Search

The worldwide pandemic caused by the new coronavirus (COVID-19) has encouraged the development of multiple computer-aided diagnosis systems to automate daily clinical tasks, such as abnormality detection and classification. Among these tasks, the segmentation of COVID lesions is of high interest to the scientific community, enabling further lesion characterization. Automating the segmentation process can be a useful strategy to provide a fast and accurate second opinion to the physicians, and thus increase the reliability of the diagnosis and disease stratification. The current work explores a CNN-based approach to segment multiple COVID lesions. It includes the implementation of a U-Net structure with a ResNet34 encoder able to deal with the highly imbalanced nature of the problem, as well as the great variability of the COVID lesions, namely in terms of size, shape, and quantity. This approach yields a Dice score of 64.1%, when evaluated on the publicly available COVID-19-20 Lung CT Lesion Segmentation GrandChallenge data set.

We propose iW-Net, a deep learning model that allows for both automatic and interactive segmentation of lung nodules in computed tomography images. iW-Net is composed of two blocks: the first one provides an automatic segmentation and the second one allows to correct it by analyzing 2 points introduced by the user in the nodule's boundary. For this purpose, a physics inspired weight map that takes the user input into account is proposed, which is used both as a feature map and in the system's loss function. Our approach is extensively evaluated on the public LIDC-IDRI dataset, where we achieve a state-of-the-art performance of 0.55 intersection over union vs the 0.59 inter-observer agreement. Also, we show that iW-Net allows to correct the segmentation of small nodules, essential for proper patient referral decision, as well as improve the segmentation of the challenging non-solid nodules and thus may be an important tool for increasing the early diagnosis of lung cancer., Comment: Pre-print submitted to IEEE Transactions on Biomedical Engineering

Lung cancer is the deadliest type of cancer worldwide and late detection is the major factor for the low survival rate of patients. Low dose computed tomography has been suggested as a potential screening tool but manual screening is costly and time-consuming. This has fuelled the development of automatic methods for the detection, segmentation and characterisation of pulmonary nodules. In spite of promising results, the application of automatic methods to clinical routine is not straightforward and only a limited number of studies have addressed the problem in a holistic way. With the goal of advancing the state of the art, the Lung Nodule Database (LNDb) Challenge on automatic lung cancer patient management was organized. The LNDb Challenge addressed lung nodule detection, segmentation and characterization as well as prediction of patient follow-up according to the 2017 Fleischner society pulmonary nodule guidelines. 294 CT scans were thus collected retrospectively at the Centro Hospitalar e Universitrio de So Joo in Porto, Portugal and each CT was annotated by at least one radiologist. Annotations comprised nodule centroids, segmentations and subjective characterization. 58 CTs and the corresponding annotations were withheld as a separate test set. A total of 947 users registered for the challenge and 11 successful submissions for at least one of the sub-challenges were received. For patient follow-up prediction, a maximum quadratic weighted Cohen's kappa of 0.580 was obtained. In terms of nodule detection, a sensitivity below 0.4 (and 0.7) at 1 false positive per scan was obtained for nodules identified by at least one (and two) radiologist(s). For nodule segmentation, a maximum Jaccard score of 0.567 was obtained, surpassing the interobserver variability. In terms of nodule texture characterization, a maximum quadratic weighted Cohen's kappa of 0.733 was obtained, with part solid nodules being particularly challenging to classify correctly. Detailed analysis of the proposed methods and the differences in performance allow to identify the major challenges remaining and future directions - data collection, augmentation/generation and evaluation of under-represented classes, the incorporation of scan-level information for better decision-making and the development of tools and challenges with clinical-oriented goals. The LNDb Challenge and associated data remain publicly available so that future methods can be tested and benchmarked, promoting the development of new algorithms in lung cancer medical image analysis and patient follow-up recommendation.

The optic disc (OD) and the fovea are relevant landmarks in fundus images. Their localization and segmentation can facilitate the detection of some retinal lesions and the assessment of their importance to the severity and progression of several eye disorders. Distinct methodologies have been developed for detecting these structures, mainly based on color and vascular information. The methodology herein described combines the entropy of the vessel directions with the image intensities for finding the OD center and uses a sliding band filter for segmenting the OD. The fovea center corresponds to the darkest point inside a region defined from the OD position and radius. Both the Messidor and the IDRiD datasets are used for evaluating the performance of the developed methods. In the first one, a success rate of 99.56% and 100.00% are achieved for OD and fovea localization. Regarding the OD segmentation, the mean Jaccard index and Dice’s coefficient obtained are 0.87 and 0.94, respectively. The proposed methods are also amongst the top-3 performing solutions submitted to the IDRiD online challenge.

We propose a pixel color amplification theory and family of enhancement methods to facilitate segmentation tasks on retinal images. Our novel re-interpretation of the image distortion model underlying dehazing theory shows how three existing priors commonly used by the dehazing community and a novel fourth prior are related. We utilize the theory to develop a family of enhancement methods for retinal images, including novel methods for whole image brightening and darkening. We show a novel derivation of the Unsharp Masking algorithm. We evaluate the enhancement methods as a pre-processing step to a challenging multi-task segmentation problem and show large increases in performance on all tasks, with Dice score increases over a no-enhancement baseline by as much as 0.491. We provide evidence that our enhancement preprocessing is useful for unbalanced and difficult data. We show that the enhancements can perform class balancing by composing them together.

