Accurate Segmentation Method Research Articles

Cucumber Leaf Segmentation Based on Bilayer Convolutional Network

When monitoring crop growth using top-down images of the plant canopies, leaves in agricultural fields appear very dense and significantly overlap each other. Moreover, the image can be affected by external conditions such as background environment and light intensity, impacting the effectiveness of image segmentation. To address the challenge of segmenting dense and overlapping plant leaves under natural lighting conditions, this study employed a Bilayer Convolutional Network (BCNet) method for accurate leaf segmentation across various lighting environments. The major contributions of this study are as follows: (1) Utilized Fully Convolutional Object Detection (FCOS) for plant leaf detection, incorporating ResNet-50 with the Convolutional Block Attention Module (CBAM) and Feature Pyramid Network (FPN) to enhance Region of Interest (RoI) feature extraction from canopy top-view images. (2) Extracted the sub-region of the RoI based on the position of the detection box, using this region as input for the BCNet, ensuring precise segmentation. (3) Utilized instance segmentation of canopy top-view images using BCNet, improving segmentation accuracy. (4) Applied the Varifocal Loss Function to improve the classification loss function in FCOS, leading to better performance metrics. The experimental results on cucumber canopy top-view images captured in glass greenhouse and plastic greenhouse environments show that our method is highly effective. For cucumber leaves at different growth stages and under various lighting conditions, the Precision, Recall and Average Precision (AP) metrics for object recognition are 97%, 94% and 96.57%, respectively. For instance segmentation, the Precision, Recall and Average Precision (AP) metrics are 87%, 83% and 84.71%, respectively. Our algorithm outperforms commonly used deep learning algorithms such as Faster R-CNN, Mask R-CNN, YOLOv4 and PANet, showcasing its superior capability in complex agricultural settings. The results of this study demonstrate the potential of our method for accurate recognition and segmentation of highly overlapping leaves in diverse agricultural environments, significantly contributing to the application of deep learning algorithms in smart agriculture.

Nuclear instance segmentation and tracking for preimplantation mouse embryos.

For investigations into fate specification and morphogenesis in time-lapse images of preimplantation embryos, automated 3D instance segmentation and tracking of nuclei are invaluable. Low signal-to-noise ratio, high voxel anisotropy, high nuclear density, and variable nuclear shapes can limit the performance of segmentation methods, while tracking is complicated by cell divisions, low frame rates, and sample movements. Supervised machine learning approaches can radically improve segmentation accuracy and enable easier tracking, but they often require large amounts of annotated 3D data. Here we first report a novel mouse line expressing near-infrared nuclear reporter H2B-miRFP720. We then generate a dataset (termed BlastoSPIM) of 3D images of H2B-miRFP720-expressing embryos with ground truth for nuclear instances. Using BlastoSPIM, we benchmark seven convolutional neural networks and identify Stardist-3D as the most accurate instance segmentation method. With our BlastoSPIM-trained Stardist-3D models, we construct a complete pipeline for nuclear instance segmentation and lineage tracking from the 8-cell stage to the end of preimplantation development (>100 nuclei). Finally, we demonstrate BlastoSPIM's usefulness as pre-train data for related problems, both for a different imaging modality and for different model systems.

Multiple myeloma segmentation net (MMNet): an encoder-decoder-based deep multiscale feature fusion model for multiple myeloma segmentation in magnetic resonance imaging.

