Detail-preserving image warping by enforcing smooth image sampling.

Multi-phase dynamic contrast-enhanced magnetic resonance imaging image registration makes a substantial contribution to medical image analysis. However, existing methods (e.g., VoxelMorph, CycleMorph) often encounter the problem of image information misalignment in deformable registration tasks, posing challenges to the practical application. To address this issue, we propose a novel smooth image sampling method to align full organic information to realize detail-preserving image warping. In this paper, we clarify that the phenomenon about image information mismatch is attributed to imbalanced sampling. Then, a sampling frequency map constructed by sampling frequency estimators is utilized to instruct smooth sampling by reducing the spatial gradient and discrepancy between all-ones matrix and sampling frequency map. In addition, our estimator determines the sampling frequency of a grid voxel in the moving image by aggregating the sum of interpolation weights from warped non-grid sampling points in its vicinity and vectorially constructs sampling frequency map through projection and scatteration. We evaluate the effectiveness of our approach through experiments on two in-house datasets. The results showcase that our method preserves nearly complete details with ideal registration accuracy compared with several state-of-the-art registration methods. Additionally, our method exhibits a statistically significant difference in the regularity of the registration field compared to other methods, at a significance level of p < 0.05. Our code will be released at https://github.com/QingRui-Sha/SFM.

Response of microbial communities and biogeochemical cycling functions to sediment physicochemical properties and microplastic pollution under damming and water diversion projects.

Understanding the interactions among flow-sediment, microorganisms, and biogeochemical cycles is crucial for comprehending the ecological response mechanisms of dams and water diversion. This study focused on the spatial patterns of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycle functional genes in the water resource for the middle route of the South-to-North Water Diversion Project in China, specifically the Danjiangkou Reservoir (comprising the Han and Dan reservoirs). The investigation incorporated sediment physicochemical properties and microplastic pollution. Numerous microbial species were identified, revealing that microbial communities demonstrated sensitivity to changes in sedimentary mud content. The communities exhibited greater ß diversity due to finer sediment particles in the Han Reservoir (HR), whereas in the Dan Reservoir (DR), despite having higher sediment nutrient content and MPs pollution, did not display this pattern. Regarding the composition and structure of microbial communities, the study highlighted that sediment N and P content had a more significant influence compared to particle size and MPs. The quantitative microbial element cycling (QMEC) results confirmed the presence of extensive chemolithotrophic microbes and strong nitrogen cycle activity stemming from long-term water storage and diversion operations. The denitrification intensity in the HR surpassed that of the DR. Notably, near the pre-dam area, biological nitrogen fixation, phosphorus removal, and sulfur reduction exhibited noticeable increases. Dam construction refined sediment, fostering the growth of different biogeochemical cycling bacteria and increasing the abundance of CNPS cycling genes. Furthermore, the presence of MPs exhibited a positive correlation with S cycling genes and a negative correlation with C and N cycling genes. These findings suggest that variations in flow-sediment dynamics and MPs pollution have significant impact the biogeochemical cycle of the reservoir.

Development and validation of a radiomics model based on T2-weighted imaging for predicting the efficacy of high intensity focused ultrasound ablation in uterine fibroids.

Background: The heterogeneity of uterine fibroids in magnetic resonance imaging (MRI) is complex for a subjective visual evaluation, therefore it is difficult for an accurate prediction of the efficacy of high intensity focused ultrasound (HIFU) ablation in fibroids before the treatment. The purpose of this study was to set up a radiomics model based on MRI T2-weighted imaging (T2WI) for predicting the efficacy of HIFU ablation in uterine fibroids, and it would be used in preoperative screening of the fibroids for achieving high non-perfused volume ratio (NPVR). Methods: A total of 178 patients with uterine fibroids were consecutively enrolled and treated with ultrasound-guided HIFU under conscious sedation between February 2017 and December 2021. Among them, 96 patients with 108 uterine fibroids with high ablation efficacy (NPVR ≥80%, h_NPVR) and 82 patients with 92 fibroids with lower ablation efficacy (NPVR <80%, l_NPVR) were retrospectively analyzed. The transverse T2WI images of fibroids were selected, and the fibroids were delineated slice by slice using ITK-SNAP software. The radiomics analysis was performed to find the imaging biomarker for the construction of a predicting model for the evaluation of the ablation efficacy, including the feature extraction, feature selection and model construction. The prediction model was built by logistic regression and assessed by receiver operating characteristic (ROC) curve, and the prediction efficiency of the two models was compared by Delong test. The ratio of the training set to the testing set was 8:2. Results: The logistic regression model showed that the mean area under the curve (AUC) of the training set was 0.817 [95% confidence interval (CI): 0.755-0.882], and the testing set was 0.805 (95% CI: 0.670-0.941), respectively, which indicated a strong classification ability. The Delong test showed that there was no significant difference in the area under the ROC curve between the training set and testing set (P>0.05). Conclusions: The radiomics model based on T2WI is feasible and effective for predicting the efficacy of HIFU ablation in treatment of uterine fibroids.