A new approach for robust edge detection on B-mode ultrasound images of the carotid artery is proposed in this paper. The proposed method uses anisotropic Gaussian derivative filters along with non-maximum suppression over the overall artery wall orientation in local regions. The anisotropic filters allow using a wider integration scale along the edges while preserving the edge location precision. They also perform edge continuation, resulting in the connection of isolated edge points along linear segments, which is a valuable feature for the segmentation of the artery wall layers. However, this usually results in false edges being detected near convex contours and isolated points. The use of non-maximum suppression over pooled local orientations is proposed to solve this issue. Experimental results are provided to demonstrate that the proposed edge detector outperforms other common methods in the detection of the lumen-intima and media-adventia layer interfaces of the carotid vessel walls. Additionally, the resulting edges are more continuous and precisely located.

Ovarian cancer is one of the most commonly occurring cancer in women. Transvaginal ultrasound is used as a screening test to detect the presence of tumors but, for specific types of ovarian tumors, malignancy can only be asserted through surgery. An automatic method to perform the detection and malignancy assessment of these tumours is thus necessary to prevent unnecessary oophorectomies.This work explores the U-Net’s architecture and investigates the selection of different hyperparameters for the ovary and the ovarian follicles segmentation. The effect of applying different post-processing methods on beam-formed radio-frequency (BRF) data is also investigated.Results show that models trained only with BRF data have the worst performance. On the other hand, the combination of B-mode with BRF data performs better for ovary segmentation. As for the hyperparameter study, results show that the U-Net with 4 levels is the architecture with the worst performance. This shows that to achieve better performance in the segmentation of ovarian structures, it is important to select an architecture that takes into account the spatial context of the regions of interest. It is also possible to conclude that the method used to analyse BRF data should be designed to take advantage of the fine-resolution of BRF data.

Lung cancer is the deadliest type of cancer worldwide and late detection is one of the major factors for the low survival rate of patients. Low dose computed tomography has been suggested as a potential early screening tool but manual screening is costly, time-consuming and prone to interobserver variability. This has fueled the development of automatic methods for the detection, segmentation and characterisation of pulmonary nodules but its application to the clinical routine is challenging. In this study, a platform for the development, deployment and testing of pulmonary nodule computer-aided strategies is presented: LNDetector. LNDetector integrates image exploration and nodule annotation tools as well as advanced nodule detection, segmentation and classification methods and gaze characterisation. Different processing modules can easily be implemented or replaced to test their efficiency in clinical environments and the use of gaze analysis allows for the development of collaborative strategies. The potential use of this platform is shown through a combination of visual search, gaze characterisation and automatic nodule detection tools for an efficient and collaborative computer-aided strategy for pulmonary nodule screening.

The automatic differentiation of retinal vessels into arteries and veins (A/V) is a highly relevant task within the field of retinal image analysis. However, due to limitations of retinal image acquisition devices, specialists can find it impossible to label certain vessels in eye fundus images. In this paper, we introduce a method that takes into account such uncertainty by design. For this, we formulate the A/V classification task as a four-class segmentation problem, and a Convolutional Neural Network is trained to classify pixels into background, A/V, or uncertain classes. The resulting technique can directly provide pixelwise uncertainty estimates. In addition, instead of depending on a previously available vessel segmentation, the method automatically segments the vessel tree. Experimental results show a performance comparable or superior to several recent A/V classification approaches. In addition, the proposed technique also attains state-of-the-art performance when evaluated for the task of vessel segmentation, generalizing to data that was not used during training, even with considerable differences in terms of appearance and resolution.

Lung volume segmentation is a key step in the design of Computer-Aided Diagnosis systems for automated lung pathology analysis. However, isolating the lung from CT volumes can be a challenging process due to considerable deformations and the potential presence of pathologies. Convolutional Neural Networks (CNN) are effective tools for modeling the spatial relationship between lung voxels. Unfortunately, they typically require large quantities of annotated data, and manually delineating the lung from volumetric CT scans can be a cumbersome process. We propose to train a 3D CNN to solve this task based on semi-automatically generated annotations. For this, we introduce an extension of the well-known V-Net architecture that can handle higher-dimensional input data. Even if the training set labels are noisy and contain errors, our experiments show that it is possible to learn to accurately segment the lung relying on them. Numerical comparisons on an external test set containing lung segmentations provided by a medical expert demonstrate that the proposed model generalizes well to new data, reaching an average 98.7% Dice coefficient. The proposed approach results in a superior performance with respect to the standard V-Net model, particularly on the lung boundary.

Diabetic Retinopathy (DR) is the most common cause of avoidable vision loss, predominantly affecting the working-age population across the globe. Screening for DR, coupled with timely consultation and treatment, is a globally trusted policy to avoid vision loss. However, implementation of DR screening programs is challenging due to the scarcity of medical professionals able to screen a growing global diabetic population at risk for DR. Computer-aided disease diagnosis in retinal image analysis could provide a sustainable approach for such large-scale screening effort. The recent scientific advances in computing capacity and machine learning approaches provide an avenue for biomedical scientists to reach this goal. Aiming to advance the state-of-the-art in automatic DR diagnosis, a grand challenge on "Diabetic Retinopathy - Segmentation and Grading" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2018). In this paper, we report the set-up and results of this challenge that is primarily based on Indian Diabetic Retinopathy Image Dataset (IDRiD). There were three principal sub-challenges: lesion segmentation, disease severity grading, and localization of retinal landmarks and segmentation. These multiple tasks in this challenge allow to test the generalizability of algorithms, and this is what makes it different from existing ones. It received a positive response from the scientific community with 148 submissions from 495 registrations effectively entered in this challenge. This paper outlines the challenge, its organization, the dataset used, evaluation methods and results of top-performing participating solutions. The top-performing approaches utilized a blend of clinical information, data augmentation, and an ensemble of models. These findings have the potential to enable new developments in retinal image analysis and image-based DR screening in particular.