Patients with multiple myeloma (MM), a malignant disease involving bone marrow plasma cells, shows significant susceptibility to bone degradation, impairing normal hematopoietic function. The accurate and effective segmentation of MM lesion areas is crucial for the early detection and diagnosis of myeloma. However, the presence of complex shape variations, boundary ambiguities, and multiscale lesion areas, ranging from punctate lesions to extensive bone damage, presents a formidable challenge in achieving precise segmentation. This study thus aimed to develop a more accurate and robust segmentation method for MM lesions by extracting rich multiscale features. In this paper, we propose a novel, multiscale feature fusion encoding-decoding model architecture specifically designed for MM segmentation. In the encoding stage, our proposed multiscale feature extraction module, dilated dense connected net (DCNet), is employed to systematically extract multiscale features, thereby augmenting the model's sensing field. In the decoding stage, we propose the CBAM-atrous spatial pyramid pooling (CASPP) module to enhance the extraction of multiscale features, enabling the model to dynamically prioritize both channel and spatial information. Subsequently, these features are concatenated with the final output feature map to optimize segmentation outcomes. At the feature fusion bottleneck layer, we incorporate the dynamic feature fusion (DyCat) module into the skip connection to dynamically adjust feature extraction parameters and fusion processes. We assessed the efficacy of our approach using a proprietary dataset of MM, yielding notable advancements. Our dataset comprised 753 magnetic resonance imaging (MRI) two-dimensional (2D) slice images of the spinal regions from 45 patients with MM, along with their corresponding ground truth labels. These images were primarily obtained from three sequences: T1-weighted imaging (T1WI), T2-weighted imaging (T2WI), and short tau inversion recovery (STIR). Using image augmentation techniques, we expanded the dataset to 3,000 images, which were employed for both model training and prediction. Among these, 2,400 images were allocated for training purposes, while 600 images were reserved for validation and testing. Our method showed increase in the intersection over union (IoU) and Dice coefficients by 7.9 and 6.7 percentage points, respectively, as compared to the baseline model. Furthermore, we performed comparisons with alternative image segmentation methodologies, which confirmed the sophistication and efficacy of our proposed model. Our proposed multiple myeloma segmentation net (MMNet), can effectively extract multiscale features from images and enhance the correlation between channel and spatial information. Furthermore, a systematic evaluation of the proposed network architecture was conducted on a self-constructed, limited dataset. This endeavor holds promise for offering valuable insights into the development of algorithms for future clinical applications.

EFS-Former: An Efficient Network for Fruit Tree Leaf Disease Segmentation and Severity Assessment

Fruit is a major source of vitamins, minerals, and dietary fiber in people’s daily lives. Leaf diseases caused by climate change and other factors have significantly reduced fruit production. Deep learning methods for segmenting leaf diseases can effectively mitigate this issue. However, challenges such as leaf folding, jaggedness, and light shading make edge feature extraction difficult, affecting segmentation accuracy. To address these problems, this paper proposes a method based on EFS-Former. The expanded local detail (ELD) module extends the model’s receptive field by expanding the convolution, better handling fine spots and effectively reducing information loss. H-attention reduces computational redundancy by superimposing multi-layer convolutions, significantly improving feature filtering. The parallel fusion architecture effectively utilizes the different feature extraction intervals of the convolutional neural network (CNN) and Transformer encoders, achieving comprehensive feature extraction and effectively fusing detailed and semantic information in the channel and spatial dimensions within the feature fusion module (FFM). Experiments show that, compared to DeepLabV3+, this method achieves 10.78%, 9.51%, 0.72%, and 8.00% higher scores for mean intersection over union (mIoU), mean pixel accuracy (mPA), accuracy (Acc), and F_score, respectively, while having 1.78 M fewer total parameters and 0.32 G lower floating point operations per second (FLOPS). Additionally, it effectively calculates the ratio of leaf area occupied by spots. This method is also effective in calculating the disease period by analyzing the ratio of leaf area occupied by diseased spots. The method’s overall performance is evaluated using mIoU, mPA, Acc, and F_score metrics, achieving 88.60%, 93.49%, 98.60%, and 95.90%, respectively. In summary, this study offers an efficient and accurate method for fruit tree leaf spot segmentation, providing a solid foundation for the precise analysis of fruit tree leaves and spots, and supporting smart agriculture for precision pesticide spraying.

Accurate neuron segmentation method for one-photon calcium imaging videos combining convolutional neural networks and clustering

One-photon fluorescent calcium imaging helps understand brain functions by recording large-scale neural activities in freely moving animals. Automatic, fast, and accurate active neuron segmentation algorithms are essential to extract and interpret information from these videos. One-photon imaging videos’ low resolution, high noise, and high background fluctuation pose significant challenges. Here, we develop a software pipeline to address the challenges of processing one-photon calcium imaging videos. We extend our previous two-photon active neuron segmentation algorithm, Shallow U-Net Neuron Segmentation (SUNS), to better suppress background fluctuations in one-photon videos. We also develop additional neuron extraction (ANE) to locate small or dim neurons missed by SUNS. To train our segmentation method, we create ground truth neurons by developing a manual labeling pipeline assisted with semi-automatic refinement. Our method is more accurate and faster than state-of-the-art techniques when processing simulated videos and multiple experimental datasets acquired over various brain regions with different imaging conditions.

