Existing prompt-based approaches have demonstrated impressive performance in continual learning, leveraging pre-trained large-scale models for classification tasks; however, the tight coupling between foreground-background information and the coupled attention between prompts and image-text tokens present significant challenges in incremental medical object detection tasks, due to the conceptual gap between medical and natural domains. To overcome these challenges, we introduce the \method~framework, which comprises two main components: 1) Instance-level Prompt Generation (\ipg), which decouples fine-grained instance-level knowledge from images and generates prompts that focus on dense predictions, and 2) Decoupled Prompt Attention (\dpa), which decouples the original prompt attention, enabling a more direct and efficient transfer of prompt information while reducing memory usage and mitigating catastrophic forgetting. We collect 13 clinical, cross-modal, multi-organ, and multi-category datasets, referred to as \dataset, and experiments demonstrate that \method~outperforms existing SOTA methods, with FAP improvements of 5.44\%, 4.83\%, 12.88\%, and 4.59\% in full data, 1-shot, 10-shot, and 50-shot settings, respectively.
Object detection is of paramount importance in biomedical image analysis, particularly for lesion identification. While current methodologies are proficient in identifying and pinpointing lesions, they often lack the precision needed to detect minute biomedical entities (e.g., abnormal cells, lung nodules smaller than 3 mm), which are critical in blood and lung pathology. To address this challenge, we propose CAF-YOLO, based on the YOLOv8 architecture, a nimble yet robust method for medical object detection that leverages the strengths of convolutional neural networks (CNNs) and transformers. To overcome the limitation of convolutional kernels, which have a constrained capacity to interact with distant information, we introduce an attention and convolution fusion module (ACFM). This module enhances the modeling of both global and local features, enabling the capture of long-term feature dependencies and spatial autocorrelation. Additionally, to improve the restricted single-scale feature aggregation inherent in feed-forward networks (FFN) within transformer architectures, we design a multi-scale neural network (MSNN). This network improves multi-scale information aggregation by extracting features across diverse scales. Experimental evaluations on widely used datasets, such as BCCD and LUNA16, validate the rationale and efficacy of CAF-YOLO. This methodology excels in detecting and precisely locating diverse and intricate micro-lesions within biomedical imagery. Our codes are available at https://github.com/xiaochen925/CAF-YOLO.
Diagnosing and treating abnormalities in the wrist, specifically distal radius, and ulna fractures, is a crucial concern among children, adolescents, and young adults, with a higher incidence rate during puberty. However, the scarcity of radiologists and the lack of specialized training among medical professionals pose a significant risk to patient care. This problem is further exacerbated by the rising number of imaging studies and limited access to specialist reporting in certain regions. This highlights the need for innovative solutions to improve the diagnosis and treatment of wrist abnormalities. Automated wrist fracture detection using object detection has shown potential, but current studies mainly use two-stage detection methods with limited evidence for single-stage effectiveness. This study employs state-of-the-art single-stage deep neural network-based detection models YOLOv5, YOLOv6, YOLOv7, and YOLOv8 to detect wrist abnormalities. Through extensive experimentation, we found that these YOLO models outperform the commonly used two-stage detection algorithm, Faster R-CNN, in fracture detection. Additionally, compound-scaled variants of each YOLO model were compared, with YOLOv8m demonstrating a highest fracture detection sensitivity of 0.92 and mean average precision (mAP) of 0.95. On the other hand, YOLOv6m achieved the highest sensitivity across all classes at 0.83. Meanwhile, YOLOv8x recorded the highest mAP of 0.77 for all classes on the GRAZPEDWRI-DX pediatric wrist dataset, highlighting the potential of single-stage models for enhancing pediatric wrist imaging.