Our goal in this chapter is to describe the recent application of deep learning and artificial intelligence (AI) techniques to retinal image analysis. Automatic retinal image analysis (ARIA) is a complex task that has significant applications for diagnostic purposes for a host of retinal, neurological, and vascular diseases. A number of approaches for the automatic analysis of the retinal images have been studied for the past two decades but the recent success of deep learning (DL) for a range of computer vision and image analysis tasks has now permeated medical imaging and ARIA. Since 2016, major improvements were reported using DL discriminative methods (deep convolutional neural networks or autoencoder convolutional networks), and generative methods, in combination with other image analysis methods, that have demonstrated the ability of algorithms to perform on par with ophthalmologists and retinal specialists, for tasks such as automated classification, diagnostics, and segmentation. We review these recent developments in this chapter.

The segmentation and characterization of the ovarian structures are important tasks in gynecological and reproductive medicine. Ultrasound imaging is typically used for the medical diagnosis within this field but the understanding of the images can be difficult due to their characteristics. Furthermore, the complexity of ultrasound data may lead to a heavy image processing, which makes the application of classical methods of computer vision difficult. This work presents the first supervised fully convolutional neural network (fCNN) for the automatic segmentation of ovarian structures in B-mode ultrasound images. Due to the small dataset available, only 57 images were used for training. In order to overcome this limitation, several regularization techniques were used and are discussed in this paper. The experiments show the ability of the fCNN to learn features to distinguish ovarian structures, achieving a Dice similarity coefficient (DSC) of 0.855 for the segmentation of the stroma and a DSC of 0.955 for the follicles. When compared with a semi-automatic commercial application for follicle segmentation, the proposed fCNN achieved an average improvement of 19%.

Ovarian cancer is one of the pathologies with the worst prognostic in adult women and it has a very difficult early diagnosis. Clinical evaluation of gynaecological ultrasound images is performed visually, and it is dependent on the experience of the medical doctor. Besides the dependency on the specialists, the malignancy of specific types of ovarian tumors cannot be asserted until their surgical removal. This work explores the use of ultrasound data for the segmentation of the ovary and the ovarian follicles, using two different convolutional neural networks, a fully connected residual network and a U-Net, with a binary and multi-class approach. Five different types of ultrasound data (from beam-formed radio-frequency to brightness mode) were used as input. The best performance was obtained using B-mode, for both ovary and follicles segmentation. No significant differences were found between the two convolutional neural networks. The use of the multi-class approach was beneficial as it provided the model information on the spatial relation between follicles and the ovary. This study demonstrates the suitability of combining convolutional neural networks with beam-formed radio-frequency data and with brightness mode data for segmentation of ovarian structures. Future steps involve the processing of pathological data and investigation of biomarkers of pathological ovaries.

This paper proposes a new methodology to automatically segment and measure the volume of pulmonary nodules in lung computed tomography (CT) scans. Estimating the malignancy likelihood of a pulmonary nodule based on lesion characteristics motivated the development of an unsupervised pulmonary nodule segmentation and volume measurement as a preliminary stage for pulmonary nodule characterization. The idea is to optimally cluster a set of feature vectors composed by intensity and shape-related features in a given feature data space extracted from a pre-detected nodule. For that purpose, a metaheuristic search based on evolutionary computation is used for clustering the corresponding feature vectors. The proposed method is simple, unsupervised and is able to segment different types of nodules in terms of location and texture without the need for any manual annotation. We validate the proposed segmentation and volume measurement on the Lung Image Database Consortium and Image Database Resource Initiative – LIDC-IDRI dataset. The first dataset is a group of 705 solid and sub-solid (assessed as part-solid and non-solid) nodules located in different regions of the lungs, and the second, more challenging, is a group of 59 sub-solid nodules. The average Dice scores of 82.35% and 71.05% for the two datasets show the good performance of the segmentation proposal. Comparisons with previous state-of-the-art techniques also show acceptable and comparable segmentation results. The volumes of the segmented nodules are measured via ellipsoid approximation. The correlation and statistical significance between the measured volumes of the segmented nodules and the ground-truth are obtained by Pearson correlation coefficient value, obtaining an R-value ≥ 92.16% with a significance level of 5%.

