Automated peripancreatic vessel segmentation and labeling based on iterative trunk growth and weakly supervised mechanism.

Peripancreatic vessel segmentation and anatomical labeling are pivotal aspects in aiding surgical planning and prognosis for patients with pancreatic tumors. Nevertheless, prevailing techniques often fall short in achieving satisfactory segmentation performance for the peripancreatic vein (PPV), leading to predictions characterized by poor integrity and connectivity. Besides, unsupervised labeling algorithms usually cannot deal with complex anatomical variation while fully supervised methods require a large number of voxel-wise annotations for training, which is very labor-intensive and time-consuming. To address these two problems, we propose an Automated Peripancreatic vEssel Segmentation and lAbeling (APESA) framework, to not only highly improve the segmentation performance for PPV, but also efficiently identify the peripancreatic artery (PPA) branches. There are two core modules in our proposed APESA framework: iterative trunk growth module (ITGM) for vein segmentation and weakly supervised labeling mechanism (WSLM) for artery labeling. The ITGM is composed of a series of iterative submodules, each of which chooses the largest connected component of the previous PPV segmentation as the trunk of a tree structure, seeks for the potential missing branches around the trunk by our designed branch proposal network, and facilitates trunk growth under the connectivity constraint. The WSLM incorporates the rule-based pseudo label generation with less expert participation, an anatomical labeling network to learn the branch distribution voxel by voxel, and adaptive radius-based postprocessing to refine the branch structures of the labeling predictions. Our achieved Dice of 94.01% for PPV segmentation on our collected dataset represents an approximately 10% accuracy improvement compared to state-of-the-art methods. Additionally, we attained a Dice of 97.01% for PPA segmentation and competitive labeling performance for PPA labeling compared to prior works. Our source codes will be publicly available at https://github.com/ZouLiwen-1999/APESA.

Rib segmentation in chest x-ray images based on unsupervised domain adaptation.

Rib segmentation in 2D chest x-ray images is a crucial and challenging task. On one hand, chest x-ray images serve as the most prevalent form of medical imaging due to their convenience, affordability, and minimal radiation exposure. However, on the other hand, these images present intricate challenges including overlapping anatomical structures, substantial noise and artifacts, inherent anatomical complexity. Currently, most methods employ deep convolutional networks for rib segmentation, necessitating an extensive quantity of accurately labeled data for effective training. Nonetheless, achieving precise pixel-level labeling in chest x-ray images presents a notable difficulty. Additionally, many methods neglect the challenge of predicting fractured results and subsequent post-processing difficulties. In contrast, CT images benefit from being able to directly label as the 3D structure and patterns of organs or tissues. In this paper, we redesign rib segmentation task for chest x-ray images and propose a concise and efficient cross-modal method based on unsupervised domain adaptation with centerline loss function to prevent result discontinuity and address rigorous post-processing. We utilize digital reconstruction radiography images and the labels generated from 3D CT images to guide rib segmentation on unlabeled 2D chest x-ray images. Remarkably, our model achieved a higher dice score on the test samples and the results are highly interpretable, without requiring any annotated rib markings on chest x-ray images. Our code and demo will be released in 'https://github.com/jialin-zhao/RibsegBasedonUDA'.

Progress and opportunities for metal-organic framework composites in electrochemical sensors.

Metal-organic framework composites have the advantages of large surface area, high porosity, strong catalytic efficiency and good stability, which provide a great possibility of finding excellent electrode materials for electrochemical sensors. However, MOF composites still face various challenges and difficulties, which limit their development and application. This paper reviews the application of MOF composites in electrochemical sensors, including MOF/carbon composites, MOF/metal nanoparticle composites, MOF/metal oxide composites and MOF/enzyme composites. In addition, the application challenges of MOF composites in electrochemical sensors are summarized. Finally, the application prospect for MOF composites is considered to promote the synthesis of more MOF composites with excellent properties.

Splitting proximate algorithm for deformable image registration based on functions of bounded deformation.

