimpose at a single point in the 2-D image. Removal of particular superimposed structures may improve interpretation of these images, both by humans and by computers. This work therefore presents a general method to isolate and suppress structures in 2-D projection images. The focus is on elongated structures, which allows an intensity model of a structure of interest to be extracted using local information only. The model is created from profiles sampled perpendicular to the structure. Profiles containing other structures are detected and removed to reduce the influence on the model. Subspace filtering, using blind source separation techniques, is applied to separate the structure to be suppressed from other structures. By subtracting the modeled structure from the original image a structure suppressed image is created. The method is evaluated in four experiments. In the first experiment ribs are suppressed in 20 artificial radiographs simulated from 3-D lung computed tomography (CT) images. The proposed method with blind source separation and outlier detection shows superior suppression of ribs in simulated radiographs, compared to a simplified approach without these techniques. Additionally, the ability of three observers to discriminate between patches containing ribs and containing no ribs, as measured by the area under the receiver operating characteristic curve (AUC), reduced from 0.99-1.00 on original images to 0.75-0.84 on suppressed images. In the second experiment clavicles are suppressed in 253 chest radiographs. The effect of suppression on clavicle visibility is evaluated using the clavicle contrast and border response, showing a reduction of 78 and 34 , respectively. In the third experiment nodules extracted from CT were simulated close to the clavicles in 100 chest radiographs. It was found that after suppression contrast of the nodules was higher than of the clavicles (1.35 and 0.55, respectively) than on original images (1.83 and 2.46, respectively). In the fourth experiment catheters were suppressed in chest radiographs. The ability of three observers to discriminate between patches originating from 36 images with and 21 images without catheters, as measured by the AUC, reduced from 0.98-0.99 on original images to 0.64-0.74 on suppressed images. We conclude that the presented method can markedly reduce the visibility of elongated structures in chest radiographs and shows potential to enhance diagnosis. Abstract We propose the use of second-harmonic generation (SHG) microscopy for imaging collagen fibers in porcine femoral cortical bone. The technique is compared with scanning electron microscopy (SEM). SHG microscopy is shown to have excellent potential for bone imaging primarily due its intrinsic specificity to collagen fibers, which results in high contrast images without the need for specimen staining. Furthermore, this technique's ability to quantitatively assess collagen fiber organization is evaluated through an exploratory examination of bone structure as a function of age, from very young to mature bone. In particular, four different age groups: 1 month, 3.5 months, 6 months, and 30 months, were studied. Specifically, we employ the recently developed Fourier transform-second harmonic generation (FT-SHG) imaging technique for the quantification of the structural changes, and observe that as the bone develops, there is an overall reduction in porosity, the number of osteons increases, and the collagen fibers become comparatively more organized. It is also observed that the variations in structure across the whole cross-section of the bone increase with age. The results of this work show that quantitative SHG microscopy can serve as a valuable tool for evaluating the structural organization of collagen fibers in ex vivo bone studies. tion. Generally, finger-vein images have low contrast and uneven illumination due to finger-vein imaging manner and finger-shape variation. So, finger-vein enhancement is indispensable for reliable finger-vein network extraction. This paper proposes a new method based on combination of Gray-Level Grouping (GLG) and Circular Gabor Filter (CGF) for finger-vein image enhancement. First, GLG is used to reduce illumination fluctuation and improve the contrast of finger-vein images. Then a circular Gabor filter is used to further strengthen vein ridges in images. The experimental results show that this proposed method is capable of enhancing finger-vein image effectively. In this study, the Gabor filter bank technique was applied to the biceps and gastrocnemius ultrasound images to longitudinally enhance the coherently oriented and hyperechoic perimysiums regions. The method involved three steps, orientation field estimation, frequency map computation and Gabor filtering. The method was evaluated using a simulated image distorted with multiplicative speckle noises, where the “muscles” were arranged in a bipennate fashion with a central “aponeurosis”. After the enhancement using the proposed method, most of the original hyperechoic bands in the simulated image could be recovered and the noises in other locations were greatly reduced. The proposed method was also tested on biceps sonograms collected from 4 healthy adult subjects. Based on the filtering results, the hyperechoic regions, especially the fibroadipose septas, could be enhanced in several aspects, such as the completion of broken but coherently oriented regions. It is believed that the proposed method have potentials in assisting the visualization of strongly oriented patterns in ultrasound images and especially the quantitative estimation of muscle thickness, muscle fiber pennation angle and fascicle length. Automatic retinal image analysis is emerging as an important screening tool for early detection of eye diseases. Glaucoma is one of the most common