In the design of computer-aided diagnosis systems for lung cancer diagnosis, an appropriate and accurate segmentation of the pulmonary nodules in computerized tomography (CT) is one of the most relevant and difficult tasks. An accurate segmentation is crucial for the posterior measurement of nodule characteristics and for lung cancer diagnosis. This paper proposes different approaches that use Hessian-based strategies for lung nodule segmentation in chest CT scans. We propose a multiscale segmentation process that uses the central medialness adaptive principle, a Hessian-based strategy that was originally formulated for tubular extraction but it also provides good segmentation results in blob-like structures as is the case of lung nodules. We compared this proposal with a well established Hessian-based strategy that calculates the Shape Index (SI) and Curvedness (CV). We adapted the SI and CV approach for multiscale nodule segmentation. Moreover, we propose the combination of both strategies by combining the results, in order to take benefit of the advantages of both strategies. Different cases with pulmonary nodules from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) database were taken and used to analyze and validate the approaches. The chest CT images present a large variability in nodule characteristics and image conditions. Our proposals provide an accurate lung nodule segmentation, similar to radiologists performance. Our Hessian-based approaches were validated with 569 solid and mostly solid nodules demonstrating that these novel strategies have good results when compared with the radiologists segmentations, providing accurate pulmonary nodule volumes for posterior characterization and appropriate diagnosis.

The segmentation and characterization of the lung lobes are important tasks for Computer Aided Diagnosis (CAD) systems related to pulmonary disease. The detection of the fissures that divide the lung lobes is non-trivial when using classical methods that rely on anatomical information like the localization of the airways and vessels. This work presents a fully automatic and supervised approach to the problem of the segmentation of the five pulmonary lobes from a chest Computer Tomography (CT) scan using a Fully RegularizedV-Net (FRV- Net), a 3D Fully Convolutional Neural Network trained end-to- end. Our network was trained and tested in a custom dataset that we make publicly available. It can correctly separate the lobes even in cases when the fissure is not well delineated, achieving 0.93 in per-lobe Dice Coefficient and 0.85 in the inter-lobar Dice Coefficient in the test set. Both quantitative and qualitative results show that the proposed method can learn to produce correct lobe segmentations even when trained on a reduced dataset.

We propose UOLO, a novel framework for the simultaneous detection and segmentation of structures of interest in medical images. UOLO consists of an object segmentation module which intermediate abstract representations are processed and used as input for object detection. The resulting system is optimized simultaneously for detecting a class of objects and segmenting an optionally different class of structures. UOLO is trained on a set of bounding boxes enclosing the objects to detect, as well as pixel-wise segmentation information, when available. A new loss function is devised, taking into account whether a reference segmentation is accessible for each training image, in order to suitably backpropagate the error. We validate UOLO on the task of simultaneous optic disc (OD) detection, fovea detection, and OD segmentation from retinal images, achieving state-of-the-art performance on public datasets.

Due to inevitable differences between the data used for training modern CAD systems and the data encountered when they are deployed in clinical scenarios, the ability to automatically assess the quality of predictions when no expert annotation is available can be critical. In this paper, we propose a new method for quality assessment of retinal vessel tree segmentations in the absence of a reference ground-truth. For this, we artificially degrade expert-annotated vessel map segmentations and then train a CNN to predict the similarity between the degraded images and their corresponding ground-truths. This similarity can be interpreted as a proxy to the quality of a segmentation. The proposed model can produce a visually meaningful quality score, effectively predicting the quality of a vessel tree segmentation in the absence of a manually segmented reference. We further demonstrate the usefulness of our approach by applying it to automatically find a threshold for soft probabilistic segmentations on a per-image basis. For an independent state-of-the-art unsupervised vessel segmentation technique, the thresholds selected by our approach lead to statistically significant improvements in F1-score \((+2.67\%)\) and Matthews Correlation Coefficient (+\(3.11\%\)) over the thresholds derived from ROC analysis on the training set. The score is also shown to correlate strongly with F1 and MCC when a reference is available.

Given a retinal image, can we automatically determine whether it is of high quality (suitable for medical diagnosis)? Can we also explain our decision, pinpointing the region or regions that led to our decision? Images from human retinas are vital for the diagnosis of multiple health issues, like hypertension, diabetes, and Alzheimer’s; low quality images may force the patient to come back again for a second scanning, wasting time and possibly delaying treatment. However, existing retinal image quality assessment methods are either black boxes without explanations of the results or depend heavily on feature engineering or on complex and error-prone anatomical structures’ segmentation. Therefore, we propose EyeQual, that solves exactly this problem. EyeQual is novel, fast for inference, accurate and explainable, pinpointing low-quality regions on the image. We evaluated EyeQual on two real datasets where it achieved 100% accuracy taking just 36 milliseconds for each image.

A method for the detection of juxta-pleural lung nodules with radius ≤ 5mm in chest computed tomography images is proposed. The lung volume is segmented using region-growing and refined with morphological operations and active contours to include juxta-pleural nodules. Nodule candidates are searched slice-wise inside the lung volume segmentation. Solid nodules are detected by selecting an appropriate threshold inside a representative sliding window. Sub-solid and non-solid nodules are enhanced with a multiscale Laplacian-of-Gaussian filtering prior to their detection. Obvious non-nodule candidates, namely small blood vessels, are discarded using fixed rules. Then, a support vector machine with radial basis function is trained with the remaining candidates to further reduce the number of false positives (FPs). The final system sensitivity is 57.4% with 4 FPs/scan.The performance is similar or better than state-of-the-art methods, especially when considering the high number and small radius of the studied juxta-pleural nodules.

Retinal vessel segmentation is a fundamental and well-studied problem in the retinal image analysis field. The standard images in this context are color photographs acquired with standard fundus cameras. Several vessel segmentation techniques have been proposed in the literature that perform successfully on this class of images. However, for other retinal imaging modalities, blood vessel extraction has not been thoroughly explored. In this paper, we propose a vessel segmentation technique for Scanning Laser Opthalmoscopy (SLO) retinal images. Our method adapts a Deep Neural Network (DNN) architecture initially devised for segmentation of biological images (U-Net), to perform the task of vessel segmentation. The model was trained on a recent public dataset of SLO images. Results show that our approach efficiently segments the vessel network, achieving a performance that outperforms the current state-of-the-art on this particular class of images.