TaG-Net: Topology-Aware Graph Network for Centerline-Based Vessel Labeling.

Anatomical labeling of head and neck vessels is a vital step for cerebrovascular disease diagnosis. However, it remains challenging to automatically and accurately label vessels in computed tomography angiography (CTA) since head and neck vessels are tortuous, branched, and often spatially close to nearby vasculature. To address these challenges, we propose a novel topology-aware graph network (TaG-Net) for vessel labeling. It combines the advantages of volumetric image segmentation in the voxel space and centerline labeling in the line space, wherein the voxel space provides detailed local appearance information, and line space offers high-level anatomical and topological information of vessels through the vascular graph constructed from centerlines. First, we extract centerlines from the initial vessel segmentation and construct a vascular graph from them. Then, we conduct vascular graph labeling using TaG-Net, in which techniques of topology-preserving sampling, topology-aware feature grouping, and multi-scale vascular graph are designed. After that, the labeled vascular graph is utilized to improve volumetric segmentation via vessel completion. Finally, the head and neck vessels of 18 segments are labeled by assigning centerline labels to the refined segmentation. We have conducted experiments on CTA images of 401 subjects, and experimental results show superior vessel segmentation and labeling of our method compared to other state-of-the-art methods.

Deep learning empowered volume delineation of whole-body organs-at-risk for accelerated radiotherapy.

In radiotherapy for cancer patients, an indispensable process is to delineate organs-at-risk (OARs) and tumors. However, it is the most time-consuming step as manual delineation is always required from radiation oncologists. Herein, we propose a lightweight deep learning framework for radiotherapy treatment planning (RTP), named RTP-Net, to promote an automatic, rapid, and precise initialization of whole-body OARs and tumors. Briefly, the framework implements a cascade coarse-to-fine segmentation, with adaptive module for both small and large organs, and attention mechanisms for organs and boundaries. Our experiments show three merits: 1) Extensively evaluates on 67 delineation tasks on a large-scale dataset of 28,581 cases; 2) Demonstrates comparable or superior accuracy with an average Dice of 0.95; 3) Achieves near real-time delineation in most tasks with <2 s. This framework could be utilized to accelerate the contouring process in the All-in-One radiotherapy scheme, and thus greatly shorten the turnaround time of patients.

Evaluation of an automated intracranial aneurysm detection and rupture analysis approach using cascade detection and classification networks.

Intracranial aneurysm is commonly found in human brains especially for the elderly, and its rupture accounts for a high rate of subarachnoid hemorrhages. However, it is time-consuming and requires special expertise to pinpoint small aneurysms from computed tomography angiography (CTA) images. Deep learning-based detection has helped improve much efficiency but false-positives still render difficulty to be ruled out. To study the feasibility of deep learning algorithms for aneurysm analysis in clinical applications, this paper proposes a pipeline for aneurysm detection, segmentation, and rupture classification and validates its performance using CTA images of 1508 subjects. A cascade aneurysm detection model is employed by first using a fine-tuned feature pyramid network (FPN) for candidate detection and then applying a dual-channel ResNet aneurysm classifier to further reduce false positives. Detected aneurysms are then segmented by applying a traditional 3D V-Net to their image patches. Radiomics features of aneurysms are extracted after detection and segmentation. The machine-learning-based and deep learning-based rupture classification can be used to distinguish ruptured and un-ruptured ones. Experimental results show that the dual-channel ResNet aneurysm classifier utilizing image and vesselness information helps boost sensitivity of detection compared to single image channel input. Overall, the proposed pipeline can achieve a sensitivity of 90 % for 1 false positive per image, and 95 % for 2 false positives per image. For rupture classification the area under curve (AUC) of 0.906 can be achieved for the testing dataset. The results suggest feasibility of the pipeline for potential clinical use to assist radiologists in aneurysm detection and classification of ruptured and un-ruptured aneurysms.