Detection of Brain Tumor Employing Residual Network-based Optimized Deep Learning

Diagnosis and treatment planning play a very vital role in improving the survival of oncological patients. However, there is high variability in the shape, size, and structure of the tumor, making automatic segmentation difficult. The automatic and accurate detection and segmentation methods for Brain tumors are proposed in this paper. A modified ResNet50 model was used for tumor detection, and a ResUNetmodel-based convolutional neural network for segmentation is proposed in this paper. The detection and segmentation were performed on the same dataset consisting of pre-contrast, FLAIR, and postcontrast MRI images of 110 patients collected from the Cancer Imaging Archive. Due to the use of Residual Networks, the authors observed improvement in evaluation parameters, such as accuracy for tumor detection and dice similarity coefficient for tumor segmentation. The accuracy of tumor detection and Dice Similarity Coefficient achieved by the segmentation model were 96.77% and 0.893, respectively, for the TCIA dataset. The results were compared based on manual segmentation and existing segmentation techniques. The tumor mask was also individually compared to the ground truth using the SSIM value. The proposed detection and segmentation models were validated on BraTS2015 and BraTS2017 datasets, and the results were consensus. The use of residual networks in both the detection and the segmentation model resulted in improved accuracy and DSC score. DSC score was increased by 5.9% compared to the UNet model, and the accuracy of the model was increased from 92% to 96.77% for the test set.

EfficientQ: An efficient and accurate post-training neural network quantization method for medical image segmentation

Model quantization is a promising technique that can simultaneously compress and accelerate a deep neural network by limiting its computation bit-width, which plays a crucial role in the fast-growing AI industry. Despite model quantization’s success in producing well-performing low-bit models, the quantization process itself can still be expensive, which may involve a long fine-tuning stage on a large, well-annotated training set. To make the quantization process more efficient in terms of both time and data requirements, this paper proposes a fast and accurate post-training quantization method, namely EfficientQ. We develop this new method with a layer-wise optimization strategy and leverage the powerful alternating direction method of multipliers (ADMM) algorithm to ensure fast convergence. Furthermore, a weight regularization scheme is incorporated to provide more guidance for the optimization of the discrete weights, and a self-adaptive attention mechanism is proposed to combat the class imbalance problem. Extensive comparison and ablation experiments are conducted on two publicly available medical image segmentation datasets, i.e., LiTS and BraTS2020, and the results demonstrate the superiority of the proposed method over various existing post-training quantization methods in terms of both accuracy and optimization speed. Remarkably, with EfficientQ, the quantization of a practical 3D UNet only requires less than 5 min on a single GPU and one data sample. The source code is available at https://github.com/rongzhao-zhang/EfficientQ.

FCM-DCS: Fuzzy C means distorted contour-based segmentation model for breast cancer detection

Breast cancer (BC) is a commonly diagnosed cancer among women nowadays. The cancer cells in the breast tissues are known as BC. Comprehensive research on early-stage BC detection helped to increase the survival rate and reduce the amortality rate associated with this disease. Mammogram scan analysis is a commonly used breast tissue visualization method. This image data is analyzed adequately for accurate BC diagnosis. Region of interest (ROI) identification is crucial in an image-based BC detection system. The ROI detection helps to segment the cancer tissues from the mammogram images by analyzing the heterogeneity among cancerous and normal breast tissues. Early-stage BC issues have homogeneous features as normal breast tissues. So, it is an open challenge for the researchers to develop a more accurate segmentation method during the automatic BC stages detection system. This study introduced fuzzy C means (FCM) distorted contour-based segmentation (FCM DCS) method to address the real detection issues in present studies. It uses the distorted contour (DC) based method to identify the contour of the cancer tissue from mammogram images. The DC method is performed with the help of FCM to identify the cancer tissues. Moreover, a histogram and adaptive equalization method were utilized to reduce image noise and preserve the edge features. The result analysis shows that the FCM-DC methods achieved a maximum accuracy rate (98.76 %) than comparison methods in BC detection.

