Hover-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images

Goal: In this work, we present an extensive description and evaluation of our method for blood vessel segmentation in fundus images based on a discriminatively trained fully connected conditional random field model. Methods: Standard segmentation priors such as a Potts model or total variation usually fail when dealing with thin and elongated structures. We overcome this difficulty by using a conditional random field model with more expressive potentials, taking advantage of recent results enabling inference of fully connected models almost in real time. Parameters of the method are learned automatically using a structured output support vector machine, a supervised technique widely used for structured prediction in a number of machine learning applications. Results: Our method, trained with state of the art features, is evaluated both quantitatively and qualitatively on four publicly available datasets: DRIVE, STARE, CHASEDB1, and HRF. Additionally, a quantitative comparison with respect to other strategies is included. Conclusion: The experimental results show that this approach outperforms other techniques when evaluated in terms of sensitivity, F1-score, G-mean, and Matthews correlation coefficient. Additionally, it was observed that the fully connected model is able to better distinguish the desired structures than the local neighborhood-based approach. Significance: Results suggest that this method is suitable for the task of segmenting elongated structures, a feature that can be exploited to contribute with other medical and biological applications.

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A Discriminatively Trained Fully Connected Conditional Random Field Model for Blood Vessel Segmentation in Fundus Images

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.

A fully convolutional neural network based structured prediction approach towards the retinal vessel segmentation

Objective: Many common eye diseases and cardiovascular diseases can be diagnosed through retinal imaging. However, due to uneven illumination, image blurring, and low contrast, retinal images with poor quality are not useful for diagnosis, especially in automated image analyzing systems. Here, we propose a new image enhancement method to improve color retinal image luminosity and contrast. Methods: A luminance gain matrix, which is obtained by gamma correction of the value channel in the HSV (hue, saturation, and value) color space, is used to enhance the R, G, and B (red, green and blue) channels, respectively. Contrast is then enhanced in the luminosity channel of L*a*b* color space by CLAHE (contrast-limited adaptive histogram equalization). Image enhancement by the proposed method is compared to other methods by evaluating quality scores of the enhanced images. Results: The performance of the method is mainly validated on a dataset of 961 poor-quality retinal images. Quality assessment (range 0–1) of image enhancement of this poor dataset indicated that our method improved color retinal image quality from an average of 0.0404 (standard deviation 0.0291) up to an average of 0.4565 (standard deviation 0.1000). Conclusion: The proposed method is shown to achieve superior image enhancement compared to contrast enhancement in other color spaces or by other related methods, while simultaneously preserving image naturalness. Significance: This method of color retinal image enhancement may be employed to assist ophthalmologists in more efficient screening of retinal diseases and in development of improved automated image analysis for clinical diagnosis.

Color Retinal Image Enhancement Based on Luminosity and Contrast Adjustment

Retinal vessel segmentation is a key step towards the accurate visualization, diagnosis, early treatment and surgery planning of ocular diseases. For the last two decades, a tremendous amount of research has been dedicated in developing automated methods for segmentation of blood vessels from retinal fundus images. Despite the fact, segmentation of retinal vessels still remains a challenging task due to the presence of abnormalities, varying size and shape of the vessels, non-uniform illumination and anatomical variability between subjects. In this paper, we carry out a systematic review of the most recent advancements in retinal vessel segmentation methods published in last five years. The objectives of this study are as follows: first, we discuss the most crucial preprocessing steps that are involved in accurate segmentation of vessels. Second, we review most recent state-of-the-art retinal vessel segmentation techniques which are classified into different categories based on their main principle. Third, we quantitatively analyse these methods in terms of its sensitivity, specificity, accuracy, area under the curve and discuss newly introduced performance metrics in current literature. Fourth, we discuss the advantages and limitations of the existing segmentation techniques. Finally, we provide an insight into active problems and possible future directions towards building successful computer-aided diagnostic system.

Recent Advancements in Retinal Vessel Segmentation

Retinal vessels play an important role in the diagnostic procedure of retinopathy. A new retinal vessel enhancement method is proposed in this paper. Firstly, the optimal bright and dim image features of an original retinal image are extracted by a multi-scale top-hat transformation. Then, the retinal image is enhanced preliminarily by adding the optimal bright image features and removing the optimal dim image features. Finally, the preliminarily enhanced image is further processed by linear stretching with histogram Gaussian curve fitting. The experiments results on the DRIVE and STARE databases show that the proposed method improves the contrast and enhances the details of the retinal vessels effectively.