Assessment of retinal vessels is fundamental for the diagnosis of many disorders such as heart diseases, diabetes and hypertension. The imaging of retina using advanced fundus camera has become a standard in computer-assisted diagnosis of opthalmic disorders. Modern cameras produce high quality color digital images, but during the acquisition process the light reflected by the retinal surface generates a luminosity and contrast variation. Irregular illumination can introduce severe distortions in the resulting images, decreasing the visibility of anatomical structures and consequently demoting the performance of the automated segmentation of these structures. In this paper, a novel approach for illumination correction of color fundus images is proposed and applied as preprocessing step for retinal vessel segmentation. Our method builds on the connection between two different phenomena, shadows and haze, and works by removing the haze from the image in the inverted intensity domain. This is shown to be equivalent to correct the nonuniform illumination in the original intensity domain. We tested the proposed method as preprocessing stage of two vessel segmentation methods, one unsupervised based on mathematical morphology, and one supervised based on deep learning Convolutional Neural Networks (CNN). Experiments were performed on the publicly available retinal image database DRIVE. Statistically significantly better vessel segmentation performance was achieved in both test cases when illumination correction was applied.

In this paper, a Hessian-based strategy, based on the central medialness adaptive principle, was adapted and proposed in a multiscale approach for the 3D segmentation of pulmonary nodules in chest CT scans. This proposal is compared with another well stated Hessian based strategy of the literature, for nodule extraction, in order to demonstrate its accuracy.

A new algorithm is proposed for the semi-automatic segmentation of the near-end and the far-end adventitia boundary of the common carotid artery in ultrasound images. It uses the random sample consensus method to estimate the most significant cubic splines fitting the edge map of a longitudinal section. The consensus of the geometric model (a spline) is evaluated through a new gain function, which integrates the responses to different discriminating features of the carotid boundary: the proximity of the geometric model to any edge or to valley shaped edges; the consistency between the orientation of the normal to the geometric model and the intensity gradient; and the distance to a rough estimate of the lumen boundary. A set of 50 longitudinal B-mode images of the common carotid and their manual segmentations performed by two medical experts were used to assess the performance of the method. The image set was taken from 25 different subjects, most of them having plaques of different classes (class II to class IV), sizes and shapes. The quantitative evaluation showed promising results, having detection errors similar to the ones observed in manual segmentations for 95% of the far-end boundaries and 73% of the near-end boundaries.

Microscopy cell image analysis is a fundamental tool for biological research. In particular, multivariate fluorescence microscopy is used to observe different aspects of cells in cultures. It is still common practice to perform analysis tasks by visual inspection of individual cells which is time consuming, exhausting and prone to induce subjective bias. This makes automatic cell image analysis essential for large scale, objective studies of cell cultures. Traditionally the task of automatic cell analysis is approached through the use of image segmentation methods for extraction of cells' locations and shapes. Image segmentation, although fundamental, is neither an easy task in computer vision nor is it robust to image quality changes. This makes image segmentation for cell detection semi-automated requiring frequent tuning of parameters. We introduce a new approach for cell detection and shape estimation in multivariate images based on the sliding band filter (SBF). This filter's design makes it adequate to detect overall convex shapes and as such it performs well for cell detection. Furthermore, the parameters involved are intuitive as they are directly related to the expected cell size. Using the SBF filter we detect cells' nucleus and cytoplasm location and shapes. Based on the assumption that each cell has the same approximate shape center in both nuclei and cytoplasm fluorescence channels, we guide cytoplasm shape estimation by the nuclear detections improving performance and reducing errors. Then we validate cell detection by gathering evidence from nuclei and cytoplasm channels. Additionally, we include overlap correction and shape regularization steps which further improve the estimated cell shapes. The approach is evaluated using two datasets with different types of data: a 20 images benchmark set of simulated cell culture images, containing 1000 simulated cells; a 16 images Drosophila melanogaster Kc167 dataset containing 1255 cells, stained for DNA and actin. Both image datasets present a difficult problem due to the high variability of cell shapes and frequent cluster overlap between cells. On the Drosophila dataset our approach achieved a precision/recall of 95%/69% and 82%/90% for nuclei and cytoplasm detection respectively and an overall accuracy of 76%.

This paper proposes a new approach for the segmentation of both near-end and far-end intima-media regions of the common carotid artery in ultrasound images. The method requires minimal user interaction and is able to segment the near-end wall in arteries with large, hypoechogenic and irregular plaques, issues usually not considered previously due to the increased segmentation difficulty. The adventitia is detected by searching for the best fit of a cubic spline to edges having features compatible with the adventitia boundary. The algorithm uses a global smoothness constraint and integrates discriminating features of the adventitia to reduce the attraction by other edges. Afterwards, using the information of the adventitia location, the lumen boundary is detected by combining dynamic programming, smooth intensity thresholding surfaces and geometric snakes. Smooth contours that correctly adapt to the intima are produced, even in the presence of deep concavities. Moreover, unlike balloon-based snakes, the propagation force does not depend on gradients and does not require a predefined direction. An extensive statistical evaluation is computed, using a set of 47 images from 24 different symptomatic patients, including several classes, sizes and shapes of plaques. Bland-Altman plots of the mean intima-media thickness, for manual segmentations of two medical experts, show a high intra-observer and inter-observer agreement, with mean differences close to zero (mean between -0.10mm and 0.18mm) and with the large majority of differences within the limits of agreement (standard deviation between 0.10mm and 0.12mm). Similar plots reveal a good agreement between the automatic and the manual segmentations (mean between -0.07mm and 0.11mm and standard deviation between 0.11mm and 0.12mm).

