Region growing on frangi vesselness values in 3

Region growing on frangi vesselness values in 3

The segmentation of coronary arteries is a vital process that helps cardiovascular radiologists detect and quantify stenosis. In this paper, we propose a fully automated coronary artery segmentation from cardiac data volume. The method is built on a statistics region growing together with a heuristic decision. First, the heart region is extracted using a multi-atlas-based approach. Second, the vessel structures are enhanced via a 3D multiscale line filter.

Next, seed points are detected automatically through a threshold preprocessing and a subsequent morphological operation. Based on the set of detected seed points, a statistics-based region growing is applied.

Finally, results are obtained by setting conservative parameters. A heuristic decision method is then used to obtain the desired result automatically because parameters in region growing vary in different patients, and the segmentation requires full automation. The experiments are carried out on a dataset that includes eight-patient multivendor cardiac computed tomography angiography CTA volume data.

The DICE similarity index, mean distance, and Hausdorff distance metrics are employed to compare the proposed algorithm with two state-of-the-art methods. Experimental results indicate that the proposed algorithm is capable of performing complete, robust, and accurate extraction of coronary arteries. Over the past decades, coronary artery disease CAD has been the main cause of human deaths in the world [ 1 ].

Many factors can lead to CAD, and, of these, stenosis caused by atherosclerosis is the most common.

Robust Vessel Segmentation in Fundus Images

Coronary arteries are usually extracted first to diagnose stenosis. An inaccurate segmentation of coronary arteries can result in fatal false treatments because a missing segment or mixed extraction of other structures can lead to the oversight of existing stenosis or improper narrow lumen detections. Many studies have been conducted on automated or semiautomated segmentation of coronary arteries on computed tomography angiography CTA images.

Automated segmentation methods can automatically segment regions of interest of images, without any human intervention. However, the complexity of such methods is usually relatively high [ 23 ]. Compared with automated segmentation methods, semiautomated segmentation methods [ 45 ] require the interactions of therapists, making the methods less convenient than automated methods.

However, the performances of semiautomated methods are sometimes better than those of the automated methods. Threshold preprocessing in this method retains many uninterested regions. In addition, traditional 3D region growing requires human interactions and lacks accuracy. Thus, the precision and automation of this method must be improved.

Kitamura et al. However, the method derives a limitation from the Hessian-based features, which cannot distinguish a very wide variety of structures. In addition, the method requires human interactions.

Research on automated segmentation methods has been making great progress recently, and automated methods are gradually becoming popular in clinical diagnosis. However, automated methods have problems in both efficiency and accuracy.

To solve this problem, Lugauer et al. They utilized a Markov random field formulation with convex priors that rely on the training of a large dataset. Their method is sensitive to the dataset and its training and also proved to be inefficient because the dataset analysis is time-consuming.

Zheng et al. Zhou et al.

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However, the EM algorithm used in the heart region extraction has low efficiency because of the huge amount of points in the CTA volume.Updated 02 Mar This function uses the eigenvectors of the Hessian to compute the likeliness of an image region to contain vessels or other image ridgesaccording to the method described by Frangi The 3D method contains an c-code file which can calculate fast the eigenvectors and eigenvalues of a list of image Hessians. First compile this code with "mex eig3volume.

Try the examples. Dirk-Jan Kroon Retrieved October 12, I am having trouble applying this filter on my angiogram. I am able to run the filter on the example image vessel. I have been playing around with this and just wanted to say, that it works very well, other than for the hideous edge effects which can be neatly dealt with by adding the 'replicate' argument to the imfilter call in Hessian2D.

A quick fix is to change the function imgaussian. I think there is a problem with the imgaussian function. I am trying to run on a 10xx CT image and get this error:. Error using imgaussian Requested xx See array size limit or preference panel for more information.

I have tried casting the data to different types single, double, int16, int32, etc. I think there is a bug in the 2d analysis. Hi everyone, Thanks for the discusion. This Frangi-filter enhances individual line-like structures, not their intersections. To enhance or detect junctions what should be done?? This does not implement the algorithm described in Frangi's paper - there are several conceptual issues with the code, such that this "kind of" detects vessels, but not with the same results as one would with the correct algorithm.

The Matlab code run successfully. But a problem that "Undefined function or variable "Dxy". Is there any help? Thanks a lot. This is exactly the filter that I need. I only have one problem with running the script, I do not know how to compile the eig3volume. Have tried googling it and tried using the mex function but it all didn't work out for me.One of the most common modalities to examine the human eye is the eye-fundus photograph.