BACKGROUND: Deformable image registration is a crucial task in the field of medical image analysis. Functions of bounded deformation (BD) have been proved effective for modeling the displacement fields between medical images since they can capture the discontinuity of displacement fields along edges of organs and tissues. PURPOSE: However, we find that at the same time, BD functions-based models tend to obtain discontinuous displacement fields inside the regions of organs and tissues due to image noises in some cases and the presented gradient descent algorithm is time-consuming. To alleviate these problems, we propose a faster algorithm named SPA: splitting proximate algorithm. METHODS: In the framework of variable-splitting scheme, we incorporate a proximal term in the deformable registration energy based on functions of BD. RESULTS: The proposed algorithm can efficiently solve the original model and obtain displacement fields, which look more natural and plausible. Numerical experiments show the effectiveness and stability of the proposed algorithm. CONCLUSIONS: The proposed SPA is able to drastically register the images with a plausible deformation field and not sensitive to noise.

Automated segmentation of normal and diseased coronary arteries - The ASOCA challenge.

Cardiovascular disease is a major cause of death worldwide. Computed Tomography Coronary Angiography (CTCA) is a non-invasive method used to evaluate coronary artery disease, as well as evaluating and reconstructing heart and coronary vessel structures. Reconstructed models have a wide array of for educational, training and research applications such as the study of diseased and non-diseased coronary anatomy, machine learning based disease risk prediction and in-silico and in-vitro testing of medical devices. However, coronary arteries are difficult to image due to their small size, location, and movement, causing poor resolution and artefacts. Segmentation of coronary arteries has traditionally focused on semi-automatic methods where a human expert guides the algorithm and corrects errors, which severely limits large-scale applications and integration within clinical systems. International challenges aiming to overcome this barrier have focussed on specific tasks such as centreline extraction, stenosis quantification, and segmentation of specific artery segments only. Here we present the results of the first challenge to develop fully automatic segmentation methods of full coronary artery trees and establish the first large standardized dataset of normal and diseased arteries. This forms a new automated segmentation benchmark allowing the automated processing of CTCAs directly relevant for large-scale and personalized clinical applications.

Detection and analysis of cerebral aneurysms based on X-ray rotational angiography - the CADA 2020 challenge.

The Cerebral Aneurysm Detection and Analysis (CADA) challenge was organized to support the development and benchmarking of algorithms for detecting, analyzing, and risk assessment of cerebral aneurysms in X-ray rotational angiography (3DRA) images. 109 anonymized 3DRA datasets were provided for training, and 22 additional datasets were used to test the algorithmic solutions. Cerebral aneurysm detection was assessed using the F2 score based on recall and precision, and the fit of the delivered bounding box was assessed using the distance to the aneurysm. The segmentation quality was measured using the Jaccard index and a combination of different surface distance measures. Systematic errors were analyzed using volume correlation and bias. Rupture risk assessment was evaluated using the F2 score. 158 participants from 22 countries registered for the CADA challenge. The U-Net-based detection solutions presented by the community show similar accuracy compared to experts (F2 score 0.92), with a small number of missed aneurysms with diameters smaller than 3.5 mm. In addition, the delineation of these structures, based on U-Net variations, is excellent, with a Jaccard score of 0.92. The rupture risk estimation methods achieved an F2 score of 0.71. The performance of the detection and segmentation solutions is equivalent to that of human experts. The best results are obtained in rupture risk estimation by combining different image-based, morphological, and computational fluid dynamic parameters using machine learning methods. Furthermore, we evaluated the best methods pipeline, from detecting and delineating the vessel dilations to estimating the risk of rupture. The chain of these methods achieves an F2-score of 0.70, which is comparable to applying the risk prediction to the ground-truth delineation (0.71).

Toward data-efficient learning: A benchmark for COVID-19 CT lung and infection segmentation.