Children often suffer wrist injuries in daily life, while fracture injuring radiologists usually need to analyze and interpret X-ray images before surgical treatment by surgeons. The development of deep learning has enabled neural network models to work as computer-assisted diagnosis (CAD) tools to help doctors and experts in diagnosis. Since the YOLOv8 models have obtained the satisfactory success in object detection tasks, it has been applied to fracture detection. The Global Context (GC) block effectively models the global context in a lightweight way, and incorporating it into YOLOv8 can greatly improve the model performance. This paper proposes the YOLOv8+GC model for fracture detection, which is an improved version of the YOLOv8 model with the GC block. Experimental results demonstrate that compared to the original YOLOv8 model, the proposed YOLOv8-GC model increases the mean average precision calculated at intersection over union threshold of 0.5 (mAP 50) from 63.58% to 66.32% on the GRAZPEDWRI-DX dataset, achieving the state-of-the-art (SOTA) level. The implementation code for this work is available on GitHub at https://github.com/RuiyangJu/YOLOv8_Global_Context_Fracture_Detection.
The introduction of YOLOv9, the latest version of the You Only Look Once (YOLO) series, has led to its widespread adoption across various scenarios. This paper is the first to apply the YOLOv9 algorithm model to the fracture detection task as computer-assisted diagnosis (CAD) to help radiologists and surgeons to interpret X-ray images. Specifically, this paper trained the model on the GRAZPEDWRI-DX dataset and extended the training set using data augmentation techniques to improve the model performance. Experimental results demonstrate that compared to the mAP 50-95 of the current state-of-the-art (SOTA) model, the YOLOv9 model increased the value from 42.16% to 43.73%, with an improvement of 3.7%. The implementation code is publicly available at https://github.com/RuiyangJu/YOLOv9-Fracture-Detection.
Wrist trauma and even fractures occur frequently in daily life, particularly among children who account for a significant proportion of fracture cases. Before performing surgery, surgeons often request patients to undergo X-ray imaging first and prepare for it based on the analysis of the radiologist. With the development of neural networks, You Only Look Once (YOLO) series models have been widely used in fracture detection as computer-assisted diagnosis (CAD). In 2023, Ultralytics presented the latest version of the YOLO models, which has been employed for detecting fractures across various parts of the body. Attention mechanism is one of the hottest methods to improve the model performance. This research work proposes YOLOv8-AM, which incorporates the attention mechanism into the original YOLOv8 architecture. Specifically, we respectively employ four attention modules, Convolutional Block Attention Module (CBAM), Global Attention Mechanism (GAM), Efficient Channel Attention (ECA), and Shuffle Attention (SA), to design the improved models and train them on GRAZPEDWRI-DX dataset. Experimental results demonstrate that the mean Average Precision at IoU 50 (mAP 50) of the YOLOv8-AM model based on ResBlock + CBAM (ResCBAM) increased from 63.6% to 65.8%, which achieves the state-of-the-art (SOTA) performance. Conversely, YOLOv8-AM model incorporating GAM obtains the mAP 50 value of 64.2%, which is not a satisfactory enhancement. Therefore, we combine ResBlock and GAM, introducing ResGAM to design another new YOLOv8-AM model, whose mAP 50 value is increased to 65.0%. The implementation code for this study is available on GitHub at https://github.com/RuiyangJu/Fracture_Detection_Improved_YOLOv8.
Object detection and localization are crucial tasks for biomedical image analysis, particularly in the field of hematology where the detection and recognition of blood cells are essential for diagnosis and treatment decisions. While attention-based methods have shown significant progress in object detection in various domains, their application in medical object detection has been limited due to the unique challenges posed by medical imaging datasets. To address this issue, we propose ADA-YOLO, a light-weight yet effective method for medical object detection that integrates attention-based mechanisms with the YOLOv8 architecture. Our proposed method leverages the dynamic feature localisation and parallel regression for computer vision tasks through \textit{adaptive head} module. Empirical experiments were conducted on the Blood Cell Count and Detection (BCCD) dataset to evaluate the effectiveness of ADA-YOLO. The results showed that ADA-YOLO outperforms the YOLOv8 model in mAP (mean average precision) on the BCCD dataset by using more than 3 times less space than YOLOv8. This indicates that our proposed method is effective. Moreover, the light-weight nature of our proposed method makes it suitable for deployment in resource-constrained environments such as mobile devices or edge computing systems. which could ultimately lead to improved diagnosis and treatment outcomes in the field of hematology.