Accurate Segmentation Method for Roadside Lampposts Based on Vehicle-Mounted Lidar Point Clouds

Abstract. The extraction of roadside lampposts constitutes a significant research focus within the domain of vehicular LiDAR point cloud object retrieval. Addressing the complexities inherent in discerning lampposts amidst convoluted vegetation in diverse roadway settings, this study introduces an innovative, progressive technique for the individualized extraction of lampposts utilizing vehicular LiDAR point clouds. The proposed method initiates with a bifurcation of the primary point cloud into terrestrial and aerial subsets via the Cloth Simulation Filter (CSF) algorithm. Subsequent processes involve the extraction of distinct lamppost structures from aerial point clouds through a methodology integrating elevation-normalized spatial partitioning and directional coverage analysis, thereby facilitating precise lamppost localization. The culmination of this process involves the refinement of lamppost point clouds through supervoxel clustering complemented by a non-discretization filter grounded in Principal Component Analysis (PCA). The efficacy of this novel approach is substantiated through empirical studies employing a LiDAR dataset encompassing extensive adhesive scenarios, whereupon comparative analysis with extant methodologies reveals its enhanced proficiency in isolating individual lampposts in complex environments.

Semi or fully automatic tooth segmentation in CBCT images: a review.

Cone beam computed tomography (CBCT) is widely employed in modern dentistry, and tooth segmentation constitutes an integral part of the digital workflow based on these imaging data. Previous methodologies rely heavily on manual segmentation and are time-consuming and labor-intensive in clinical practice. Recently, with advancements in computer vision technology, scholars have conducted in-depth research, proposing various fast and accurate tooth segmentation methods. In this review, we review 55 articles in this field and discuss the effectiveness, advantages, and disadvantages of each approach. In addition to simple classification and discussion, this review aims to reveal how tooth segmentation methods can be improved by the application and refinement of existing image segmentation algorithms to solve problems such as irregular morphology and fuzzy boundaries of teeth. It is assumed that with the optimization of these methods, manual operation will be reduced, and greater accuracy and robustness in tooth segmentation will be achieved. Finally, we highlight the challenges that still exist in this field and provide prospects for future directions.

Light3DHS: A lightweight 3D hippocampus segmentation method using multiscale convolution attention and vision transformer

The morphological analysis and volume measurement of the hippocampus are crucial to the study of many brain diseases. Therefore, an accurate hippocampal segmentation method is beneficial for the development of clinical research in brain diseases. U-Net and its variants have become prevalent in hippocampus segmentation of Magnetic Resonance Imaging (MRI) due to their effectiveness, and the architecture based on Transformer has also received some attention. However, some existing methods focus too much on the shape and volume of the hippocampus rather than its spatial information, and the extracted information is independent of each other, ignoring the correlation between local and global features. In addition, many methods cannot be effectively applied to practical medical image segmentation due to many parameters and high computational complexity. To this end, we combined the advantages of CNNs and ViTs (Vision Transformer) and proposed a simple and lightweight model: Light3DHS for the segmentation of the 3D hippocampus. In order to obtain richer local contextual features, the encoder first utilizes a multi-scale convolutional attention module (MCA) to learn the spatial information of the hippocampus. Considering the importance of local features and global semantics for 3D segmentation, we used a lightweight ViT to learn high-level features of scale invariance and further fuse local-to-global representation. To evaluate the effectiveness of encoder feature representation, we designed three decoders of different complexity to generate segmentation maps. Experiments on three common hippocampal datasets demonstrate that the network achieves more accurate hippocampus segmentation with fewer parameters. Light3DHS performs better than other state-of-the-art algorithms.

Automatic segmentation of fat metaplasia on sacroiliac joint MRI using deep learning

ObjectiveTo develop a deep learning (DL) model for segmenting fat metaplasia (FM) on sacroiliac joint (SIJ) MRI and further develop a DL model for classifying axial spondyloarthritis (axSpA) and non-axSpA.Materials and methodsThis study retrospectively collected 706 patients with FM who underwent SIJ MRI from center 1 (462 axSpA and 186 non-axSpA) and center 2 (37 axSpA and 21 non-axSpA). Patients from center 1 were divided into the training, validation, and internal test sets (n = 455, 64, and 129). Patients from center 2 were used as the external test set. We developed a UNet-based model to segment FM. Based on segmentation results, a classification model was built to distinguish axSpA and non-axSpA. Dice Similarity Coefficients (DSC) and area under the curve (AUC) were used for model evaluation. Radiologists’ performance without and with model assistance was compared to assess the clinical utility of the models.ResultsOur segmentation model achieved satisfactory DSC of 81.86% ± 1.55% and 85.44% ± 6.09% on the internal cross-validation and external test sets. The classification model yielded AUCs of 0.876 (95% CI: 0.811–0.942) and 0.799 (95% CI: 0.696–0.902) on the internal and external test sets, respectively. With model assistance, segmentation performance was improved for the radiological resident (DSC, 75.70% vs. 82.87%, p < 0.05) and expert radiologist (DSC, 85.03% vs. 85.74%, p > 0.05).ConclusionsDL is a novel method for automatic and accurate segmentation of FM on SIJ MRI and can effectively increase radiologist’s performance, which might assist in improving diagnosis and progression of axSpA.Critical relevance statementDL models allowed automatic and accurate segmentation of FM on sacroiliac joint MRI, which might facilitate quantitative analysis of FM and have the potential to improve diagnosis and prognosis of axSpA.Key points• Deep learning was used for automatic segmentation of fat metaplasia on MRI.• UNet-based models achieved automatic and accurate segmentation of fat metaplasia.• Automatic segmentation facilitates quantitative analysis of fat metaplasia to improve diagnosis and prognosis of axial spondyloarthritis.Graphical

