The vast volume of medical image data necessitates efficient compression techniques to support remote healthcare services. This paper explores Region of Interest (ROI) coding to address the balance between compression rate and image quality. By leveraging UNET segmentation on the Brats 2020 dataset, we accurately identify tumor regions, which are critical for diagnosis. These regions are then subjected to High Efficiency Video Coding (HEVC) for compression, enhancing compression rates while preserving essential diagnostic information. This approach ensures that critical image regions maintain their quality, while non-essential areas are compressed more. Our method optimizes storage space and transmission bandwidth, meeting the demands of telemedicine and large-scale medical imaging. Through this technique, we provide a robust solution that maintains the integrity of vital data and improves the efficiency of medical image handling.
In the past decades, deep neural networks, particularly convolutional neural networks, have achieved state-of-the-art performance in a variety of medical image segmentation tasks. Recently, the introduction of the vision transformer (ViT) has significantly altered the landscape of deep segmentation models. There has been a growing focus on ViTs, driven by their excellent performance and scalability. However, we argue that the current design of the vision transformer-based UNet (ViT-UNet) segmentation models may not effectively handle the heterogeneous appearance (e.g., varying shapes and sizes) of objects of interest in medical image segmentation tasks. To tackle this challenge, we present a structured approach to introduce spatially dynamic components to the ViT-UNet. This adaptation enables the model to effectively capture features of target objects with diverse appearances. This is achieved by three main components: \textbf{(i)} deformable patch embedding; \textbf{(ii)} spatially dynamic multi-head attention; \textbf{(iii)} deformable positional encoding. These components were integrated into a novel architecture, termed AgileFormer. AgileFormer is a spatially agile ViT-UNet designed for medical image segmentation. Experiments in three segmentation tasks using publicly available datasets demonstrated the effectiveness of the proposed method. The code is available at \href{https://github.com/sotiraslab/AgileFormer}{https://github.com/sotiraslab/AgileFormer}.
Identifying neutral hydrogen (\hi) galaxies from observational data is a significant challenge in \hi\ galaxy surveys. With the advancement of observational technology, especially with the advent of large-scale telescope projects such as FAST and SKA, the significant increase in data volume presents new challenges for the efficiency and accuracy of data processing.To address this challenge, in this study, we present a machine learning-based method for extracting \hi\ sources from the three-dimensional (3D) spectral data obtained from the Commensal Radio Astronomy FAST Survey (CRAFTS). We have carefully assembled a specialized dataset, HISF, rich in \hi\ sources, specifically designed to enhance the detection process. Our model, Unet-LK, utilizes the advanced 3D-Unet segmentation architecture and employs an elongated convolution kernel to effectively capture the intricate structures of \hi\ sources. This strategy ensures a reliable identification and segmentation of \hi\ sources, achieving notable performance metrics with a recall rate of 91.6\% and an accuracy of 95.7\%. These results substantiate the robustness of our dataset and the effectiveness of our proposed network architecture in the precise identification of \hi\ sources. Our code and dataset is publicly available at \url{https://github.com/fishszh/HISF}.
Crashes and delays at Railroad Highway Grade Crossings (RHGC), where highways and railroads intersect, pose significant safety concerns for the U.S. Federal Railroad Administration (FRA). Despite the critical importance of addressing accidents and traffic delays at highway-railroad intersections, there is a notable dearth of research on practical solutions for managing these issues. In response to this gap in the literature, our study introduces an intelligent system that leverages machine learning and computer vision techniques to enhance safety at Railroad Highway Grade crossings (RHGC). This research proposed a Non-Maximum Suppression (NMS)- based ensemble model that integrates a variety of YOLO variants, specifically YOLOv5S, YOLOv5M, and YOLOv5L, for grade-crossing object detection, utilizes segmentation techniques from the UNet architecture for detecting approaching rail at a grade crossing. Both methods are implemented on a Raspberry Pi. Moreover, the strategy employs high-definition cameras installed at the RHGC. This framework enables the system to monitor objects within the Region of Interest (ROI) at crossings, detect the approach of trains, and clear the crossing area before a train arrives. Regarding accuracy, precision, recall, and Intersection over Union (IoU), the proposed state-of-the-art NMS-based object detection ensemble model achieved 96% precision. In addition, the UNet segmentation model obtained a 98% IoU value. This automated railroad grade crossing system powered by artificial intelligence represents a promising solution for enhancing safety at highway-railroad intersections.