PURPOSE: Accurate segmentation of lung and infection in COVID-19 computed tomography (CT) scans plays an important role in the quantitative management of patients. Most of the existing studies are based on large and private annotated datasets that are impractical to obtain from a single institution, especially when radiologists are busy fighting the coronavirus disease. Furthermore, it is hard to compare current COVID-19 CT segmentation methods as they are developed on different datasets, trained in different settings, and evaluated with different metrics. METHODS: To promote the development of data-efficient deep learning methods, in this paper, we built three benchmarks for lung and infection segmentation based on 70 annotated COVID-19 cases, which contain current active research areas, for example, few-shot learning, domain generalization, and knowledge transfer. For a fair comparison among different segmentation methods, we also provide standard training, validation and testing splits, evaluation metrics and, the corresponding code. RESULTS: Based on the state-of-the-art network, we provide more than 40 pretrained baseline models, which not only serve as out-of-the-box segmentation tools but also save computational time for researchers who are interested in COVID-19 lung and infection segmentation. We achieve average dice similarity coefficient (DSC) scores of 97.3%, 97.7%, and 67.3% and average normalized surface dice (NSD) scores of 90.6%, 91.4%, and 70.0% for left lung, right lung, and infection, respectively. CONCLUSIONS: To the best of our knowledge, this work presents the first data-efficient learning benchmark for medical image segmentation, and the largest number of pretrained models up to now. All these resources are publicly available, and our work lays the foundation for promoting the development of deep learning methods for efficient COVID-19 CT segmentation with limited data.

Active contour regularized semi-supervised learning for COVID-19 CT infection segmentation with limited annotations.

Infection segmentation on chest CT plays an important role in the quantitative analysis of COVID-19. Developing automatic segmentation tools in a short period with limited labelled images has become an urgent need. Pseudo label-based semi-supervised method is a promising way to leverage unlabelled data to improve segmentation performance. Existing methods usually obtain pseudo labels by first training a network with limited labelled images and then inferring unlabelled images. However, these methods may generate obviously inaccurate labels and degrade the subsequent training process. To address these challenges, in this paper, an active contour regularized semi-supervised learning framework was proposed to automatically segment infections with few labelled images. The active contour regularization was realized by the region-scalable fitting (RSF) model which is embedded to the loss function of the network to regularize and refine the pseudo labels of the unlabelled images. We further designed a splitting method to separately optimize the RSF regularization term and the segmentation loss term with iterative convolution-thresholding method and stochastic gradient descent, respectively, which enable fast optimization of each term. Furthermore, we built a statistical atlas to show the infection spatial distribution. Extensive experiments on a small public dataset and a large scale dataset showed that the proposed method outperforms state-of-the-art methods with up to 5% in dice similarity coefficient and normalized surface dice, 10% in relative absolute volume difference and 8 mm in 95% Hausdorff distance. Moreover, we observed that the infections tend to occur at the dorsal subpleural lung and posterior basal segments that are not mentioned in current radiology reports and are meaningful to advance our understanding of COVID-19.

Deformable Image Registration Using Functions of Bounded Deformation.

Deformable image registration is a widely used technique in the field of computer vision and medical image processing. Basically, the task of deformable image registration is to find the displacement field between the moving image and the fixed image. Many variational models are proposed for deformable image registration, under the assumption that the displacement field is continuous and smooth. However, displacement fields may be discontinuous, especially for medical images with intensity inhomogeneity, pathological tissues, or heavy noises. In the mathematical theory of elastoplasticity, when the displacement fields are possibly discontinuous, a suitable framework for describing the displacement fields is the space of functions of bounded deformation (BD). Inspired by this, we propose a novel deformable registration model, called the BD model, which allows discontinuities of displacement fields in images. The BD model is formulated in a variational framework by supposing the displacement field to be a function of BD. The existence of solutions of this model is proven. Numerical experiments on 2D images show that the BD model outperforms the classical demons model, the log-domain diffeomorphic demons model, and the state-of-the-art vectorial total variation model. Numerical experiments on two public 3D databases show that the target registration error of the BD model is competitive compared with more than ten other models.