YOLO2U-Net: Detection-guided 3D instance segmentation for microscopy

Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and low resolution in the z-axis may pose challenges (even for human experts) to detect individual cells in 3D volumes as these non-overlapping cells may appear as overlapping. A comprehensive method for accurate 3D instance segmentation of cells in the brain tissue is introduced here. The proposed method combines the 2D YOLO detection method with a multi-view fusion algorithm to construct a 3D localization of the cells. Next, the 3D bounding boxes along with the data volume are input to a 3D U-Net network that is designed to segment the primary cell in each 3D bounding box, and in turn, to carry out instance segmentation of cells in the entire volume. The promising performance of the proposed method is shown in comparison with current deep learning-based 3D instance segmentation methods.

EAIS-Former: An efficient and accurate image segmentation method for fruit leaf diseases

Fruit leaf disease segmentation is an essential foundation for achieving accurate disease diagnosis and identification. However, shadows caused by folded leaves and serrations on leaves can lead to difficulty in extracting edge features, affecting the accuracy of leaf segmentation. In addition, the varying shapes and blurred boundaries of disease spots can further lead to poor segmentation performance of spots. To address the above problems, this work proposes a method called EAIS-Former by combining the advantages of global modeling of Transformer, local processing and positional coding of convolutional neural network (CNN) for accurate segmentation in fruit leaf disease images. Dual scale overlap (DSO) patch embedding is designed to effectively extract multi-scale disease features by dual paths to alleviate omission of lesions. Ultra large convolution (ULC) Transformer block is customized for performing positional encoding and global modeling to efficiently extract global and positional features of leaves and diseases. Skip convolutional local optimization (SCLO) module is proposed to optimize the local detail and edge information and improve the pixel classification ability of the model so that the segmentation results of leaves and spots can be finer and more tiny spots can be extracted. Double layer upsampling (DLU) decoder is built to efficiently fuse the detail information with the semantic information and output the accurate segmentation results of leaves and spots. The experimental results show that the proposed method reach 99.04%, 98.64%, 99.24%, 99.42%, 98.59% and 98.58% intersection over union (IoU) for leaf segmentation on apple rust, pomegranate cercospora spot, mango anthracnose, jamun fungal disease, apple alternaria blotch and apple gray spot datasets, respectively. The IoU of lesion segmentation achieve 94.47%, 94.54%, 83.83%, 86.60%, 89.59% and 88.76%, respectively. In contrast to DeepLabv3+, the accuracy of disease segmentation is raised by 5.25%, 5.15%, 5.55%, 7.64%, 7.04% and 9.35%, respectively. Compared with U-Net, the proposed method improves the accuracy of disease spot segmentation by 4.3%, 4.44%, 5.26%, 9.42%, 5.87% and 6.53% under the six fruit leaf test sets, respectively. In addition, total parameters and FLOPs of the proposed method are only 18.44% and 8.47% of U-Net, respectively. Therefore, this study can provide an efficient and accurate method for the task of fruit leaf disease spot segmentation, which provides a sufficient basis for the accurate analysis of fruit leaves and diseases.

Accurate Lung Nodule Segmentation With Detailed Representation Transfer and Soft Mask Supervision.