The evaluation of fundus photographs is carried out by medical experts during time-consuming visual inspection. Our aim is to accelerate this process using computer aided diagnosis. As a first step, it is necessary to segment structures in the images for tissue differentiation. As the eye is the only organ, where the vasculature can be imaged in an in vivo and noninterventional way without using expensive scanners, the vessel tree is one of the most interesting and important structures to analyze.

The quality and resolution of fundus images are rapidly increasing. Thus, segmentation methods need to be adapted to the new challenges of high resolutions. In this paper, we present a method to reduce calculation time, achieve high accuracy, and increase sensitivity compared to the original Frangi method.

This method contains approaches to avoid potential problems like specular reflexes of thick vessels. This outperforms state-of-the-art methods. In ophthalmology the most common way to examine the human eye is to take an eye-fundus photograph and to analyse it. During this kind of eye examinations a medical expert acquires a photo of the eye-background through the pupil with a fundus camera.

The analysis of these images is commonly done by visual inspection. This process can require hours in front of a computer screen, in particular in case of medical screening. An example fundus image is shown in Figure 1.

An example of eye-fundus image: the macula is shown in the middle, the optic disk is to the right, and the blood vessels are entering and leaving the eye through the optic disk.

Our goal is to speed up the diagnosis by processing the images using computer algorithms to find and highlight the most important details. In addition we aim to automatically identify abnormalities and diseases with minimal human interaction. Due to the rapidly increasing spatial resolution of fundus images, the common image processing methods which were developed and tested using low resolution images have shown drawbacks in clinical use. For this purpose, a new generation of methods needs to be developed.

These methods need to be able to operate on high resolution images with low computational complexity. In this paper, we would like to introduce a novel vessel segmentation method with low computational needs and a public available high resolution fundus database with manually generated gold standards for evaluation of retinal structure segmentation methods. The proposed algorithms include modifications to the method proposed by Frangi et al.

The structure of the paper is as follows. We describe the proposed methods in detail in Section 3. In Section 4we present the evaluation methods and databases, including our proposed high resolution fundus database, while Section 5 presents the quantitative results. In Sections 6 and 7the computational complexity and robustness of the proposed algorithm are analyzed.

This is followed by a Discussion in Section 8 and the Conclusions in Section 9. Retinal vessel segmentation is a challenging task and has been in the focus of researches all over the world for years. During this time many different algorithms were published [ 2 ].

The segmentation algorithms can be classified into two main groups: in unsupervised and supervised methods. Unsupervised methods classify vessels using heuristics, while supervised methods learn a criteria system automatically using prelabeled data as gold standard. We focus on heuristic methods, as supervised methods need a large training set for each camera setup. Heuristic methods instead require a set of parameters, which need to be adapted to the camera setup. Thus, they are much more independent from the test dataset during their development.

A more detailed review of the segmentation and other retinal image processing algorithms can be found in the articles published by Kirbas and Quek [ 2 ] and Patton et al. Early, but one of the most common approaches for fundus images are the matched-filter approaches. One of the first methods was presented by Chaudhuri et al.The segmentation of coronary arteries is a vital process that helps cardiovascular radiologists detect and quantify stenosis. In this paper, we propose a fully automated coronary artery segmentation from cardiac data volume.

The method is built on a statistics region growing together with a heuristic decision. First, the heart region is extracted using a multi-atlas-based approach. Second, the vessel structures are enhanced via a 3D multiscale line filter.

Next, seed points are detected automatically through a threshold preprocessing and a subsequent morphological operation. Based on the set of detected seed points, a statistics-based region growing is applied. Finally, results are obtained by setting conservative parameters. A heuristic decision method is then used to obtain the desired result automatically because parameters in region growing vary in different patients, and the segmentation requires full automation.

The experiments are carried out on a dataset that includes eight-patient multivendor cardiac computed tomography angiography CTA volume data. The DICE similarity index, mean distance, and Hausdorff distance metrics are employed to compare the proposed algorithm with two state-of-the-art methods. Experimental results indicate that the proposed algorithm is capable of performing complete, robust, and accurate extraction of coronary arteries.

Over the past decades, coronary artery disease CAD has been the main cause of human deaths in the world [ 1 ]. Many factors can lead to CAD, and, of these, stenosis caused by atherosclerosis is the most common. Coronary arteries are usually extracted first to diagnose stenosis. An inaccurate segmentation of coronary arteries can result in fatal false treatments because a missing segment or mixed extraction of other structures can lead to the oversight of existing stenosis or improper narrow lumen detections.

Many studies have been conducted on automated or semiautomated segmentation of coronary arteries on computed tomography angiography CTA images. Automated segmentation methods can automatically segment regions of interest of images, without any human intervention. However, the complexity of such methods is usually relatively high [ 23 ].