Retinal vessel enhancement based on multi-scale top-hat transformation and histogram fitting stretching

Retinal fundus image plays an important role in the diagnosis of retinal related diseases. The detailed information of the retinal fundus image such as small vessels, microaneurysms, and exudates may be in low contrast, and retinal image enhancement usually gives help to analyze diseases related to retinal fundus image. Current image enhancement methods may lead to artificial boundaries, abrupt changes in color levels, and the loss of image detail. In order to avoid these side effects, a new retinal fundus image enhancement method is proposed. First, the original retinal fundus image was processed by the normalized convolution algorithm with a domain transform to obtain an image with the basic information of the background. Then, the image with the basic information of the background was fused with the original retinal fundus image to obtain an enhanced fundus image. Lastly, the fused image was denoised by a two-stage denoising method including the fourth order PDEs and the relaxed median filter. The retinal image databases, including the DRIVE database, the STARE database, and the DIARETDB1 database, were used to evaluate image enhancement effects. The results show that the method can enhance the retinal fundus image prominently. And, different from some other fundus image enhancement methods, the proposed method can directly enhance color images.

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Retinal Fundus Image Enhancement Using the Normalized Convolution and Noise Removing

Automatic segmentation for cell images based on bottleneck detection and ellipse fitting

Vessel segmentation in retinal fundus images is a preliminary step to clinical diagnosis for some systemic diseases and some eye diseases. The performances of existing methods for segmenting small vessels which are usually of more importance than the main vessels in a clinical diagnosis are not satisfactory in clinical use. In this paper, we present a method for both main and peripheral vessel segmentation. A local gray-level change enhancement algorithm called gray-voting is used to enhance the small vessels, while a two-dimensional Gabor wavelet is used to extract the main vessels. We fuse the gray-voting results with the 2D-Gabor filter results as pre-processing outcome. A Gaussian mixture model is then used to extract vessel clusters from the pre-processing outcome, while small vessels fragments are obtained using another gray-voting process, which complements the vessel cluster extraction already performed. At the last step, we eliminate the fragments that do not belong to the vessels based on the shape of the fragments. We evaluated the approach with two publicly available DRIVE (Staal et al., 2004) and STARE (Hoover et at., 2000) datasets with manually segmented results. For the STARE dataset, when using the second manually segmented results which include much more small vessels than the first manually segmented results as the “gold standard,” this approach achieved an average sensitivity, accuracy and specificity of 65.0%, 92.1% and 97.0%, respectively. The sensitivities of this approach were much higher than those of the other existing methods, with comparable specificities; these results thus demonstrated that this approach was sensitive to detection of small vessels.

A New Approach to Segment Both Main and Peripheral Retinal Vessels Based on Gray-Voting and Gaussian Mixture Model

Objective. This study is aimed at investigating differences in local brain activity and functional connectivity (FC) between children with unilateral amblyopia and healthy controls (HCs) by using resting state functional magnetic resonance imaging (rs-fMRI). Methods. Local activity and FC analysis methods were used to explore the altered spontaneous brain activity of children with unilateral amblyopia. Local brain function analysis methods included the amplitude of low-frequency fluctuation (ALFF). FC analysis methods consisted of the FC between the primary visual cortex (PVC-FC) and other brain regions and the FC network between regions of interest (ROIs-FC) selected by independent component analysis. Results. The ALFF in the bilateral frontal, temporal, and occipital lobes in the amblyopia group was lower than that in the HCs. The weakened PVC-FC was mainly concentrated in the frontal lobe and the angular gyrus. The ROIs-FC between the default mode network, salience network, and primary visual cortex network (PVCN) were significantly reduced, whereas the ROIs-FC between the PVCN and the high-level visual cortex network were significantly increased in amblyopia. Conclusions. Unilateral amblyopia may reduce local brain activity and FC in the dorsal and ventral visual pathways and affect the top-down attentional control. Amblyopia may also alter FC between brain functional networks. These findings may help understand the pathological mechanisms of children with amblyopia.

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Peishan Dai

Papers

Retinal vessel enhancement based on multi-scale top-hat transformation and histogram fitting stretching

Retinal Fundus Image Enhancement Using the Normalized Convolution and Noise Removing

Automatic segmentation for cell images based on bottleneck detection and ellipse fitting

A New Approach to Segment Both Main and Peripheral Retinal Vessels Based on Gray-Voting and Gaussian Mixture Model

Altered Spontaneous Brain Activity of Children with Unilateral Amblyopia: A Resting State fMRI Study.