Accurate lung lesion segmentation from computed tomography (CT) images is crucial to the analysis and diagnosis of lung diseases, such as COVID-19 and lung cancer. However, the smallness and variety of lung nodules and the lack of high-quality labeling make the accurate lung nodule segmentation difficult. To address these issues, we first introduce a novel segmentation mask named "soft mask", which has richer and more accurate edge details description and better visualization, and develop a universal automatic soft mask annotation pipeline to deal with different datasets correspondingly. Then, a novel network with detailed representation transfer and soft mask supervision (DSNet) is proposed to process the input low-resolution images of lung nodules into high-quality segmentation results. Our DSNet contains a special detailed representation transfer module (DRTM) for reconstructing the detailed representation to alleviate the small size of lung nodules images and an adversarial training framework with soft mask for further improving the accuracy of segmentation. Extensive experiments validate that our DSNet outperforms other state-of-the-art methods for accurate lung nodule segmentation, and has strong generalization ability in other accurate medical segmentation tasks with competitive results. Besides, we provide a new challenging lung nodules segmentation dataset for further studies (https://drive.google.com/file/d/15NNkvDTb_0Ku0IoPsNMHezJR TH1Oi1wm/view?usp=sharing).

Organ-Level Instance Segmentation of Oilseed Rape at Seedling Stage Based on 3D Point Cloud

Highlights Provides a low-cost, fast, accurate, and non-destructive method for segmenting stems and leaves of oilseed rape at the seedling stage. Different varieties and leaf shapes of oilseed rape can all be accurately and efficiently segmented at organ level. The results of accurate organ instance segmentation are used for further organ morphological structure analysis and organ-level phenotype extraction. The calculated phenotypic data is highly correlated with the true phenotypic data. Abstract. Organ-level plant point cloud instance segmentation is crucial for three-dimensional (3D) plant structure investigations and plant phenotypic formations. Due to the complexity of 3D plant structures, accurate plant organ segmentation methods remain a bottleneck in current development of plant organ phenotypes. In this work, we present a fast, accurate, low-cost, and non-destructive method of stem and leaf instance segmentation at the organ level for oilseed rape point cloud. Firstly, we use a 3D scanner to obtain the point cloud of oilseed rape plants. Then, principal component analysis (PCA) is used to perform surface feature extraction on the point cloud after preprocessing. Subsequently, the stems and leaves in different features are segmented by region growing. The irrational segmentation results are finally optimized. Segmentation results of stems and leaves of oilseed rape of different sizes and leaf shapes are evaluated using manually segmented oilseed rape point clouds as a benchmark. The precision, recall, F-score, and average accuracy of the proposed stem and leave segmentation method are 0.983, 0.897, 0.937, and 0.883, respectively. The experimental results suggest that the proposed method can accurately segment an oilseed rape 3D point cloud into instances corresponding to the organs of the plant. Additionally, the separated leaf and stem organs of oilseed rape can be further used for plant structure studies and organ phenotype extraction. The organ phenotypic parameters of oilseed rape are calculated based on the results of stem and leaf instances segmentation. The leaf area, stem length and stem angle of oilseed rape calculated from the point cloud are also compared with the corresponding manual measurements, which are highly correlated with coefficients of determination R2 (0.82-0.97). In conclusion, the proposed segmentation method can be applied as a fundamental segmentation step to extract organ phenotype data from oilseed rape plants. Namely, our research is valuable for precision breeding and basic plant research. Keywords: 3D point cloud, Oilseed rape plant, Phenotypic traits, Stem-leaf segmentation.

Accurate malocclusion tooth segmentation method based on a level set with adaptive edge feature enhancement

ObjectiveThis study aimed to accurately segment teeth under complex oral conditions, including complex structural interference among adjacent teeth or malocclusion conditions, such as tooth rotation and displacement caused by dental crowding. Study designCone-beam computed tomography (CBCT) images were obtained from 19 patients with complex oral conditions, and a three-step solution was proposed. This study used a global convex level-set model to extract bony tissue and developed a flexible curve extraction method for separating neighbouring teeth under complex structural interference. In addition, a local level-set model with adaptive edge feature enhancement was proposed to segment individual teeth precisely. This model adaptively enhances edge features based on the structure of the root boundary and accurately distinguishes between the close-contact root and alveolar bone resulting from tooth rotation or displacement. ResultsThe experimental results showed that the average Dice similarity coefficient values for incisors, canines, premolars, and molars were 93.30%, 93.47%, 93.24%, and 93.89%, respectively, and the average tooth centroid distances were 0.66, 0.61, 0.87, and 0.80 mm, respectively. ConclusionThe proposed method can effectively segment teeth without relying on highly precise annotated datasets, yielding satisfactory results even under complex structural interference between adjacent teeth or tooth rotation and displacement caused by dental crowding. It is more robust than the other methods and provides valuable data for further research and clinical practice.