To obtain development information of individual plant cells, it is necessary to perform in vivo imaging of the specimen under study, through time-lapse confocal microscopy. Automation of cell detection/marking process is important to provide research tools in order to ease the search for special events, such as cell division. In this paper we discuss an automatic cell detection approach for Arabidopsis thaliana based on segmentation, which selects the best cell candidates from a starting watershed-based image segmentation and improves the result by merging adjacent regions. The selection of individual cells is obtained using a support vector machine (SVM) classifier, based on a cell descriptor constructed from the shape and edge strength of the cells' contour. In addition we proposed a novel cell merging criterion based on edge strength along the line that connects adjacent cells' centroids, which is a valuable tool in the reduction of cell over-segmentation. The result is largely pruned of badly segmented and over-segmented cells, thus facilitating the study of cells. When comparing the results after merging with the basic watershed segmentation, we obtain 1.5% better coverage (increase in F-measure) and up to 27% better precision in correct cell segmentation.

The Arteriolar-to-Venular Ratio (AVR) is an index used for the early diagnosis of diseases such as diabetes, hypertension or cardiovascular pathologies. This paper presents three automatic approaches for the estimation of the AVR in retinal images that result from the combination of different methodologies in some of the processing phases used for AVR estimation. Each one of these methods includes vessel segmentation, vessel caliber estimation, optic disc detection or segmentation, region of interest determination, vessel classification into arteries and veins and finally AVR calculation. The values produced by the proposed methods on 40 images of the INSPIRE-AVR dataset were compared with a ground-truth obtained by two medical experts using a semi-automated system. The results showed that the measured AVRs are not statistically different from the reference, with mean errors similar to those achieved by the two experts, thus demonstrating the reliability of the herein proposed approach for AVR estimation.

Background: The optic disc (OD) centre and boundary are important landmarks in retinal images and are essential for automating the calculation of health biomarkers related with some prevalent systemic disorders, such as diabetes, hypertension, cerebrovascular and cardiovascular diseases.Methods: This paper presents an automatic approach for OD segmentation using a multiresolution sliding band filter (SBF). After the preprocessing phase, a low-resolution SBF is applied on a downsampled retinal image and the locations of maximal filter response are used for focusing the analysis on a reduced region of interest (ROI). A high-resolution SBF is applied to obtain a set of pixels associated with the maximum response of the SBF, giving a coarse estimation of the OD boundary, which is regularized using a smoothing algorithm.Results: Our results are compared with manually extracted boundaries from public databases (ONHSD, MESSIDOR and INSPIRE-AVR datasets) outperforming recent approaches for OD segmentation. For the ONHSD, 44% of the results are classified as Excellent, while the remaining images are distributed between the Good (47%) and Fair (9%) categories. An average overlapping area of 83%, 89% and 85% is achieved for the images in ONHSD, MESSIDOR and INSPIR-AVR datasets, respectively, when comparing with the manually delineated OD regions.Discussion: The evaluation results on the images of three datasets demonstrate the better performance of the proposed method compared to recently published OD segmentation approaches and prove the independence of this method when from changes in image characteristics such as size, quality and camera field of view.

Lung nodule segmentation allows for automatic measurement of the nodule’s size or volume which is of utmost importance in lung cancer diagnosis. It is a challenging task since there are many different types of nodules (solid or non-solid, solitary or multiple, etc). A supervised lung nodule segmentation method uses a shape-based, contrast-based and intensity-based feature set to produce three preliminary segmentations and an artificial neural network to obtain a more accurate segmentation. This method was applied to 20 computer tomography studies, all containing nodules. The data has 10 images of solid nodules and 10 images of ground glass opacity nodules, all with ground-truth. The segmentation uses a region growing approach and the volumetric shape index is used for nodule detection and providing a seed point. In the first and second segmentation the probability of each neighbor belonging to the nodule is estimated using the volumetric shape index and the convergence index filter, respectively. The third segmentation is obtained using a feature set region regression method where for each neighbor the probability of belonging to the nodule or not is obtained using k nearest neighbor regression. Then, using a leave-one out method, an artificial neural network uses the three preliminary segmentations as input and is trained to obtain a more accurate segmentation.

In a lung nodule detection task, parenchyma segmentation is crucial to obtain the region of interest containing all the nodules. Thus, the challenge is to devise a methodology that includes all the lung nodules, particularly those close to the walls, as the juxtapleural nodules. In this paper, different region growing approaches are proposed for the automatic segmentation of the lung parenchyma. The methodology is organized in five different steps: first, the image intensity is corrected to improve the contrast of the lungs. With that, the fat area is obtained, automatically deriving the interior of the lung region. Then, the traquea is extracted by a 3D region growing, being subtracted from the lung region results. The next step is the division of the two lungs to guarantee that both are separated. And finally, the lung contours are refined to provide appropriate final results.