You Only Look Once (YOLO)-based object detectors have shown remarkable accuracy for automated brain tumor detection. In this paper, we develop a novel BGF-YOLO architecture by incorporating Bi-level routing attention, Generalized feature pyramid networks, and Fourth detecting head into YOLOv8. BGF-YOLO contains an attention mechanism to focus more on important features, and feature pyramid networks to enrich feature representation by merging high-level semantic features with spatial details. Furthermore, we investigate the effect of different attention mechanisms and feature fusions, detection head architectures on brain tumor detection accuracy. Experimental results show that BGF-YOLO gives a 4.7% absolute increase of mAP$_{50}$ compared to YOLOv8x, and achieves state-of-the-art on the brain tumor detection dataset Br35H. The code is available at https://github.com/mkang315/BGF-YOLO.
Both CNN-based and Transformer-based object detection with bounding box representation have been extensively studied in computer vision and medical image analysis, but circular object detection in medical images is still underexplored. Inspired by the recent anchor free CNN-based circular object detection method (CircleNet) for ball-shape glomeruli detection in renal pathology, in this paper, we present CircleFormer, a Transformer-based circular medical object detection with dynamic anchor circles. Specifically, queries with circle representation in Transformer decoder iteratively refine the circular object detection results, and a circle cross attention module is introduced to compute the similarity between circular queries and image features. A generalized circle IoU (gCIoU) is proposed to serve as a new regression loss of circular object detection as well. Moreover, our approach is easy to generalize to the segmentation task by adding a simple segmentation branch to CircleFormer. We evaluate our method in circular nuclei detection and segmentation on the public MoNuSeg dataset, and the experimental results show that our method achieves promising performance compared with the state-of-the-art approaches. The effectiveness of each component is validated via ablation studies as well. Our code is released at https://github.com/zhanghx-iim-ahu/CircleFormer.
With an excellent balance between speed and accuracy, cutting-edge YOLO frameworks have become one of the most efficient algorithms for object detection. However, the performance of using YOLO networks is scarcely investigated in brain tumor detection. We propose a novel YOLO architecture with Reparameterized Convolution based on channel Shuffle (RCS-YOLO). We present RCS and a One-Shot Aggregation of RCS (RCS-OSA), which link feature cascade and computation efficiency to extract richer information and reduce time consumption. Experimental results on the brain tumor dataset Br35H show that the proposed model surpasses YOLOv6, YOLOv7, and YOLOv8 in speed and accuracy. Notably, compared with YOLOv7, the precision of RCS-YOLO improves by 1%, and the inference speed by 60% at 114.8 images detected per second (FPS). Our proposed RCS-YOLO achieves state-of-the-art performance on the brain tumor detection task. The code is available at https://github.com/mkang315/RCS-YOLO.
The accurate detection of suspicious regions in medical images is an error-prone and time-consuming process required by many routinely performed diagnostic procedures. To support clinicians during this difficult task, several automated solutions were proposed relying on complex methods with many hyperparameters. In this study, we investigate the feasibility of DEtection TRansformer (DETR) models for volumetric medical object detection. In contrast to previous works, these models directly predict a set of objects without relying on the design of anchors or manual heuristics such as non-maximum-suppression to detect objects. We show by conducting extensive experiments with three models, namely DETR, Conditional DETR, and DINO DETR on four data sets (CADA, RibFrac, KiTS19, and LIDC) that these set prediction models can perform on par with or even better than currently existing methods. DINO DETR, the best-performing model in our experiments demonstrates this by outperforming a strong anchor-based one-stage detector, Retina U-Net, on three out of four data sets.