A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data

BackgroundBone marrow adipose tissue (BMAT) represents > 10% fat mass in healthy humans and can be measured by magnetic resonance imaging (MRI) as the bone marrow fat fraction (BMFF). Human MRI studies have identified several diseases associated with BMFF but have been relatively small scale. Population-scale studies therefore have huge potential to reveal BMAT’s true clinical relevance. The UK Biobank (UKBB) is undertaking MRI of 100,000 participants, providing the ideal opportunity for such advances. ObjectiveTo establish deep learning for high-throughput multi-site BMFF analysis from UKBB MRI data. Materials and methodsWe studied males and females aged 60–69. Bone marrow (BM) segmentation was automated using a new lightweight attention-based 3D U-Net convolutional neural network that improved segmentation of small structures from large volumetric data. Using manual segmentations from 61–64 subjects, the models were trained to segment four BM regions of interest: the spine (thoracic and lumbar vertebrae), femoral head, total hip and femoral diaphysis. Models were tested using a further 10–12 datasets per region and validated using datasets from 729 UKBB participants. BMFF was then quantified and pathophysiological characteristics assessed, including site- and sex-dependent differences and the relationships with age, BMI, bone mineral density, peripheral adiposity, and osteoporosis. ResultsModel accuracy matched or exceeded that for conventional U-Nets, yielding Dice scores of 91.2% (spine), 94.5% (femoral head), 91.2% (total hip) and 86.6% (femoral diaphysis). One case of severe scoliosis prevented segmentation of the spine, while one case of Non-Hodgkin Lymphoma prevented segmentation of the spine, femoral head and total hip because of T2 signal depletion; however, successful segmentation was not disrupted by any other pathophysiological variables. The resulting BMFF measurements confirmed expected relationships between BMFF and age, sex and bone density, and identified new site- and sex-specific characteristics. ConclusionsWe have established a new deep learning method for accurate segmentation of small structures from large volumetric data, allowing high-throughput multi-site BMFF measurement in the UKBB. Our findings reveal new pathophysiological insights, highlighting the potential of BMFF as a novel clinical biomarker. Applying our method across the full UKBB cohort will help to reveal the impact of BMAT on human health and disease.

Merizo: a rapid and accurate protein domain segmentation method using invariant point attention

The AlphaFold Protein Structure Database, containing predictions for over 200 million proteins, has been met with enthusiasm over its potential in enriching structural biological research and beyond. Currently, access to the database is precluded by an urgent need for tools that allow the efficient traversal, discovery, and documentation of its contents. Identifying domain regions in the database is a non-trivial endeavour and doing so will aid our understanding of protein structure and function, while facilitating drug discovery and comparative genomics. Here, we describe a deep learning method for domain segmentation called Merizo, which learns to cluster residues into domains in a bottom-up manner. Merizo is trained on CATH domains and fine-tuned on AlphaFold2 models via self-distillation, enabling it to be applied to both experimental and AlphaFold2 models. As proof of concept, we apply Merizo to the human proteome, identifying 40,818 putative domains that can be matched to CATH representative domains.

Combining Color and Spatial Image Features for Unsupervised Image Segmentation with Mixture Modelling and Spectral Clustering

The demand for accurate and reliable unsupervised image segmentation methods is high. Regardless of whether we are faced with a problem for which we do not have a usable training dataset, or whether it is not possible to obtain one, we still need to be able to extract the desired information from images. In such cases, we are usually gently pushed towards the best possible clustering method, as it is often more robust than simple traditional image processing methods. We investigate the usefulness of combining two clustering methods for unsupervised image segmentation. We use the mixture models to extract the color and spatial image features based on the obtained output segments. Then we construct a similarity matrix (adjacency matrix) based on these features to perform spectral clustering. In between, we propose a label noise correction using Markov random fields. We investigate the usefulness of our method on many hand-crafted images of different objects with different shapes, colorization, and noise. Compared to other clustering methods, our proposal performs better, with 10% higher accuracy. Compared to state-of-the-art supervised image segmentation methods based on deep convolutional neural networks, our proposal proves to be competitive.