Blood Vessel Segmentation Research Articles

Retraction Note: Features fusion based novel approach for efficient blood vessel segmentation from fundus images

Retraction Note: Features fusion based novel approach for efficient blood vessel segmentation from fundus images

Retina Blood Vessels Segmentation and Classification with the Multi-featured Approach.

Segmenting retinal blood vessels poses a significant challenge due to the irregularities inherent in small vessels. The complexity arises from the intricate task of effectively merging features at multiple levels, coupled with potential spatial information loss during successive down-sampling steps. This particularly affects the identification of small and faintly contrasting vessels. To address these challenges, we present a model tailored for automated arterial and venous (A/V) classification, complementing blood vessel segmentation. This paper presents an advanced methodology for segmenting and classifying retinal vessels using a series of sophisticated pre-processing and feature extraction techniques. The ensemble filter approach, incorporating Bilateral and Laplacian edge detectors, enhances image contrast and preserves edges. The proposed algorithm further refines the image by generating an orientation map. During the vessel extraction step, a complete convolution network processes the input image to create a detailed vessel map, enhanced by attention operations that improve modeling perception and resilience. The encoder extracts semantic features, while the Attention Module refines blood vessel depiction, resulting in highly accurate segmentation outcomes. The model was verified using the STARE dataset, which includes 400 images; the DRIVE dataset with 40 images; the HRF dataset with 45 images; and the INSPIRE-AVR dataset containing 40 images. The proposed model demonstrated superior performance across all datasets, achieving an accuracy of 97.5% on the DRIVE dataset, 99.25% on the STARE dataset, 98.33% on the INSPIREAVR dataset, and 98.67% on the HRF dataset. These results highlight the method's effectiveness in accurately segmenting and classifying retinal vessels.

Automatic Segmentation of Mediastinal Lymph Nodes and Blood Vessels in Endobronchial Ultrasound (EBUS) Images Using Deep Learning.

Endobronchial ultrasound (EBUS) is used in the minimally invasive sampling of thoracic lymph nodes. In lung cancer staging, the accurate assessment of mediastinal structures is essential but challenged by variations in anatomy, image quality, and operator-dependent image interpretation. This study aimed to automatically detect and segment mediastinal lymph nodes and blood vessels employing a novel U-Net architecture-based approach in EBUS images. A total of 1161 EBUS images from 40 patients were annotated. For training and validation, 882 images from 30 patients and 145 images from 5 patients were utilized. A separate set of 134 images was reserved for testing. For lymph node and blood vessel segmentation, the mean ± standard deviation (SD) values of the Dice similarity coefficient were 0.71 ± 0.35 and 0.76 ± 0.38, those of the precision were 0.69 ± 0.36 and 0.82 ± 0.22, those of the sensitivity were 0.71 ± 0.38 and 0.80 ± 0.25, those of the specificity were 0.98 ± 0.02 and 0.99 ± 0.01, and those of the F1 score were 0.85 ± 0.16 and 0.81 ± 0.21, respectively. The average processing and segmentation run-time per image was 55 ± 1 ms (mean ± SD). The new U-Net architecture-based approach (EBUS-AI) could automatically detect and segment mediastinal lymph nodes and blood vessels in EBUS images. The method performed well and was feasible and fast, enabling real-time automatic labeling.

Liver vessel MRI image segmentation based on dual-path diffusion model

Accurate segmentation of liver blood vessels in magnetic resonance imaging (MRI) images is a challenging task due to the complex tree-like structure and anisotropic diffusion properties of blood vessels. To solve this problem, we propose a new Dual-Path Diffusion Model (DPDM) framework. The framework consists of two collaborative diffusion paths: a local feature learning path based on convolution operations and a global context modeling path based on transform blocks. Local path encodes rich shape priors and preserve spatial details, while global path captures long-distance dependencies and enhance representation. In the decoding phase, the boundary features from the boundary path are fused with the features of the ordinary path decoding, which further enhances the shape sensitivity. In addition, we leverage a multi-task learning scheme to jointly optimize vascular segmentation and boundary prediction tasks in an end-to-end manner. Experiments on retrospective clinical dataset demonstrate that the proposed DPDM framework achieves excellent performance on the liver vessel segmentation task. Compared with state-of-the-art methods, our approach achieved a 6.0% and 7.3% performance improvement in Dice coefficient and IoU index, respectively. Our approach offers a promising solution for automated blood vessel segmentation in precision medicine.