This chapter surveys methodologies for the segmentation of carotid ultrasound images and describes a method for the semiautomatic detection of the lumen–intima and the media–adventitia interfaces of the near and far common carotid wall. The approach is based on feature extraction, fitting of cubic splines, dynamic programming, smooth intensity thresholding surfaces, and geometric snakes. A set of 47 B-mode images of the common carotid were used to assess the performance of the method. The detection errors are similar to the ones observed in manual segmentations for 95% of the far wall interfaces and 73% of the near wall interfaces.

This paper describes a new methodology for lane detection in Thin-Layer Chromatography images. An approach based on the continuous wavelet transform is used to enhance the relevant lane information contained in the intensity profile obtained from image data projection. Lane detection proceeds in three phases: the first obtains a set of candidate lanes, which are validated or removed in the second phase; in the third phase, lane limits are calculated, and subtle lanes are recovered. The superior performance of the new solution was confirmed by a comparison with three other methodologies previously described in the literature.

This paper presents a methodology for correcting band distortions in Thin-Layer Chromatography (TLC) images. After the segmentation of image lanes, the intensity profile of each lane column is spatially aligned with a reference profile using a modified version of the Correlation Optimized Warping (COW) algorithm. As the initial partition of the profile into equal length segments proposed by COW can result in the separation of a single band between two segments to be disjointedly aligned, in the proposed method the warping function is only applied to selected profile regions containing groups of adjacent bands. The proposed band correction methodology was assessed using 105 profiles of 105 TLC lanes. A set of features for band characterization was extracted from each lane profile, before and after band distortion correction, and was used as input for three distinct one-class classifiers aiming at band identification. In all cases, the best results of band classification were obtained for the set lanes after band distortion correction.

In this paper we present a study of evaluation measures that enable the quantification of the quality of an image segmentation result. Despite significant advances in image segmentation techniques, evaluation of these techniques thus far has been largely subjective. Typically, the effectiveness of a new algorithm is demonstrated only by the presentation of a few segmented images and is otherwise left to subjective evaluation by the reader. Such an evaluation criterion can be useful for different applications: the comparison of segmentation results, the automatic choice of the best fitted parameters of a segmentation method for a given image, or the definition of new segmentation methods by optimization. We first present the state of art of distance evaluation measures, and then, we compare several evaluation criteria.

This paper describes a segmentation method for automating the region of interest (ROI) delineation in chromatographic images, thus allowing the definition of the image area that contains the fundamental information for further processing while excluding the frame of the chromatographic plate that does not contain relevant data for disease identification. This is the first component of a screening tool for Fabry disease, which will be based on the automatic analysis of the chromatographic patterns extracted from the image ROI. Image segmentation is performed in two phases, where each individual pixel is finally considered as frame or ROI. In the first phase, an unsupervised learning method is used for classifying image pixels into three classes: frame, ROI or unknown. In the second phase, distance features are used for deciding which class the unknown pixels belong to. The segmentation result is post-processed using a sequence of morphological operators in order to obtain the final ROI rectangular area. The proposed methodology was successfully evaluated in a dataset of 41 chromatographic images.

This paper proposes a classification-based method for automating the segmentation of the region of interest (ROI) in digital images of chromatographic plates. Image segmentation is performed in two phases. In the first phase an unsupervised learning method classifies the image pixels into three classes: frame, ROI or unknown. In the second phase, distance features calculated for the members of the three classes are used for deciding on the new label, ROI or frame, for each individual connected segment previously classified as unknown.The segmentation result is post-processed using a sequence of morphological operators beforeobtaining the final ROI rectangular area. The proposed methodology, which is the initial step for the development of a screening tool for Fabry disease, was successfully evaluated in a dataset of 58 chromatographic images.

The study of cell nuclei is fundamental for plant cell Biology research. To obtain information at cellular level, researchers image cells' nuclei which were modified with fluorescence proteins, through laser scanning confocal microscopy. These images are normally noisy and suffer from high background fluorescence, making grey-scale segmentation approaches inadequate for a usable detection. To obtain a successful detection even at low contrast we investigate the use of a particular convergence filter, the Symmetric Sliding Band filter (SSBF), for cell detection. This filter is based on gradient convergence and not intensity. As such it can detect low contrast cell nuclei which otherwise would be lost in the background noise. Due to the characteristics of cell nuclei morphology, a symmetry constrain is integrated in the filter which corrects some inadequate detections and results in a filter response that is more discriminative. We evaluate the use of this filter for cell nuclei detection on the Arabidopsis thaliana root tip, where the nuclei were stained using yellow fluorescence protein. The resulting cell nuclei detection precision is 89%.

In vivoobservation and tracking of the Arabidopsis thalianaroot meristem, by time-lapse confocal microscopy, is important to understand mechanisms like cell division and elongation. The research herein described is based on a large amount of image data, which must be analyzed to determine the location and state of cells. The automation of the process of cell detection/marking is an important step to provide research tools for the biologists in order to ease the search for special events, such as cell division. This paper discusses a hybrid approach for automatic cell segmentation, which selects the best cell candidates from a starting watershed-based image segmentation and improves the result by merging adjacent regions. The selection of individual cells is obtained using a Support Vector Machine (SVM) classifier, based on the shape and edge strength of the cells' contour. The merging criterion is based on edge strength along the line that connects adjacent cells' centroids. The resulting segmentation is largely pruned of badly segmented and over-segmented cells, thus facilitating the study of cell division.