Clinical evaluation of deep learning-based clinical target volume three-channel auto-segmentation algorithm for adaptive radiotherapy in cervical cancer.

OBJECTIVES: Accurate contouring of the clinical target volume (CTV) is a key element of radiotherapy in cervical cancer. We validated a novel deep learning (DL)-based auto-segmentation algorithm for CTVs in cervical cancer called the three-channel adaptive auto-segmentation network (TCAS). METHODS: A total of 107 cases were collected and contoured by senior radiation oncologists (ROs). Each case consisted of the following: (1) contrast-enhanced CT scan for positioning, (2) the related CTV, (3) multiple plain CT scans during treatment and (4) the related CTV. After registration between (1) and (3) for the same patient, the aligned image and CTV were generated. Method 1 is rigid registration, method 2 is deformable registration, and the aligned CTV is seen as the result. Method 3 is rigid registration and TCAS, method 4 is deformable registration and TCAS, and the result is generated by a DL-based method. RESULTS: From the 107 cases, 15 pairs were selected as the test set. The dice similarity coefficient (DSC) of method 1 was 0.8155 ± 0.0368; the DSC of method 2 was 0.8277 ± 0.0315; the DSCs of method 3 and 4 were 0.8914 ± 0.0294 and 0.8921 ± 0.0231, respectively. The mean surface distance and Hausdorff distance of methods 3 and 4 were markedly better than those of method 1 and 2. CONCLUSIONS: The TCAS achieved comparable accuracy to the manual delineation performed by senior ROs and was significantly better than direct registration.

A consistent deep registration network with group data modeling.

Medical image registration is a critical process for automated image computing, and ideally, the deformation field from one image to another should be smooth and inverse-consistent in order to bidirectionally align anatomical structures and to preserve their topology. Consistent registration can reduce bias caused by the order of input images, increase robustness, and improve reliability of subsequent quantitative analysis. Rigorous differential geometry constraints have been used in traditional methods to enforce the topological consistency but require comprehensive optimization and are time consuming. Recent studies show that deep learning-based registration methods can achieve comparable accuracy and are much faster than traditional registration. However, the estimated deformation fields do not necessarily possess inverse consistency when the order of two input images is swapped. To tackle this problem, we propose a new deep registration algorithm by employing the inverse consistency training strategy, so the forward and backward deformations of a pair of images can consistently align anatomical structures. In addition, since fine-tuned deformations among the training images reflect variability of shapes and appearances in a high-dimensional space, we formulate a group prior data modeling framework so that such statistics can be used to improve accuracy and consistency for registering new input image pairs. Specifically, we implement the wavelet principle component analysis (w-PCA) model of deformation fields and incorporate such prior constraints into the inverse-consistent deep registration network. We refer the proposed algorithm as consistent deep registration with group data modeling. Experiments on 3D brain magnetic resonance (MR) images showed that the unsupervised consistent deep registration and data modeling strategy yield consistent deformations after switching the input images and tolerated image variations well.

HF-UNet: Learning Hierarchically Inter-Task Relevance in Multi-Task U-Net for Accurate Prostate Segmentation in CT Images.