causes of blindness. The manual examination of optic disk (OD) is a standard procedure used for detecting glaucoma. In this paper, we present an automatic OD parameterization technique based on segmented OD and cup regions obtained from monocular retinal images. A novel OD segmentation method is proposed which integrates the local image information around each point of interest in multidimensional feature space to provide robustness against variations found in and around the OD region. We also propose a novel cup segmentation method which is based on anatomical evidence such as vessel bends at the cup boundary, considered relevant by glaucoma experts. Bends in a vessel are robustly detected using a region of support concept, which automatically selects the right scale for analysis. A multi-stage strategy is employed to derive a reliable subset of vessel bends called r-bends followed by a local spline fitting to derive the desired cup boundary. The method has been evaluated on 138 images comprising 33 normal and 105 glaucomatous images against three glaucoma experts. The obtained segmentation results show consistency in handling various geometric and photometric variations found across the dataset. The estimation error of the method for vertical cup-to-disk diameter ratio is 0.09 0.08 (mean standard deviation) while for cup-to-disk area ratio it is 0.12 0.10. Overall, the obtained qualitative and quantitative results show effectiveness in both segmentation and subsequent OD parameterization for glaucoma assessment. Automatic segmentation of retinal blood vessels from fundus images plays an important role in the computer aided diagnosis of retinal diseases. The task of blood vessel segmentation is challenging due to the extreme variations in morphology of the vessels against noisy background. In this paper, we formulate the segmentation task as a multi-label inference task and utilize the implicit advantages of the combination of convolutional neural networks and structured prediction. Our proposed convolutional neural network based model achieves strong performance and significantly outperforms the state-of-the-art for automatic retinal blood vessel segmentation on DRIVE dataset with 95.33 accuracy and 0.974 AUC score. Abstract Compressive sensing (CS) theory makes it possible – under certain assumptions – to recover a signal or an image sampled below the Nyquist sampling limit. In medical ultrasound imaging, CS could allow lowering the amount of acquired data needed to reconstruct the echographic image. CS thus offers the perspective of speeding up echographic acquisitions and could have many applications, e.g. triplex acquisitions for CFM B-mode Doppler imaging, high-frame-rate echocardiography, 3D imaging using matrix probes, etc. The objective of this paper is to study the feasibility of CS for the reconstruction of channel RF data, i.e. the 2D set of raw RF lines gathered at the receive elements. Successful application of CS implies selecting a representation basis where the data to be reconstructed have a sparse expansion. Because they consist mainly in warped oscillatory patterns, channel RF data do not easily lend themselves to a sparse representation and thus represent a specific challenge. Within this perspective, we propose to perform and assess CS reconstruction of channel RF data using the recently introduced wave atoms [1] representation, which exhibit advantageous properties for sparsely representing such oscillatory patterns. Reconstructions obtained using wave atoms are compared with the reconstruction performed with two conventional representation bases, namely Fourier and Daubechies wavelets. The first experiment was conducted on simulated channel RF data acquired from a numerical cyst phantom. The quality of the reconstructions was quantified through the mean absolute error at varying subsampling rates by removing 50–90 of the original samples. The results obtained for channel RF data reconstruction yield error ranges of [0.6–3.0] × 10−2, [0.2–2.6] × 10−2, [0.1–1.5] × 10−2, for wavelets, Fourier and wave atoms respectively. The error ranges observed for the associated beamformed log-envelope images are [2.4–20.6] dB, [1.1–12.2] dB, and [0.5–8.8 dB] using wavelets, Fourier, and wave atoms, respectively. These results thus show the superiority of the wave atom representation and the feasibility of CS for the reconstruction of US RF data. The second experiment aimed at showing the experimental feasibility of the method proposed using a data set acquired by imaging a general-purpose phantom (CIRS Model 054GS) using an Ultrasonix MDP scanner. The reconstruction was performed by removing 80 of the initial samples and using wave atoms. The reconstructed image was found to reliably preserve the speckle structure and was associated with an error of 5.5 dB. We work towards efficient methods of categorizing visual content in medical images as a precursor step to segmentation and anatomy recognition. In this paper, we address the problem of automatic detection of level position for a given cardiac CT slice. Specifically, we divide the body area depicted in chest CT into nine semantic categories each representing an area most relevant to the study of a disease and or key anatomic cardiovascular feature. Using a set of handcrafted image features together with features derived form a deep convolutional neural network (CNN), we build a classification scheme to map a given CT slice to the relevant level. Each feature group is used to train a separate support vector machine classifier. The resulting labels are then combined in a linear model, also learned from training data. We report margin zero and margin one accuracy of 91.7 and 98.8 and show that this hybrid approach is a very effective methodology for assigning a given CT image to a relatively narrow