Compared with automated segmentation methods, semiautomated segmentation methods [ 45 ] require the interactions of therapists, making the methods less convenient than automated methods.

However, the performances of semiautomated methods are sometimes better than those of the automated methods. Threshold preprocessing in this method retains many uninterested regions. In addition, traditional 3D region growing requires human interactions and lacks accuracy. Thus, the precision and automation of this method must be improved. Kitamura et al. However, the method derives a limitation from the Hessian-based features, which cannot distinguish a very wide variety of structures.

In addition, the method requires human interactions. Research on automated segmentation methods has been making great progress recently, and automated methods are gradually becoming popular in clinical diagnosis. However, automated methods have problems in both efficiency and accuracy. To solve this problem, Lugauer et al. They utilized a Markov random field formulation with convex priors that rely on the training of a large dataset.

Their method is sensitive to the dataset and its training and also proved to be inefficient because the dataset analysis is time-consuming. Zheng et al. Zhou et al. However, the EM algorithm used in the heart region extraction has low efficiency because of the huge amount of points in the CTA volume.

Meanwhile, Bouraoui et al. They employed a blurry grey-level hit-or-miss transform method to detect seed points automatically. However, the 13 structure candidates employed in their method occasionally fail to detect seed points because they cannot cover all patient conditions.Electroporation-based treatments rely on increasing the permeability of the cell membrane by high voltage electric pulses delivered to tissue via electrodes.

To ensure that the whole tumor is covered by the sufficiently high electric field, accurate numerical models are built based on individual patient geometry.

For the purpose of reconstruction of hepatic vessels from MRI images we searched for an optimal segmentation method that would meet the following initial criteria: identify major hepatic vessels, be robust and work with minimal user input.

We tested the approaches based on vessel enhancement filtering, thresholding, and their combination in local thresholding. The methods were evaluated on a phantom and clinical data. Results show that thresholding based on variance minimization provides less error than the one based on entropy maximization.

Best results were achieved by performing local thresholding of the original de-biased image in the regions of interest which were determined through previous vessel-enhancement filtering. In evaluation on clinical cases the proposed method scored in average sensitivity of The proposed method to segment hepatic vessels from MRI images based on local thresholding meets all the initial criteria set at the beginning of the study and necessary to be used in treatment planning of electroporation-based treatments: it identifies the major vessels, provides results with consistent accuracy and works completely automatically.

Whether the achieved accuracy is acceptable or not for treatment planning models remains to be verified through numerical modeling of effects of the segmentation error on the distribution of the electric field. Exposing a biological cell to a sufficiently high electric field causes increased permeability of the cell membrane.

Vesselness-guided Active Contour: A Coronary Vessel Extraction Method

This increased permeability of the membrane allows transfer of molecules which normally lack membrane transport mechanism into the cell.

The described effect of the electric field on the cell is called electroporation. In reversible electroporation, the cell membrane eventually returns to its normal state. Irreversible electroporation however leads to cell death because the cell membrane is permanently disrupted or due to the extensive loss of the intracellular components. Combination of reversible electroporation with traditional methods of chemotherapy has resulted in a new method for tumor treatment named electro-chemotherapy ECT.

Tumor treatments based on electroporation like ECT and IRE include placement of the electrodes in the tissue and delivery of the electric pulses. In order for the treatment to be successful the whole tumor must be covered by a sufficiently high electric field. The magnitude and distribution of the electric field depends on the number and the position of the electrodes, the amplitudes of pulses applied per electrode pair and the electric properties of the tissue, especially conductivity.

Prediction of parameters needed for successful treatment is easier for surface tumors which is why the ECT was first performed on skin tumors. The reasons which reduce predictability of the electric field distribution in deep-seated tumors are the tumor position, high diversity in tumor size and shape, and presence of the surrounding tissues with different electric conductivities.

Predictability of an adequate distribution of the electric field can be best achieved by calculating a patient-specific treatment plan as a part of an electroporation-based treatment procedure. Correctness of a treatment plan is ensured by an accurate model of the patient which includes the tumor with critical surrounding tissues and structures.

The patient model is built by segmenting the medical images and then used to perform numerical calculations of the electric field distribution. A proof-of-concept was provided in a clinical study in which colorectal metastases in the liver were treated by means of ECT.

Other than liver and tumor tissue, critical structures that need to be included in the model for both RFA and electroporation-based treatments of the liver are hepatic vessels. For the purpose of radiofrequency ablation, vessels which measure more than 3 mm in diameter size have been described as critical because of their influence on heat propagation. Firstly, the electric conductivity of the vessels is different than that of the liver tissue and tumors, which can have an impact on the electric field distribution, especially in cases when a tumor is situated close to large vessels.