Precision improvement of robotic bioprinting via vision-based tool path compensation

Robotic 3D bioprinting is a rapidly advancing technology with applications in organ fabrication, tissue restoration, and pharmaceutical testing. While the stepwise generation of organs characterizes bioprinting, challenges such as non-linear material behavior, layer shifting, and trajectory tracking are common in freeform reversible embedding of suspended hydrogels (FRESH) bioprinting, leading to imperfections in complex organ construction. To overcome these limitations, we propose a computer vision-based strategy to identify discrepancies between printed filaments and the reference robot path. Employing error compensation techniques, we generate an adjusted reference path, enhancing robotic 3D bioprinting by adapting the robot path based on vision system data. Experimental assessments confirm the reliability and agility of our vision-based robotic 3D bioprinting approach, showcasing precision in fabricating human blood vessel segments through case studies. Significantly, it minimizes the printing layer width disparity to just 0.15 mm compared to the 0.6 mm in traditional methods, and it decreases the average error for curved filaments to 7.0 mm2 from the previous 12.7 mm2 in conventional printing. While these results underscore the significant potential of our innovation in creating precise biomimetic constructs, further investigation is necessary to tackle challenges such as accurately distinguishing closely stacked layers using a vision system, especially under varying lighting conditions. These limitations, coupled with issues of computational complexity and scalability in larger-scale bioprinting, emphasize the importance of enhancing the reliability of the vision-based approach across various conditions. Nonetheless, our innovation demonstrates substantial promise in creating precise biomimetic constructs and paves the way for future advancements in vision-guided robotic bioprinting, including the integration of multi-material printing techniques to enhance versatility.

Unsupervised Segmentation of 3D Microvascular Photoacoustic Images Using Deep Generative Learning.

Mesoscopic photoacoustic imaging (PAI) enables label-free visualization of vascular networks in tissues with high contrast and resolution. Segmenting these networks from 3D PAI data and interpreting their physiological and pathological significance is crucial yet challenging due to the time-consuming and error-prone nature of current methods. Deep learning offers a potential solution; however, supervised analysis frameworks typically require human-annotated ground-truth labels. To address this, an unsupervised image-to-image translation deep learning model is introduced, the Vessel Segmentation Generative Adversarial Network (VAN-GAN). VAN-GAN integrates synthetic blood vessel networks that closely resemble real-life anatomy into its training process and learns to replicate the underlying physics of the PAI system in order to learn how to segment vasculature from 3D photoacoustic images. Applied to a diverse range of in silico, in vitro, and in vivo data, including patient-derived breast cancer xenograft models and 3D clinical angiograms, VAN-GAN demonstrates its capability to facilitate accurate and unbiased segmentation of 3D vascular networks. By leveraging synthetic data, VAN-GAN reduces the reliance on manual labeling, thus lowering the barrier to entry for high-quality blood vessel segmentation (F1 score: VAN-GAN vs. U-Net = 0.84 vs. 0.87) and enhancing preclinical and clinical research into vascular structure andfunction.

Deep Learning for 3D Vascular Segmentation in Phase Contrast Tomography.

Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation using a new imaging modality, Hierarchical Phase-Contrast Tomography (HiP-CT). We begin with an extensive review of current machine learning approaches for vascular segmentation across various organs. Our work introduces a meticulously curated training dataset, verified by double annotators, consisting of vascular data from three kidneys imaged using Hierarchical Phase-Contrast Tomography (HiP-CT) as part of the Human Organ Atlas Project. HiP-CT, pioneered at the European Synchrotron Radiation Facility in 2020, revolutionizes 3D organ imaging by offering resolution around 20μm/voxel, and enabling highly detailed localized zooms up to 1μm/voxel without physical sectioning. We leverage the nnU-Net framework to evaluate model performance on this high-resolution dataset, using both known and novel samples, and implementing metrics tailored for vascular structures. Our comprehensive review and empirical analysis on HiP-CT data sets a new standard for evaluating machine learning models in high-resolution organ imaging. Our three experiments yielded Dice scores of 0.9523 and 0.9410, and 0.8585, respectively. Nevertheless, DSC primarily assesses voxel-to-voxel concordance, overlooking several crucial characteristics of the vessels and should not be the sole metric for deciding the performance of vascular segmentation. Our results show that while segmentations yielded reasonably high scores-such as centerline Dice values ranging from 0.82 to 0.88, certain errors persisted. Specifically, large vessels that collapsed due to the lack of hydro-static pressure (HiP-CT is an ex vivo technique) were segmented poorly. Moreover, decreased connectivity in finer vessels and higher segmentation errors at vessel boundaries were observed. Such errors, particularly in significant vessels, obstruct the understanding of the structures by interrupting vascular tree connectivity. Through our review and outputs, we aim to set a benchmark for subsequent model evaluations using various modalities, especially with the HiP-CT imaging database.

Multi-dimensional dense attention network for pixel-wise segmentation of optic disc in colour fundus images.

Segmentation of retinal fragments like blood vessels, Optic Disc (OD), and Optic Cup (OC) enables the early detection of different retinal pathologies like Diabetic Retinopathy (DR), Glaucoma, etc. Accurate segmentation of OD remains challenging due to blurred boundaries, vessel occlusion, and other distractions and limitations. These days, deep learning is rapidly progressing in the segmentation of image pixels, and a number of network models have been proposed for end-to-end image segmentation. However, there are still certain limitations, such as limited ability to represent context, inadequate feature processing, limited receptive field, etc., which lead to the loss of local details and blurred boundaries. A multi-dimensional dense attention network, or MDDA-Net, is proposed for pixel-wise segmentation of OD in retinal images in order to address the aforementioned issues and produce more thorough and accurate segmentation results. In order to acquire powerful contexts when faced with limited context representation capabilities, a dense attention block is recommended. A triple-attention (TA) block is introduced in order to better extract the relationship between pixels and obtain more comprehensive information, with the goal of addressing the insufficient feature processing. In the meantime, a multi-scale context fusion (MCF) is suggested for acquiring the multi-scale contexts through context improvement. Specifically, we provide a thorough assessment of the suggested approach on three difficult datasets. In the MESSIDOR and ORIGA data sets, the suggested MDDA-NET approach obtains accuracy levels of 99.28% and 98.95%, respectively. The experimental results show that the MDDA-Net can obtain better performance than state-of-the-art deep learning models under the same environmental conditions.

Laddernet retinal vessel segmentation algorithm fusing attentional mechanisms

A retinal blood vessel segmentation algorithm fusing the attention mechanism is proposed to address the problems of insufficient accuracy and incorrect segmentation of minutiae in existing retinal blood vessel segmentation algorithms. The network structure used in this algorithm is Laddernet (LCT-UNet for short), which fuses the Convolutional Block Attention Module (CBAM) and Transformer, i.e., the residual module of Laddernet, which shares the weights, is structurally optimised to decrease the parameter count; After the residual module, CBAM is incorporated to adaptively adjust the weights of channels and spatial features to enhance the feature representation; Transformer with global self-attention mechanism is introduced at the bottom of the network to overcome the shortcomings of UNet's inability to model long-range relationships and spatial dependencies, and gradually refine the features so that the segmentation results have finer boundary and detail information. The model validity was verified on the public datasets DRIVE and CHASEDB1, and the experimental results showed that the ACC of LCT-UNet was 95.81% and 96.88%, SE was 79.74% and 81.12%, SP was 98.15% and 98.83%, and AUC was 98.22% and 98.99%, and the F1 values were 82.88% and 85.14%, respectively, and the comprehensive segmentation performance of the LCT-UNet network showed significant enhancement over the algorithms such as U-Net, R2UNet, and Laddernet.