Image segmentation is a branch of computer vision that is widely used in real world applications including biomedical image processing. With recent advancement of deep learning, image segmentation has achieved at a very high level performance. Recently, UNet architecture is found as the core of novel deep learning segmentation methods. In this paper we implement UNet architecture from scratch with using basic blocks in Pytorch and evaluate its performance on multiple biomedical image datasets. We also use transfer learning to apply novel modified UNet segmentation packages on the biomedical image datasets. We fine tune the pre-trained transferred model with each specific dataset. We compare its performance with our fundamental UNet implementation. We show that transferred learning model has better performance in image segmentation than UNet model that is implemented from scratch.
X-ray coronary angiography (XCA) is used to assess coronary artery disease and provides valuable information on lesion morphology and severity. However, XCA images are 2D and therefore limit visualisation of the vessel. 3D reconstruction of coronary vessels is possible using multiple views, however lumen border detection in current software is performed manually resulting in limited reproducibility and slow processing time. In this study we propose 3DAngioNet, a novel deep learning (DL) system that enables rapid 3D vessel mesh reconstruction using 2D XCA images from two views. Our approach learns a coarse mesh template using an EfficientB3-UNet segmentation network and projection geometries, and deforms it using a graph convolutional network. 3DAngioNet outperforms similar automated reconstruction methods, offers improved efficiency, and enables modelling of bifurcated vessels. The approach was validated using state-of-the-art software verified by skilled cardiologists.
CT-based bronchial tree analysis plays an important role in the computer-aided diagnosis for respiratory diseases, as it could provide structured information for clinicians. The basis of airway analysis is bronchial tree reconstruction, which consists of bronchus segmentation and classification. However, there remains a challenge for accurate bronchial analysis due to the individual variations and the severe class imbalance. In this paper, we propose a region and structure prior embedded framework named BronchusNet to achieve accurate segmentation and classification of bronchial regions in CT images. For bronchus segmentation, we propose an adaptive hard region-aware UNet that incorporates multi-level prior guidance of hard pixel-wise samples in the general Unet segmentation network to achieve better hierarchical feature learning. For the classification of bronchial branches, we propose a hybrid point-voxel graph learning module to fully exploit bronchial structure priors and to support simultaneous feature interactions across different branches. To facilitate the study of bronchial analysis, we contribute~\textbf{BRSC}: an open-access benchmark of \textbf{BR}onchus imaging analysis with high-quality pixel-wise \textbf{S}egmentation masks and the \textbf{C}lass of bronchial segments. Experimental results on BRSC show that our proposed method not only achieves the state-of-the-art performance for binary segmentation of bronchial region but also exceeds the best existing method on bronchial branches classification by 6.9\%.
Medical image segmentation, which aims to automatically extract anatomical or pathological structures, plays a key role in computer-aided diagnosis and disease analysis. Despite the problem has been widely studied, existing methods are prone to topological errors. In medical imaging, the topology of the structure, such as the kidney or lung, is usually known. Preserving the topology of the structure in the segmentation process is of utmost importance for accurate image analysis. In this work, a novel learning-based segmentation model is proposed. A {\it topology-preserving segmentation network (TPSN)} is trained to give an accurate segmentation result of an input image that preserves the prescribed topology. TPSN is a deformation-based model that yields a deformation map through a UNet, which takes the medical image and a template mask as inputs. The main idea is to deform a template mask describing the prescribed topology by a diffeomorphism to segment the object in the image. The topology of the shape in the template mask is well preserved under the diffeomorphic map. The diffeomorphic property of the map is controlled by introducing a regularization term related to the Jacobian in the loss function. As such, a topology-preserving segmentation result can be guaranteed. Furthermore, a multi-scale TPSN is developed in this paper that incorporates multi-level information of images to produce more precise segmentation results. To evaluate our method, we applied the 2D TPSN on Ham10000 and 3D TPSN on KiTS21. Experimental results illustrate our method outperforms the baseline UNet segmentation model with/without connected-component analysis (CCA) by both the dice score and IoU score. Besides, results show that our method can produce reliable results even in challenging cases, where pixel-wise segmentation models by UNet and CCA fail to obtain accurate results.
Most recent semantic segmentation methods adopt a U-Net framework with an encoder-decoder architecture. It is still challenging for U-Net with a simple skip connection scheme to model the global multi-scale context: 1) Not each skip connection setting is effective due to the issue of incompatible feature sets of encoder and decoder stage, even some skip connection negatively influence the segmentation performance; 2) The original U-Net is worse than the one without any skip connection on some datasets. Based on our findings, we propose a new segmentation framework, named UCTransNet (with a proposed CTrans module in U-Net), from the channel perspective with attention mechanism. Specifically, the CTrans module is an alternate of the U-Net skip connections, which consists of a sub-module to conduct the multi-scale Channel Cross fusion with Transformer (named CCT) and a sub-module Channel-wise Cross-Attention (named CCA) to guide the fused multi-scale channel-wise information to effectively connect to the decoder features for eliminating the ambiguity. Hence, the proposed connection consisting of the CCT and CCA is able to replace the original skip connection to solve the semantic gaps for an accurate automatic medical image segmentation. The experimental results suggest that our UCTransNet produces more precise segmentation performance and achieves consistent improvements over the state-of-the-art for semantic segmentation across different datasets and conventional architectures involving transformer or U-shaped framework. Code: https://github.com/McGregorWwww/UCTransNet.
Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.
Many cultures around the world believe that palm reading can be used to predict the future life of a person. Palmistry uses features of the hand such as palm lines, hand shape, or fingertip position. However, the research on palm-line detection is still scarce, many of them applied traditional image processing techniques. In most real-world scenarios, images usually are not in well-conditioned, causing these methods to severely under-perform. In this paper, we propose an algorithm to extract principle palm lines from an image of a person's hand. Our method applies deep learning networks (DNNs) to improve performance. Another challenge of this problem is the lack of training data. To deal with this issue, we handcrafted a dataset from scratch. From this dataset, we compare the performance of readily available methods with ours. Furthermore, based on the UNet segmentation neural network architecture and the knowledge of attention mechanism, we propose a highly efficient architecture to detect palm-lines. We proposed the Context Fusion Module to capture the most important context feature, which aims to improve segmentation accuracy. The experimental results show that it outperforms the other methods with the highest F1 Score about 99.42% and mIoU is 0.584 for the same dataset.
Deep learning (DL) has drawn tremendous attention in object localization and recognition for both natural and medical images. U-Net segmentation models have demonstrated superior performance compared to conventional handcrafted feature-based methods. Medical image modality-specific DL models are better at transferring domain knowledge to a relevant target task than those that are pretrained on stock photography images. This helps improve model adaptation, generalization, and class-specific region of interest (ROI) localization. In this study, we train chest X-ray (CXR) modality-specific U-Nets and other state-of-the-art U-Net models for semantic segmentation of tuberculosis (TB)-consistent findings. Automated segmentation of such manifestations could help radiologists reduce errors and supplement decision-making while improving patient care and productivity. Our approach uses the publicly available TBX11K CXR dataset with weak TB annotations, typically provided as bounding boxes, to train a set of U-Net models. Next, we improve the results by augmenting the training data with weak localizations, post-processed into an ROI mask, from a DL classifier that is trained to classify CXRs as showing normal lungs or suspected TB manifestations. Test data are individually derived from the TBX11K CXR training distribution and other cross-institutional collections including the Shenzhen TB and Montgomery TB CXR datasets. We observe that our augmented training strategy helped the CXR modality-specific U-Net models achieve superior performance with test data derived from the TBX11K CXR training distribution as well as from cross-institutional collections (p < 0.05).
Medical image processing is one of the most important topics in the field of the Internet of Medical Things (IoMT). Recently, deep learning methods have carried out state-of-the-art performances on medical image tasks. However, conventional deep learning have two main drawbacks: 1) insufficient training data and 2) the domain mismatch between the training data and the testing data. In this paper, we propose a distant domain transfer learning (DDTL) method for medical image classification. Moreover, we apply our methods to a recent issue (Coronavirus diagnose). Several current studies indicate that lung Computed Tomography (CT) images can be used for a fast and accurate COVID-19 diagnosis. However, the well-labeled training data cannot be easily accessed due to the novelty of the disease and a number of privacy policies. Moreover, the proposed method has two components: Reduced-size Unet Segmentation model and Distant Feature Fusion (DFF) classification model. It is related to a not well-investigated but important transfer learning problem, termed Distant Domain Transfer Learning (DDTL). DDTL aims to make efficient transfers even when the domains or the tasks are entirely different. In this study, we develop a DDTL model for COVID-19 diagnose using unlabeled Office-31, Catech-256, and chest X-ray image data sets as the source data, and a small set of COVID-19 lung CT as the target data. The main contributions of this study: 1) the proposed method benefits from unlabeled data collected from distant domains which can be easily accessed, 2) it can effectively handle the distribution shift between the training data and the testing data, 3) it has achieved 96\% classification accuracy, which is 13\% higher classification accuracy than "non-transfer" algorithms, and 8\% higher than existing transfer and distant transfer algorithms.