Blood cell detection is a typical small-scale object detection problem in computer vision. In this paper, we propose a CST-YOLO model for blood cell detection based on YOLOv7 architecture and enhance it with the CNN-Swin Transformer (CST), which is a new attempt at CNN-Transformer fusion. We also introduce three other useful modules: Weighted Efficient Layer Aggregation Networks (W-ELAN), Multiscale Channel Split (MCS), and Concatenate Convolutional Layers (CatConv) in our CST-YOLO to improve small-scale object detection precision. Experimental results show that the proposed CST-YOLO achieves 92.7%, 95.6%, and 91.1% [email omitted], respectively, on three blood cell datasets, outperforming state-of-the-art object detectors, e.g., RT-DETR, YOLOv5, and YOLOv7. Our code is available at https://github.com/mkang315/CST-YOLO.
Intracranial aneurysms are a commonly occurring and life-threatening condition, affecting approximately 3.2% of the general population. Consequently, detecting these aneurysms plays a crucial role in their management. Lesion detection involves the simultaneous localization and categorization of abnormalities within medical images. In this study, we employed the nnDetection framework, a self-configuring framework specifically designed for 3D medical object detection, to detect and localize the 3D coordinates of aneurysms effectively. To capture and extract diverse features associated with aneurysms, we utilized TOF-MRA and structural MRI, both obtained from the ADAM dataset. The performance of our proposed deep learning model was assessed through the utilization of free-response receiver operative characteristics for evaluation purposes. The model's weights and 3D prediction of the bounding box of TOF-MRA are publicly available at https://github.com/orouskhani/AneurysmDetection.
Hospital emergency departments frequently receive lots of bone fracture cases, with pediatric wrist trauma fracture accounting for the majority of them. Before pediatric surgeons perform surgery, they need to ask patients how the fracture occurred and analyze the fracture situation by interpreting X-ray images. The interpretation of X-ray images often requires a combination of techniques from radiologists and surgeons, which requires time-consuming specialized training. With the rise of deep learning in the field of computer vision, network models applying for fracture detection has become an important research topic. In this paper, we use data augmentation to improve the model performance of YOLOv8 algorithm (the latest version of You Only Look Once) on a pediatric wrist trauma X-ray dataset (GRAZPEDWRI-DX), which is a public dataset. The experimental results show that our model has reached the state-of-the-art (SOTA) mean average precision (mAP 50). Specifically, mAP 50 of our model is 0.638, which is significantly higher than the 0.634 and 0.636 of the improved YOLOv7 and original YOLOv8 models. To enable surgeons to use our model for fracture detection on pediatric wrist trauma X-ray images, we have designed the application "Fracture Detection Using YOLOv8 App" to assist surgeons in diagnosing fractures, reducing the probability of error analysis, and providing more useful information for surgery.
Multi-class cell detection and counting is an essential task for many pathological diagnoses. Manual counting is tedious and often leads to inter-observer variations among pathologists. While there exist multiple, general-purpose, deep learning-based object detection and counting methods, they may not readily transfer to detecting and counting cells in medical images, due to the limited data, presence of tiny overlapping objects, multiple cell types, severe class-imbalance, minute differences in size/shape of cells, etc. In response, we propose guided posterior regularization (DeGPR), which assists an object detector by guiding it to exploit discriminative features among cells. The features may be pathologist-provided or inferred directly from visual data. We validate our model on two publicly available datasets (CoNSeP and MoNuSAC), and on MuCeD, a novel dataset that we contribute. MuCeD consists of 55 biopsy images of the human duodenum for predicting celiac disease. We perform extensive experimentation with three object detection baselines on three datasets to show that DeGPR is model-agnostic, and consistently improves baselines obtaining up to 9% (absolute) mAP gains.