LMBiS-Net: A lightweight bidirectional skip connection based multipath CNN for retinal blood vessel segmentation

Blinding eye diseases are often related to changes in retinal structure, which can be detected by analysing retinal blood vessels in fundus images. However, existing techniques struggle to accurately segment these delicate vessels. Although deep learning has shown promise in medical image segmentation, its reliance on specific operations can limit its ability to capture crucial details such as the edges of the vessel. This paper introduces LMBiS-Net, a lightweight convolutional neural network designed for the segmentation of retinal vessels. LMBiS-Net achieves exceptional performance with a remarkably low number of learnable parameters (only 0.172 million). The network used multipath feature extraction blocks and incorporates bidirectional skip connections for the information flow between the encoder and decoder. In addition, we have optimised the efficiency of the model by carefully selecting the number of filters to avoid filter overlap. This optimisation significantly reduces training time and improves computational efficiency. To assess LMBiS-Net’s robustness and ability to generalise to unseen data, we conducted comprehensive evaluations on four publicly available datasets: DRIVE, STARE, CHASE_DB1, and HRF The proposed LMBiS-Net achieves significant performance metrics in various datasets. It obtains sensitivity values of 83.60%, 84.37%, 86.05%, and 83.48%, specificity values of 98.83%, 98.77%, 98.96%, and 98.77%, accuracy (acc) scores of 97.08%, 97.69%, 97.75%, and 96.90%, and AUC values of 98.80%, 98.82%, 98.71%, and 88.77% on the DRIVE, STARE, CHEASE_DB, and HRF datasets, respectively. In addition, it records F1 scores of 83.43%, 84.44%, 83.54%, and 78.73% on the same datasets. Our evaluations demonstrate that LMBiS-Net achieves high segmentation accuracy (acc) while exhibiting both robustness and generalisability across various retinal image datasets. This combination of qualities makes LMBiS-Net a promising tool for various clinical applications.

WITHDRAWN: LSAC-Net: A lightweight scale-aware CNN with densely connected focal modulation for retinal blood vessel segmentation

The diagnosis of sight-threatening eye conditions typically involves segmenting retinal structures in fundus images. The segmentation process enables clinicians to identify alterations in retinal morphology, facilitating the detection and diagnosis of various eye diseases. Despite recent developments in image processing, current approaches often fail to partition delicate arteries precisely. Although deep learning has great potential for segmenting medical images, the accuracy of the segmentation process may be limited due to its dependence on repetitive convolution and pooling processes, which may impair the representation of edge information. In this study, we present LSAC-Net, a pixel-level convolutional neural network (CNN) designed specifically for retinal vessel segmentation. Moreover, it is lightweight, with only 37.5 K learnable parameters. LSAC-Net integrates a unique scale-aware feature extraction block (SAFEB) and a densely connected focal modulation block (DCFMB) to improve segmentation accuracy. In addition, careful selection of filter numbers to avoid overlap effectively shortens training times and boosts computational performance, both of which improve overall model efficiency. We performed extensive tests on different aspects of retinal images to evaluate the robustness and generalizability of LSAC-Net. In particular, a thorough evaluation of the model's precision in retinal artery segmentation, a crucial task for ophthalmological diagnosis and treatment, was carried out. We evaluated the performance and efficacy of LSAC-Net with a particular focus on RBV. The model obtains 98.65% specificity, 97.54% accuracy, and 98.88% area under the curve surpassing existing approaches. Experimental results confirm that LSAC-Net is robust, generalizable, and maintains a high level of segmentation accuracy. These features highlight LSAC-Net's potential as a useful instrument for accurate and timely retinal image segmentation in a variety of therapeutic contexts.

GREnet: Gradually REcurrent Network With Curriculum Learning for 2-D Medical Image Segmentation.