Uncontrolled growth of weeds can severely affect the crop yield and quality. Unrestricted use of herbicide for weed removal alters biodiversity and cause environmental pollution. Instead, identifying weed-infested regions can aid selective chemical treatment of these regions. Advances in analyzing farm images have resulted in solutions to identify weed plants. However, a majority of these approaches are based on supervised learning methods which requires huge amount of manually annotated images. As a result, these supervised approaches are economically infeasible for the individual farmer because of the wide variety of plant species being cultivated. In this paper, we propose a deep learning-based semi-supervised approach for robust estimation of weed density and distribution across farmlands using only limited color images acquired from autonomous robots. This weed density and distribution can be useful in a site-specific weed management system for selective treatment of infected areas using autonomous robots. In this work, the foreground vegetation pixels containing crops and weeds are first identified using a Convolutional Neural Network (CNN) based unsupervised segmentation. Subsequently, the weed infected regions are identified using a fine-tuned CNN, eliminating the need for designing hand-crafted features. The approach is validated on two datasets of different crop/weed species (1) Crop Weed Field Image Dataset (CWFID), which consists of carrot plant images and the (2) Sugar Beets dataset. The proposed method is able to localize weed-infested regions a maximum recall of 0.99 and estimate weed density with a maximum accuracy of 82.13%. Hence, the proposed approach is shown to generalize to different plant species without the need for extensive labeled data.
Purpose: To enable fast and reliable assessment of subcutaneous and visceral adipose tissue compartments derived from whole-body MRI. Methods: Quantification and localization of different adipose tissue compartments from whole-body MR images is of high interest to examine metabolic conditions. For correct identification and phenotyping of individuals at increased risk for metabolic diseases, a reliable automatic segmentation of adipose tissue into subcutaneous and visceral adipose tissue is required. In this work we propose a 3D convolutional neural network (DCNet) to provide a robust and objective segmentation. In this retrospective study, we collected 1000 cases (66$\pm$ 13 years; 523 women) from the Tuebingen Family Study and from the German Center for Diabetes research (TUEF/DZD), as well as 300 cases (53$\pm$ 11 years; 152 women) from the German National Cohort (NAKO) database for model training, validation, and testing with a transfer learning between the cohorts. These datasets had variable imaging sequences, imaging contrasts, receiver coil arrangements, scanners and imaging field strengths. The proposed DCNet was compared against a comparable 3D UNet segmentation in terms of sensitivity, specificity, precision, accuracy, and Dice overlap. Results: Fast (5-7seconds) and reliable adipose tissue segmentation can be obtained with high Dice overlap (0.94), sensitivity (96.6%), specificity (95.1%), precision (92.1%) and accuracy (98.4%) from 3D whole-body MR datasets (field of view coverage 450x450x2000mm${}^3$). Segmentation masks and adipose tissue profiles are automatically reported back to the referring physician. Conclusion: Automatic adipose tissue segmentation is feasible in 3D whole-body MR data sets and is generalizable to different epidemiological cohort studies with the proposed DCNet.
Early detection of lung cancer is an effective way to improve the survival rate of patients. It is a critical step to have accurate detection of lung nodules in computed tomography (CT) images for the diagnosis of lung cancer. However, due to the heterogeneity of the lung nodules and the complexity of the surrounding environment, robust nodule detection has been a challenging task. In this study, we propose a two-stage convolutional neural network (TSCNN) architecture for lung nodule detection. The CNN architecture in the first stage is based on the improved UNet segmentation network to establish an initial detection of lung nodules. Simultaneously, in order to obtain a high recall rate without introducing excessive false positive nodules, we propose a novel sampling strategy, and use the offline hard mining idea for training and prediction according to the proposed cascaded prediction method. The CNN architecture in the second stage is based on the proposed dual pooling structure, which is built into three 3D CNN classification networks for false positive reduction. Since the network training requires a significant amount of training data, we adopt a data augmentation method based on random mask. Furthermore, we have improved the generalization ability of the false positive reduction model by means of ensemble learning. The proposed method has been experimentally verified on the LUNA dataset. Experimental results show that the proposed TSCNN architecture can obtain competitive detection performance.
This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.
Earth observation (EO) sensors deliver data with daily or weekly temporal resolution. Most land use and land cover (LULC) approaches, however, expect cloud-free and mono-temporal observations. The increasing temporal capabilities of today's sensors enables the use of temporal, along with spectral and spatial features. Domains, such as speech recognition or neural machine translation, work with inherently temporal data and, today, achieve impressive results using sequential encoder-decoder structures. Inspired by these sequence-to-sequence models, we adapt an encoder structure with convolutional recurrent layers in order to approximate a phenological model for vegetation classes based on a temporal sequence of Sentinel 2 (S2) images. In our experiments, we visualize internal activations over a sequence of cloudy and non-cloudy images and find several recurrent cells, which reduce the input activity for cloudy observations. Hence, we assume that our network has learned cloud-filtering schemes solely from input data, which could alleviate the need for tedious cloud-filtering as a preprocessing step for many EO approaches. Moreover, using unfiltered temporal series of top-of-atmosphere (TOA) reflectance data, we achieved in our experiments state-of-the-art classification accuracies on a large number of crop classes with minimal preprocessing compared to other classification approaches.