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.
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.
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 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.
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}.
The difficulties in both data acquisition and annotation substantially restrict the sample sizes of training datasets for 3D medical imaging applications. As a result, constructing high-performance 3D convolutional neural networks from scratch remains a difficult task in the absence of a sufficient pre-training parameter. Previous efforts on 3D pre-training have frequently relied on self-supervised approaches, which use either predictive or contrastive learning on unlabeled data to build invariant 3D representations. However, because of the unavailability of large-scale supervision information, obtaining semantically invariant and discriminative representations from these learning frameworks remains problematic. In this paper, we revisit an innovative yet simple fully-supervised 3D network pre-training framework to take advantage of semantic supervisions from large-scale 2D natural image datasets. With a redesigned 3D network architecture, reformulated natural images are used to address the problem of data scarcity and develop powerful 3D representations. Comprehensive experiments on four benchmark datasets demonstrate that the proposed pre-trained models can effectively accelerate convergence while also improving accuracy for a variety of 3D medical imaging tasks such as classification, segmentation and detection. In addition, as compared to training from scratch, it can save up to 60% of annotation efforts. On the NIH DeepLesion dataset, it likewise achieves state-of-the-art detection performance, outperforming earlier self-supervised and fully-supervised pre-training approaches, as well as methods that do training from scratch. To facilitate further development of 3D medical models, our code and pre-trained model weights are publicly available at https://github.com/urmagicsmine/CSPR.
The computer-aided diagnosis of focal liver lesions (FLLs) can help improve workflow and enable correct diagnoses; FLL detection is the first step in such a computer-aided diagnosis. Despite the recent success of deep-learning-based approaches in detecting FLLs, current methods are not sufficiently robust for assessing misaligned multiphase data. By introducing an attention-guided multiphase alignment in feature space, this study presents a fully automated, end-to-end learning framework for detecting FLLs from multiphase computed tomography (CT) images. Our method is robust to misaligned multiphase images owing to its complete learning-based approach, which reduces the sensitivity of the model's performance to the quality of registration and enables a standalone deployment of the model in clinical practice. Evaluation on a large-scale dataset with 280 patients confirmed that our method outperformed previous state-of-the-art methods and significantly reduced the performance degradation for detecting FLLs using misaligned multiphase CT images. The robustness of the proposed method can enhance the clinical adoption of the deep-learning-based computer-aided detection system.
Box representation has been extensively used for object detection in computer vision. Such representation is efficacious but not necessarily optimized for biomedical objects (e.g., glomeruli), which play an essential role in renal pathology. In this paper, we propose a simple circle representation for medical object detection and introduce CircleNet, an anchor-free detection framework. Compared with the conventional bounding box representation, the proposed bounding circle representation innovates in three-fold: (1) it is optimized for ball-shaped biomedical objects; (2) The circle representation reduced the degree of freedom compared with box representation; (3) It is naturally more rotation invariant. When detecting glomeruli and nuclei on pathological images, the proposed circle representation achieved superior detection performance and be more rotation-invariant, compared with the bounding box. The code has been made publicly available: https://github.com/hrlblab/CircleNet
Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of high clinical relevance because diagnostic decisions often depend on rating of objects rather than e.g. pixels. For this task, the cumbersome and iterative process of method configuration constitutes a major research bottleneck. Recently, nnU-Net has tackled this challenge for the task of image segmentation with great success. Following nnU-Net's agenda, in this work we systematize and automate the configuration process for medical object detection. The resulting self-configuring method, nnDetection, adapts itself without any manual intervention to arbitrary medical detection problems while achieving results en par with or superior to the state-of-the-art. We demonstrate the effectiveness of nnDetection on two public benchmarks, ADAM and LUNA16, and propose 11 further medical object detection tasks on public data sets for comprehensive method evaluation. Code is at https://github.com/MIC-DKFZ/nnDetection .
Universal lesion detection from computed tomography (CT) slices is important for comprehensive disease screening. Since each lesion can locate in multiple adjacent slices, 3D context modeling is of great significance for developing automated lesion detection algorithms. In this work, we propose a Modified Pseudo-3D Feature Pyramid Network (MP3D FPN) that leverages depthwise separable convolutional filters and a group transform module (GTM) to efficiently extract 3D context enhanced 2D features for universal lesion detection in CT slices. To facilitate faster convergence, a novel 3D network pre-training method is derived using solely large-scale 2D object detection dataset in the natural image domain. We demonstrate that with the novel pre-training method, the proposed MP3D FPN achieves state-of-the-art detection performance on the DeepLesion dataset (3.48% absolute improvement in the sensitivity of [email omitted]), significantly surpassing the baseline method by up to 6.06% (in [email omitted]) which adopts 2D convolution for 3D context modeling. Moreover, the proposed 3D pre-trained weights can potentially be used to boost the performance of other 3D medical image analysis tasks.
Computer-aided detection, localisation, and segmentation methods can help improve colonoscopy procedures. Even though many methods have been built to tackle automatic detection and segmentation of polyps, benchmarking of state-of-the-art methods still remains an open problem. This is due to the increasing number of researched computer vision methods that can be applied to polyp datasets. Benchmarking of novel methods can provide a direction to the development of automated polyp detection and segmentation tasks. Furthermore, it ensures that the produced results in the community are reproducible and provide a fair comparison of developed methods. In this paper, we benchmark several recent state-of-the-art methods using Kvasir-SEG, an open-access dataset of colonoscopy images for polyp detection, localisation, and segmentation evaluating both method accuracy and speed. Whilst, most methods in literature have competitive performance over accuracy, we show that the proposed ColonSegNet achieved a better trade-off between an average precision of 0.8000 and mean IoU of 0.8100, and the fastest speed of 180 frames per second for the detection and localisation task. Likewise, the proposed ColonSegNet achieved a competitive dice coefficient of 0.8206 and the best average speed of 182.38 frames per second for the segmentation task. Our comprehensive comparison with various state-of-the-art methods reveals the importance of benchmarking the deep learning methods for automated real-time polyp identification and delineations that can potentially transform current clinical practices and minimise miss-detection rates.