Medical image segmentation is a vital stage in medical image analysis. Numerous deep-learning methods are booming to improve the performance of 2-D medical image segmentation, owing to the fast growth of the convolutional neural network. Generally, the manually defined ground truth is utilized directly to supervise models in the training phase. However, direct supervision of the ground truth often results in ambiguity and distractors as complex challenges appear simultaneously. To alleviate this issue, we propose a gradually recurrent network with curriculum learning, which is supervised by gradual information of the ground truth. The whole model is composed of two independent networks. One is the segmentation network denoted as GREnet, which formulates 2-D medical image segmentation as a temporal task supervised by pixel-level gradual curricula in the training phase. The other is a curriculum-mining network. To a certain degree, the curriculum-mining network provides curricula with an increasing difficulty in the ground truth of the training set by progressively uncovering hard-to-segmentation pixels via a data-driven manner. Given that segmentation is a pixel-level dense-prediction challenge, to the best of our knowledge, this is the first work to function 2-D medical image segmentation as a temporal task with pixel-level curriculum learning. In GREnet, the naive UNet is adopted as the backbone, while ConvLSTM is used to establish the temporal link between gradual curricula. In the curriculum-mining network, UNet++ supplemented by transformer is designed to deliver curricula through the outputs of the modified UNet++ at different layers. Experimental results have demonstrated the effectiveness of GREnet on seven datasets, i.e., three lesion segmentation datasets in dermoscopic images, an optic disc and cup segmentation dataset and a blood vessel segmentation dataset in retinal images, a breast lesion segmentation dataset in ultrasound images, and a lung segmentation dataset in computed tomography (CT).

TLTNet: A novel transscale cascade layered transformer network for enhanced retinal blood vessel segmentation

Extracting global and local feature information is still challenging due to the problems of retinal blood vessel medical images like fuzzy edge features, noise, difficulty in distinguishing between lesion regions and background information, and loss of low-level feature information, which leads to insufficient extraction of feature information. To better solve these problems and fully extract the global and local feature information of the image, we propose a novel transscale cascade layered transformer network for enhanced retinal blood vessel segmentation, which consists of an encoder and a decoder and is connected between the encoder and decoder by a transscale transformer cascade module. Among them, the encoder consists of a local–global transscale transformer module, a multi-head layered transscale adaptive embedding module, and a local context(LCNet) module. The transscale transformer cascade module learns local and global feature information from the first three layers of the encoder, and multi-scale dependent features, fuses the hierarchical feature information from the skip connection block and the channel-token interaction fusion block, respectively, and inputs it to the decoder. The decoder includes a decoding module for the local context network and a transscale position transformer module to input the local and global feature information extracted from the encoder with retained key position information into the decoding module and the position embedding transformer module for recovery and output of the prediction results that are consistent with the input feature information. In addition, we propose an improved cross-entropy loss function based on the difference between the deterministic observation samples and the prediction results with the deviation distance, which is validated on the DRIVE and STARE datasets combined with the proposed network model based on the dual transformer structure in this paper, and the segmentation accuracies are 97.26% and 97.87%, respectively. Compared with other state-of-the-art networks, the results show that the proposed network model has a significant competitive advantage in improving the segmentation performance of retinal blood vessel images.

Transformer Connections: Improving Segmentation in Blurred Near‐Infrared Blood Vessel Image in Different Depth