The accurate detection of mediastinal lesions is one of the rarely explored medical object detection problems. In this work, we applied a modified version of the self-configuring method nnDetection to the Mediastinal Lesion Analysis (MELA) Challenge 2022. By incorporating automatically generated pseudo masks, training high capacity models with large patch sizes in a multi GPU setup and an adapted augmentation scheme to reduce localization errors caused by rotations, our method achieved an excellent FROC score of 0.9922 at IoU 0.10 and 0.9880 at IoU 0.3 in our cross-validation experiments. The submitted ensemble ranked third in the competition with a FROC score of 0.9897 on the MELA challenge leaderboard.
The evaluation of object detection models is usually performed by optimizing a single metric, e.g. mAP, on a fixed set of datasets, e.g. Microsoft COCO and Pascal VOC. Due to image retrieval and annotation costs, these datasets consist largely of images found on the web and do not represent many real-life domains that are being modelled in practice, e.g. satellite, microscopic and gaming, making it difficult to assert the degree of generalization learned by the model. We introduce the Roboflow-100 (RF100) consisting of 100 datasets, 7 imagery domains, 224,714 images, and 805 class labels with over 11,170 labelling hours. We derived RF100 from over 90,000 public datasets, 60 million public images that are actively being assembled and labelled by computer vision practitioners in the open on the web application Roboflow Universe. By releasing RF100, we aim to provide a semantically diverse, multi-domain benchmark of datasets to help researchers test their model's generalizability with real-life data. RF100 download and benchmark replication are available on GitHub.
Existing universal lesion detection (ULD) methods utilize compute-intensive anchor-based architectures which rely on predefined anchor boxes, resulting in unsatisfactory detection performance, especially in small and mid-sized lesions. Further, these default fixed anchor-sizes and ratios do not generalize well to different datasets. Therefore, we propose a robust one-stage anchor-free lesion detection network that can perform well across varying lesions sizes by exploiting the fact that the box predictions can be sorted for relevance based on their center rather than their overlap with the object. Furthermore, we demonstrate that the ULD can be improved by explicitly providing it the domain-specific information in the form of multi-intensity images generated using multiple HU windows, followed by self-attention based feature-fusion and backbone initialization using weights learned via self-supervision over CT-scans. We obtain comparable results to the state-of-the-art methods, achieving an overall sensitivity of 86.05% on the DeepLesion dataset, which comprises of approximately 32K CT-scans with lesions annotated across various body organs.
Incorporating data-specific domain knowledge in deep networks explicitly can provide important cues beneficial for lesion detection and can mitigate the need for diverse heterogeneous datasets for learning robust detectors. In this paper, we exploit the domain information present in computed tomography (CT) scans and propose a robust universal lesion detection (ULD) network that can detect lesions across all organs of the body by training on a single dataset, DeepLesion. We analyze CT-slices of varying intensities, generated using heuristically determined Hounsfield Unit(HU) windows that individually highlight different organs and are given as inputs to the deep network. The features obtained from the multiple intensity images are fused using a novel convolution augmented multi-head self-attention module and subsequently, passed to a Region Proposal Network (RPN) for lesion detection. In addition, we observed that traditional anchor boxes used in RPN for natural images are not suitable for lesion sizes often found in medical images. Therefore, we propose to use lesion-specific anchor sizes and ratios in the RPN for improving the detection performance. We use self-supervision to initialize weights of our network on the DeepLesion dataset to further imbibe domain knowledge. Our proposed Domain Knowledge augmented Multi-head Attention based Universal Lesion Detection Network DMKA-ULD produces refined and precise bounding boxes around lesions across different organs. We evaluate the efficacy of our network on the publicly available DeepLesion dataset which comprises of approximately 32K CT scans with annotated lesions across all organs of the body. Results demonstrate that we outperform existing state-of-the-art methods achieving an overall sensitivity of 87.16%.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{https://github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.