The hepatic vessels which were identified by surgeons as critical are vena cava and vena porta with branches up to second order, left, middle and right hepatic vein, and larger hepatic arteries. These vessels will thus be the ones we will most certainly want to include in our model.

Lastly, the model of vessels built from medical images can be used for intra-operative visualization to help surgeons navigate during the insertion of the electrodes. The problem of segmentation of vessels in general 23 and hepatic vessels in particular has been an area of interest for several decades. The interest in segmentation of hepatic vessels resulted in exploring several different approaches. First attempts were based solely on thresholding 24 and region growing.

All these methods for vessel segmentation have however been designed for and applied to CT images.

To our knowledge, no method so far was tested on MRI images. Although CT images have been considered superior for hepatic vessels, the vessels are also visible in MRI images, especially when a contrast agent is applied. With respect to the colorectal metastases of the liver, multiple studies have shown that MRI is superior to CT in sensitivity and accuracy of detecting tumor lesions. Another reason why MRI is a method of choice for planning of electroporation-based treatments is possibility to directly observe the distribution of the electric field using the magnetic resonance electric impedance tomography MREITwhich was described in the work of Kranjc et al.This article has been retracted.

Retraction in: J Med Signals Sens. Vessel extraction is a critical task in clinical practice. In this paper, we propose a new approach for vessel extraction using an active contour model by defining a novel vesselness-based term, based on accurate analysis of the vessel structure in the image. To achieve the novel term, a simple and fast directional filter bank is proposed, which does not employ down sampling and resampling used in earlier versions of directional filter banks.

The proposed model not only preserves the performance of the existing models on images with intensity inhomogeneity, but also overcomes their inability both to segment low contrast vessels and to omit non-vessel structures. Experimental results for synthetic images and coronary X-ray angiograms show desirable performance of our model. Correct assessment, especially accurate visualization and quantification of blood vessels traced in angiograms plays a significant role in a number of clinical diagnostic procedures, e.

For example, appearance of vessels of a certain width in the heart may reveal the signs of stenoses. Grading of stenoses is of importance to diagnose the extent of vascular disease which determines the treatment therapy.

Therefore, the development of automatic and accurate vessel-tree reconstruction from angiograms is highly desirable. In recent years, this has been a challenging task. The key fact is that vessels cannot be characterized uniformly.

region growing on frangi vesselness values in 3

Since the blood, either by itself or by the contrast agent injected into it, is responsible for the vessel contrast to the background, vessels with larger widths usually have high contrast while smaller ones resemble the background.

Many segmentation methods have been used to visualize the blood vessel structures in the human body. A review of vessel extraction techniques and algorithms can be found in. Then the coronary arteries are extracted again by using the maximizing entropy segmentation method based on Gaussian filter. Finally, the last segmentation result is the image obtained by fusing two extracted coronary arteries images.

A region-growing method is proposed for vessel segmentation in angiography images. The method consists of two parts: The feature map extraction based on a novel vesselness function; and the segmentation process which includes automatic seed-point selection, main branch segmentation and vessel detail repair. Both the greyscale and spatial information are extracted for segmentation based on region growing algorithm. Active contour models are among the most successful image segmentation techniques in clinical applications.

Active contours may be categorized as edge based[ 91011 ] or region based. In region-based models, the statistical information inside and outside the contour are used to control the evolution. They are less sensitive to noise and are more effective for images with weak edges or images without edges.

However, popular region-based active contour models[ 1213 ] and[ 14 ] tend to rely on intensity homogeneity of each region to be segmented.

region growing on frangi vesselness values in 3

For example, the popular piecewise constant models are based on the assumption that image intensities are statistically homogeneous roughly constant in each region. In fact, intensity inhomogeneity often occurs in real images from different modalities.

Generally for medical images, inhomogeneity is usually due to technical limitations or artifacts introduced by the object being imaged. In a study done by Li et al. When intensity inhomogeneity occurs in angiograms, each of these models can be used to segment the vessels. Therefore, LBF model is more suitable for vessel segmentation in angiograms but it may fail to extract weak vessels. In this paper, we propose a new approach for vessel extraction using LBF model by defining a novel vesselness-based term which segments low contrast vessels and omits non-vessel structures.

region growing on frangi vesselness values in 3

The results are compared with the 4 active contour models. The remainder of this paper is organized as follows: In section 2, the LBF model is described. The proposed method is stated in section 3.NextBet also provides you with over 2,000 premium football predictions every season.

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The Hessian Matrix - Definition \u0026 Worked Example (2x2)

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