Accurate segmentation of the prostate is a key step in external beam radiation therapy treatments. In this paper, we tackle the challenging task of prostate segmentation in CT images by a two-stage network with 1) the first stage to fast localize, and 2) the second stage to accurately segment the prostate. To precisely segment the prostate in the second stage, we formulate prostate segmentation into a multi-task learning framework, which includes a main task to segment the prostate, and an auxiliary task to delineate the prostate boundary. Here, the second task is applied to provide additional guidance of unclear prostate boundary in CT images. Besides, the conventional multi-task deep networks typically share most of the parameters (i.e., feature representations) across all tasks, which may limit their data fitting ability, as the specificity of different tasks are inevitably ignored. By contrast, we solve them by a hierarchically-fused U-Net structure, namely HF-UNet. The HF-UNet has two complementary branches for two tasks, with the novel proposed attention-based task consistency learning block to communicate at each level between the two decoding branches. Therefore, HF-UNet endows the ability to learn hierarchically the shared representations for different tasks, and preserve the specificity of learned representations for different tasks simultaneously. We did extensive evaluations of the proposed method on a large planning CT image dataset and a benchmark prostate zonal dataset. The experimental results show HF-UNet outperforms the conventional multi-task network architectures and the state-of-the-art methods.

Computing infection distributions and longitudinal evolution patterns in lung CT images.

BACKGROUND: Spatial and temporal lung infection distributions of coronavirus disease 2019 (COVID-19) and their changes could reveal important patterns to better understand the disease and its time course. This paper presents a pipeline to analyze statistically these patterns by automatically segmenting the infection regions and registering them onto a common template. METHODS: A VB-Net is designed to automatically segment infection regions in CT images. After training and validating the model, we segmented all the CT images in the study. The segmentation results are then warped onto a pre-defined template CT image using deformable registration based on lung fields. Then, the spatial distributions of infection regions and those during the course of the disease are calculated at the voxel level. Visualization and quantitative comparison can be performed between different groups. We compared the distribution maps between COVID-19 and community acquired pneumonia (CAP), between severe and critical COVID-19, and across the time course of the disease. RESULTS: For the performance of infection segmentation, comparing the segmentation results with manually annotated ground-truth, the average Dice is 91.6% ± 10.0%, which is close to the inter-rater difference between two radiologists (the Dice is 96.1% ± 3.5%). The distribution map of infection regions shows that high probability regions are in the peripheral subpleural (up to 35.1% in probability). COVID-19 GGO lesions are more widely spread than consolidations, and the latter are located more peripherally. Onset images of severe COVID-19 (inpatients) show similar lesion distributions but with smaller areas of significant difference in the right lower lobe compared to critical COVID-19 (intensive care unit patients). About the disease course, critical COVID-19 patients showed four subsequent patterns (progression, absorption, enlargement, and further absorption) in our collected dataset, with remarkable concurrent HU patterns for GGO and consolidations. CONCLUSIONS: By segmenting the infection regions with a VB-Net and registering all the CT images and the segmentation results onto a template, spatial distribution patterns of infections can be computed automatically. The algorithm provides an effective tool to visualize and quantify the spatial patterns of lung infection diseases and their changes during the disease course. Our results demonstrate different patterns between COVID-19 and CAP, between severe and critical COVID-19, as well as four subsequent disease course patterns of the severe COVID-19 patients studied, with remarkable concurrent HU patterns for GGO and consolidations.

An artificial-intelligence lung imaging analysis system (ALIAS) for population-based nodule computing in CT scans.

Computed tomography (CT) screening is essential for early lung cancer detection. With the development of artificial intelligence techniques, it is particularly desirable to explore the ability of current state-of-the-art methods and to analyze nodule features in terms of a large population. In this paper, we present an artificial-intelligence lung image analysis system (ALIAS) for nodule detection and segmentation. And after segmenting the nodules, the locations, sizes, as well as imaging features are computed at the population level for studying the differences between benign and malignant nodules. The results provide better understanding of the underlying imaging features and their ability for early lung cancer diagnosis.

A cascade-network framework for integrated registration of liver DCE-MR images.

Registration of hepatic dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) is an important task for evaluation of transarterial chemoembolization (TACE) or radiofrequency ablation by quantifying enhancing viable residue tumor against necrosis. However, intensity changes due to contrast agents combined with spatial deformations render technical challenges for accurate registration of DCE-MRI, and traditional deformable registration methods using mutual information are often computationally intensive in order to tolerate such intensity enhancement and shape deformation variability. To address this problem, we propose a cascade network framework composed of a de-enhancement network (DE-Net) and a registration network (Reg-Net) to first remove contrast enhancement effects and then register the liver images in different phases. In experiments, we used DCE-MRI series of 97 patients from Renji Hospital of Shanghai Jiaotong University and registered the arterial phase and the portal venous phase images onto the pre-contrast phases. The performance of the cascade network framework was compared with that of the traditional registration method SyN in the ANTs toolkit and Reg-Net without DE-Net. The results showed that the proposed method achieved comparable registration performance with SyN but significantly improved the efficiency.