AbstractHigh‐fidelity segmentation of blood vessels plays a pivotal role in numerous biomedical applications, such as injection assistance, cancer detection, various surgeries, and vein authentication. Near‐infrared (NIR) transillumination imaging is an effective and safe method to visualize the subcutaneous blood vessel network. However, such images are severely blurred because of the light scattering in body tissues. Inspired by the Vision Transformer model, this paper proposes a novel deep learning network known as transformer connection (TRC)‐Unet to capture global blurred and local clear correlations while using multi‐layer attention. Our method mainly consists of two blocks, thereby aiming to remap skip connection information flow and fuse different domain features. Specifically, the TRC extracts global blurred information from multiple layers and suppresses scattering to increase the clarity of vessel features. Transformer feature fusion eliminates the domain gap between the highly semantic feature maps of the convolutional neural network backbone and the adaptive self‐attention maps of TRCs. Benefiting from the long‐range dependencies of transformers, we achieved competitive results in relation to various competing methods on different data sets, including retinal vessel segmentation, simulated blur image segmentation, and real NIR blood vessel image segmentation. Moreover, our method remarkably improved the segmentation results of simulated blur image data sets and a real NIR vessel image data set. The quantitative results of ablation studies and visualizations are also reported to demonstrate the superiority of the TRC‐Unet design. © 2024 The Author(s). IEEJ Transactions on Electrical and Electronic Engineering published by Institute of Electrical Engineers of Japan and Wiley Periodicals LLC.

DCNet: A lightweight retinal vessel segmentation network

Retinal vessel segmentation is a crucial focus within the realm of medical image analysis, playing a pivotal role in early disease diagnosis, notably retinopathy. Deep learning has exhibited remarkable segmentation capabilities for retinal blood vessels, leveraging the advantages of contextual feature learning. However, there are still some shortcomings in fine retinal vessel segmentation due to the loss of semantic information due to too many pooling operations or limited receptive fields due to fewer pooling operations. In response to the nuanced balance required for expanding the receptive field while preserving information integrity during multiple downsampling operations, this paper introduces DCNet (Dilated Convolution Net), a novel lightweight three-layer dilated-convolution-based network tailored for retinal blood vessel segmentation. This three-layer architecture autonomously extracts crucial segmentation features from various levels of the feature map. Each layer comprises a dilated convolution Positive Sequence Block (PSB) and a dilated convolution Reverse Sequence Block (RSB). The dilated convolution operation is strategically exploited for its capacity to extend the receptive field, facilitating effective feature information extraction. Simultaneously, to alleviate semantic information loss within the deep network's feature map, this paper proposes the Nonlinear Feature Extraction Module (NFEM) to supplement shallow network feature information. Furthermore, to comprehensively leverage information from various scale features, a Feature Fusion Module (FFM) is introduced for multiscale vascular feature extraction, ultimately enhancing segmentation accuracy. DCNet undergoes rigorous evaluation on four publicly accessible retinal vascular datasets – DRIVE, STARE, CHASE_DB1, and HRF. Experimental results unequivocally demonstrate that DCNet achieves superior segmentation performance with fewer model parameters compared to existing state-of-the-art methods. The code for DCNet can be accessed on the following website: https://github.com/ChunhuiYu1/DCNet.

VascuConNet: an enhanced connectivity network for vascular segmentation.

Medical image segmentation commonly involves diverse tissue types and structures, including tasks such as blood vessel segmentation and nerve fiber bundle segmentation. Enhancing the continuity of segmentation outcomes represents a pivotal challenge in medical image segmentation, driven by the demands of clinical applications, focusing on disease localization and quantification. In this study, a novel segmentation model is specifically designed for retinal vessel segmentation, leveraging vessel orientation information, boundary constraints, and continuity constraints to improve segmentation accuracy. To achieve this, we cascade U-Net with a long-short-term memory network (LSTM). U-Net is characterized by a small number of parameters and high segmentation efficiency, while LSTM offers a parameter-sharing capability. Additionally, we introduce an orientation information enhancement module inserted into the model's bottom layer to obtain feature maps containing orientation information through an orientation convolution operator. Furthermore, we design a new hybrid loss function that consists of connectivity loss, boundary loss, and cross-entropy loss. Experimental results demonstrate that the model achieves excellent segmentation outcomes across three widely recognized retinal vessel segmentation datasets, CHASE_DB1, DRIVE, and ARIA.