anatomic window. The condition of the vascular network of human eye is an important diagnostic factor in ophthalmology. Its segmentation in fundus imaging is a nontrivial task due to variable size of vessels, relatively low contrast, and potential presence of pathologies like microaneurysms and hemorrhages. Many algorithms, both unsupervised and supervised, have been proposed for this purpose in the past. We propose a supervised segmentation technique that uses a deep neural network trained on a large (up to 400 @math 000) sample of examples preprocessed with global contrast normalization, zero-phase whitening, and augmented using geometric transformations and gamma corrections. Several variants of the method are considered, including structured prediction, where a network classifies multiple pixels simultaneously. When applied to standard benchmarks of fundus imaging, the DRIVE, STARE, and CHASE databases, the networks significantly outperform the previous algorithms on the area under ROC curve measure (up to @math ) and accuracy of classification (up to @math ). The method is also resistant to the phenomenon of central vessel reflex, sensitive in detection of fine vessels ( @math ), and fares well on pathological cases. Abstract A fundamental step in the diagnosis of cardiovascular diseases, automatic left ventricle (LV) segmentation in cardiac magnetic resonance images (MRIs) is still acknowledged to be a difficult problem. Most of the existing algorithms require either extensive training or intensive user inputs. This study investigates fast detection of the left ventricle (LV) endo- and epicardium surfaces in cardiac MRI via convex relaxation and distribution matching. The algorithm requires a single subject for training and a very simple user input, which amounts to a single point (mouse click) per target region (cavity or myocardium). It seeks cavity and myocardium regions within each 3D phase by optimizing two functionals, each containing two distribution-matching constraints: (1) a distance-based shape prior and (2) an intensity prior. Based on a global measure of similarity between distributions, the shape prior is intrinsically invariant with respect to translation and rotation. We further introduce a scale variable from which we derive a fixed-point equation (FPE), thereby achieving scale-invariance with only few fast computations. The proposed algorithm relaxes the need for costly pose estimation (or registration) procedures and large training sets, and can tolerate shape deformations, unlike template (or atlas) based priors. Our formulation leads to a challenging problem, which is not directly amenable to convex-optimization techniques. For each functional, we split the problem into a sequence of sub-problems, each of which can be solved exactly and globally via a convex relaxation and the augmented Lagrangian method. Unlike related graph-cut approaches, the proposed convex-relaxation solution can be parallelized to reduce substantially the computational time for 3D domains (or higher), extends directly to high dimensions, and does not have the grid-bias problem. Our parallelized implementation on a graphics processing unit (GPU) demonstrates that the proposed algorithm requires about 3.87 s for a typical cardiac MRI volume, a speed-up of about five times compared to a standard implementation. We report a performance evaluation over 400 volumes acquired from 20 subjects, which shows that the obtained 3D surfaces correlate with independent manual delineations. We further demonstrate experimentally that (1) the performance of the algorithm is not significantly affected by the choice of the training subject and (2) the shape description we use does not change significantly from one subject to another. These results support the fact that a single subject is sufficient for training the proposed algorithm. Imaging is a powerful tool being used in many disciplines such as engineering, physics, biology and medicine to name a few. Recent years have seen a trend that imaging modalities have been combined to create multi-modality imaging tools where different modalities acquire complementary information. For example, in medical imaging, positron emission tomography (PET) and magnetic resonance imaging (MRI) are combined to image structure and function of the human body. Another example is spectral imaging where each channel provides information about a different wave length, e.g. information about red, green and blue (RGB). Most imaging modalities do not acquire images directly but measure a quantity from which we can reconstruct an image. These inverse problems require a priori information in order to give meaningful solutions. Assumptions are often on the smoothness of the solution but other information is sometimes available, too. Many multi-modality images show a strong inter-channel correlation as they are acquired from the same anatomy in medical imaging or the same scenery in spectral imaging. However, images from different modalities are usually reconstructed separately. In this thesis we aim to exploit this correlation using the data from all modalities, that are present in the acquisition, in a joint reconstruction process with the assumption that similar structures in all channels are more likely. We propose a framework for joint reconstruction where modalities are coupled by additional information about the solution we seek. A family of priors -- called parallel level sets -- allows us to incorporate structural a priori knowledge into the reconstruction. We analyse the parallel level set priors in several aspects including their convexity and the diffusive flow generated by their variation. Several numerical examples in RGB colour imaging and in PET-MRI illustrate the gain of joint reconstruction and in particular of the parallel level set priors.