Dual-Sampling Attention Network for Diagnosis of COVID-19 From Community Acquired Pneumonia.

The coronavirus disease (COVID-19) is rapidly spreading all over the world, and has infected more than 1,436,000 people in more than 200 countries and territories as of April 9, 2020. Detecting COVID-19 at early stage is essential to deliver proper healthcare to the patients and also to protect the uninfected population. To this end, we develop a dual-sampling attention network to automatically diagnose COVID-19 from the community acquired pneumonia (CAP) in chest computed tomography (CT). In particular, we propose a novel online attention module with a 3D convolutional network (CNN) to focus on the infection regions in lungs when making decisions of diagnoses. Note that there exists imbalanced distribution of the sizes of the infection regions between COVID-19 and CAP, partially due to fast progress of COVID-19 after symptom onset. Therefore, we develop a dual-sampling strategy to mitigate the imbalanced learning. Our method is evaluated (to our best knowledge) upon the largest multi-center CT data for COVID-19 from 8 hospitals. In the training-validation stage, we collect 2186 CT scans from 1588 patients for a 5-fold cross-validation. In the testing stage, we employ another independent large-scale testing dataset including 2796 CT scans from 2057 patients. Results show that our algorithm can identify the COVID-19 images with the area under the receiver operating characteristic curve (AUC) value of 0.944, accuracy of 87.5%, sensitivity of 86.9%, specificity of 90.1%, and F1-score of 82.0%. With this performance, the proposed algorithm could potentially aid radiologists with COVID-19 diagnosis from CAP, especially in the early stage of the COVID-19 outbreak.

Effects of p-nitrophenol on enzyme activity, histology, and gene expression in Larimichthys crocea.

p-Nitrophenol (PNP) is one type of environmental pollutant, which is difficult to degrade and soluble in water. To investigate the effects of PNP on economically important marine fish species, we subjected Larimichthys crocea juvenile to five different concentrations of PNP for 96 h, and the semi-lethal concentration (LC50) was 6.218 mg/L. Then we collected the liver, kidney, and gill tissues to determine enzyme activity and gene expression levels, and analyzed histological changes. In histological analysis, the gills showed curling of lamella, epithelial lifting and hyperplasia; the parenchymal structure of hepatocytes was significantly damaged, with severe vacuolation and loss of original structure. The renal cells were damaged too, with congestion and renal tubular necrosis. Catalase and superoxide dismutase both showed an up- and down-tendency with the rise of concentration in the three tissues, and GSH-px had similar trend in the kidney, which decreased at 8 mg/L in the liver but showed no significant differences in the gills. Malondialdehyde of three tissues was increased with an increase in PNP concentration. The expression of four detoxification (cyp450, gst, gpx, hsp70) and one immune-related (mhc II) genes was induced at low PNP concentrations but inhibited at high PNP concentrations in the kidney. In liver, cyp450, hsp70 and mhc II showed similar trend but gst and gpx didn't increase at low PNP concentrations. Our results indicate that the fish possesses the ability to detoxify PNP; however, at high concentrations, PNP still causes serious damage to them. Our data not only help in understanding the ability of L. crocea to detoxify PNP but also should serve as a basis for the study of toxic effects of nitrobenzenes on marine fish.

Adversarial learning for mono- or multi-modal registration.

This paper introduces an unsupervised adversarial similarity network for image registration. Unlike existing deep learning registration methods, our approach can train a deformable registration network without the need of ground-truth deformations and specific similarity metrics. We connect a registration network and a discrimination network with a deformable transformation layer. The registration network is trained with the feedback from the discrimination network, which is designed to judge whether a pair of registered images are sufficiently similar. Using adversarial training, the registration network is trained to predict deformations that are accurate enough to fool the discrimination network. The proposed method is thus a general registration framework, which can be applied for both mono-modal and multi-modal image registration. Experiments on four brain MRI datasets and a multi-modal pelvic image dataset indicate that our method yields promising registration performance in accuracy, efficiency and generalizability compared with state-of-the-art registration methods, including those based on deep learning.