Vessel Segmentation in Fundus Images with Multi-Scale Feature Extraction and Disentangled Representation

Vessel segmentation in fundus images is crucial for diagnosing eye diseases. The rapid development of deep learning has greatly improved segmentation accuracy. However, the scale of the retinal blood-vessel structure varies greatly, and there is a lot of noise unrelated to blood-vessel segmentation in fundus images, which increases the complexity and difficulty of the segmentation algorithm. Comprehensive consideration of factors like scale variation and noise suppression is imperative to enhance segmentation accuracy and stability. Therefore, we propose a retinal vessel segmentation method based on multi-scale feature extraction and decoupled representation. Specifically, we design a multi-scale feature extraction module at the skip connections, utilizing dilated convolutions to capture multi-scale features and further emphasizing crucial information through channel attention modules. Additionally, to separate useful spatial information from redundant information and enhance segmentation performance, we introduce an image reconstruction branch to assist in the segmentation task. The specific approach involves using a disentangled representation method to decouple the image into content and style, utilizing the content part for segmentation tasks. We conducted experiments on the DRIVE, STARE, and CHASE_DB1 datasets, and the results showed that our method outperformed others, achieving the highest accuracy across all three datasets (DRIVE:0.9690, CHASE_DB1:0.9757, and STARE:0.9765).

Brain Blood Vessel Segmentation based on Region Growing and U-net Neural Network

Aiming at the problems of insufficient feature extraction in existing deep learning-based cerebrovascular segmentation methods and uneven segmentation results when the original imaging quality is poor, a cerebrovascular segmentation method that integrates region growing and an improved U-net neural network is proposed. Based on the deep learning segmentation results, automatic seed point selection for region growing is performed and fused to improve the segmentation accuracy at the pixel level. In this work, the integrated segmentation method improves the Dice coefficient from 0.805 to 0.878 and the Average Hausdorff Distance (AHD) from 3.949 to 0.903 compared to the deep learning segmentation method.

Brain vasculature accumulates tau and is spatially related to tau tangle pathology in Alzheimer’s disease

Insoluble pathogenic proteins accumulate along blood vessels in conditions of cerebral amyloid angiopathy (CAA), exerting a toxic effect on vascular cells and impacting cerebral homeostasis. In this work, we provide new evidence from three-dimensional human brain histology that tau protein, the main component of neurofibrillary tangles, can similarly accumulate along brain vascular segments. We quantitatively assessed n = 6 Alzheimer’s disease (AD), and n = 6 normal aging control brains and saw that tau-positive blood vessel segments were present in all AD cases. Tau-positive vessels are enriched for tau at levels higher than the surrounding tissue and appear to affect arterioles across cortical layers (I–V). Further, vessels isolated from these AD tissues were enriched for N-terminal tau and tau phosphorylated at T181 and T217. Importantly, tau-positive vessels are associated with local areas of increased tau neurofibrillary tangles. This suggests that accumulation of tau around blood vessels may reflect a local clearance failure. In sum, these data indicate that tau, like amyloid beta, accumulates along blood vessels and may exert a significant influence on vasculature in the setting of AD.

Intrinsically explainable deep learning architecture for semantic segmentation of histological structures in heart tissue

Background:Analysis of structures contained in tissue samples and the relevant contextual information is of utmost importance to histopathologists during diagnosis. Cardiac biopsies require in-depth analysis of the relationships between biological structures. Statistical measures are insufficient for determining a model’s viability and applicability in the diagnostic process. A deeper understanding of predictions is necessary in order to support histopathologists. Methods:We propose a method for providing supporting information in the form of segmentation of histological structures to histopathologists based on these principles. The proposed method utilizes nuclei type and density information in addition to standard image input provided at two different zoom levels for the semantic segmentation of blood vessels, inflammation, and endocardium in heart tissue. Results:The proposed method was able to reach state-of-the-art segmentation results. The overall quality and viability of the predictions was qualitatively evaluated by two pathologists and a histotechnologist. Conclusions:The decision process of the proposed deep learning model utilizes the provided information sources correctly and simulates the decision process of histopathologists via the usage of a custom-designed attention gate that provides a combination of spatial and encoder attention mechanisms. The implementation is available at https://github.com/mathali/IEDL-segmentation-of-heart-tissue.