This paper presents an automated method for the segmentation of the vascular network in retinal images. The algorithm starts with the extraction of vessel centerlines, which are used as guidelines for the subsequent vessel filling phase. For this purpose, the outputs of four directional differential operators are processed in order to select connected sets of candidate points to be further classified as centerline pixels using vessel derived features. The final segmentation is obtained using an iterative region growing method that integrates the contents of several binary images resulting from vessel width dependent morphological filters. Our approach was tested on two publicly available databases and its results are compared with recently published methods. The results demonstrate that our algorithm outperforms other solutions and approximates the average accuracy of a human observer without a significant degradation of sensitivity and specificity.

In spite of significant advances in image segmentation techniques, evaluation of these methods thus far has been largely subjective. Typically, the effectiveness of a new algorithm is demonstrated only by the presentation of a few segmented images that are evaluated by some method, or it is otherwise left to subjective evaluation by the reader. We propose a new approach for evaluation of segmentation that takes into account not only the accuracy of the boundary localization of the created segments but also the under-segmentation and over-segmentation effects, regardless to the number of regions in each partition. In addition, it takes into account the way humans perceive visual information. This new metric can be applied both to automatically provide a ranking among different segmentation algorithms and to find an optimal set of input parameters of a given algorithm.

We present a fully automated method for extracting the lung region from volumetric X-ray CT images based on material decomposition. By modeling the human thorax as a composition of different materials, the proposed method follows a threshold-based, hierarchical voxel classification strategy. The segmentation procedure involves the automatic computation of threshold values and consists on three main steps: patient segmentation and decomposition, large airways extraction and lung parenchyma decomposition, and lung region of interest segmentation. Experimental results were performed on thoracic CT images acquired from 30 patients. The method provides a reproducible set of thresholds for accurate extraction of the lung parenchyma, needed for computer aided diagnosis systems.

A new algorithm for an effective and automatic segmentation of the carotid wall in ultrasonic images is proposed. It combines the speed of thresholding algorithms with the accuracy, flexibility and robustness of a successful geometric active contour model which incorporates an optimal image segmentation model in a level set framework. Due to the multiphase nature of these images, a sequential minimum cross entropy thresholding is used to get a first approximation of the segments, reducing the problem to a two phase segmentation. This thresholding solution is then used as a starting point for a two phase piecewise constant version of a geometric active contour model to reduce noise, smooth contours, improve their position accuracy and close eventual gaps in the carotid wall.

A method is proposed to segment digital posterior-anterior chest X-ray images. The segmentation is achieved through the registration of a deformable prior model, describing the anatomical structures of interest, to the X-ray image. The deformation of the model is performed using a deformation grid. A coarse matching of the model is done using anatomical landmarks automatically extracted from the image, and maps of oriented edges are used to guide the deformation process, optimized with a probabilistic genetic algorithm. The method is applied to extract the ribcage and delineate the mediastinum and diaphragms. The segmentation is needed for defining the lungs region, used in computer-aided diagnosis systems.

Indexado ISI Grouping and segmentation of images remains a challenging problem in computer vision. Recently, a number of authors have demonstrated a good performance on this task using spectral methods that are based on the eigensolution of a similarity matrix. In this paper, we implement a variation of the existing methods that combines aspects from several of the best-known eigenvector segmentation algorithms to produce a discrete optimal solution of the relaxed continuous eigensolution.

We propose a method for segmenting the ribcage boundary of digital postero-anterior chest X-ray images. The segmentation is achieved by first defining image landmarks: the center of the ribcage and, using polar transformation from this point, two initial points belonging to the ribcage. A bank of Gabor filters (in analogy with the simple cells present in the human visual cortex) is used to obtain an orientation edges enhanced image. In this enhanced image, an edge following, starting from the landmarks previously determined, is performed for delineating the left and right sections of the ribcage. The complete segmentation is then accomplished by connecting these sections with the top section of the ribcage, obtained by means of spline interpolation.

We present a method for detecting the axis of bilateral symmetry in a digital chest X-ray image and subsequently measuring the degree of symmetry of the image. The detection is achieved by analysing rotated-reflected digital chest X-ray images and it is posed as a global optimization problem solved with a probabilistic genetic algorithm (PGA). The global search is initially based on natural peak orientation information related to the orientation of the symmetry axis. Only a few generations of the PGA are needed to achieve convergence to all the images in the database. This method is applied directly on the intensity input image and does not require any prior segmentation.

A 3-D data acquisition and scene segmentation system is described. For 3-D data acquisition a structured light technique based on the ratio of two intensity images is used. This technique avoids the correspondence problem, that appears in other structured light techniques, and allows the acquisition of dense range images. The calibration steps of the system are described. Measurement results with different scenes are presented and system accuracy is evaluated. Taking into account that this system allows the acquisition of a dense range image and an intensity image, registered with it, a new approach to the segmentation of 3-D scenes using both range and intensity information is proposed. The two images are segmented separately and iteratively. At each iteration, the segmentation results are combined. The segmentation proceeds until all segments are planar or no more splits are possible. A two-step merging procedure follows: first, planar surfaces that may have been split are "reconstructed", by merging adjacent planar regions that satisfy some constraints; then, regions belonging to curved surfaces are identified and merged, using a curvature analysis along line segments delimited by edge points, combined from both images. Finally, the resulting surfaces are described, using adequate functions.