Fast Groupwise Registration Using Multi-Level and Multi-Resolution Graph Shrinkage.

Groupwise registration aligns a set of images to a common space. It can however be inefficient and ineffective when dealing with datasets with significant anatomical variations. To mitigate these problems, we propose a groupwise registration framework based on hierarchical multi-level and multi-resolution shrinkage of a graph set. First, to deal with datasets with complex inhomogeneous image distributions, we divide the images hierarchically into multiple clusters. Since the images in each cluster have similar appearances, they can be registered effectively. Second, we employ a multi-resolution strategy to reduce computational cost. Experimental results on two public datasets show that our proposed method yields state-of-the-art registration accuracy with significantly reduced computational time.

BIRNet: Brain image registration using dual-supervised fully convolutional networks.

In this paper, we propose a deep learning approach for image registration by predicting deformation from image appearance. Since obtaining ground-truth deformation fields for training can be challenging, we design a fully convolutional network that is subject to dual-guidance: (1) Ground-truth guidance using deformation fields obtained by an existing registration method; and (2) Image dissimilarity guidance using the difference between the images after registration. The latter guidance helps avoid overly relying on the supervision from the training deformation fields, which could be inaccurate. For effective training, we further improve the deep convolutional network with gap filling, hierarchical loss, and multi-source strategies. Experiments on a variety of datasets show promising registration accuracy and efficiency compared with state-of-the-art methods.

Effects of formaldehyde on detoxification and immune responses in silver pomfret (Pampus argenteus).

Formaldehyde can effectively control ectoparasites in silver pomfret (Pampus argenteus). However, there is limited information on the effects of formaldehyde treatment at a molecular level in fishes. In the present study, transcriptome profiling was conducted to investigate the effects of formaldehyde treatment (80 mg/L, bath for 1 h every day for three consecutive days) on the liver and kidney tissues of silver pomfret. A total of 617959982 clean reads were obtained and assembled into 265760 unigenes with an N50 length of 1507 bp, and the assembled unigenes were all annotated by alignment with public databases. A total of 2204 differentially expressed genes (DEGs) were detected in the liver and kidney tissues, and they included 7 detoxification- related genes and 9 immune-related genes, such as CYP450, GST, MHC I & II, and CCR. In addition, 1440 DEGs were mapped to terms in the GO database, and 1064 DEGs were mapped to the KEGG database. The expression of 4 detoxification-related genes and 6 immune-related genes in three days formaldehyde treatment were analyzed using RT-qPCR, and the antioxidant enzyme levels were also determined. The results indicate differential expression of detoxification- and immune-related genes during the three days formaldehyde treatment. Our data could provide a reference for the treatment of parasites to avoid high mortality and help in understanding the molecular activity in fishes after formaldehyde exposure.

Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts.

Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (Larimichthy crocea), deep sequencing of olfactory epithelium was conducted to analyse olfactory-related genes in olfactory transduction. Sodium cholates (SAS) have typical bile salt chemical structures, hence we used four different concentrations of SAS to stimulate L. crocea, and the fish displayed a significant behavioural preference for 0.30% SAS. We then sequenced olfactory epithelium tissues, and identified 9938 unigenes that were significantly differentially expressed between SAS-stimulated and control groups, including 9055 up-regulated and 883 down-regulated unigenes. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found eight categories linked to the olfactory transduction pathway that was highly enriched with some differentially expressed genes (DEGs), including the olfactory receptor (OR), Adenylate cyclase type 3 (ADCY3) and Calmodulin (CALM). Genes in these categories were analysed by RT-qPCR, which revealed aspects of the pathway transformation between odor detection, and recovery and adaptation. The results provide new insight into the effects of bile salt stimulation in olfactory molecular mechanisms in fishes, and expands our knowledge of olfactory transduction, and signal generation and decline.