Circle Representation for Medical Object Detection

GloFinder: AI-empowered QuPath plugin for WSI-level glomerular detection, visualization, and curation

Artificial intelligence (AI) has demonstrated significant success in automating the detection of glomeruli-key functional units of the kidney-from whole slide images (WSIs) in kidney pathology. However, existing open-source tools are often distributed as source code or Docker containers, requiring advanced programming skills that hinder accessibility for non-programmers, such as clinicians. Additionally, current models are typically trained on a single dataset and lack flexibility in adjusting confidence levels for predictions. To overcome these challenges, we introduce GloFinder, a QuPath plugin designed for single-click automated glomerular detection across entire WSIs with online editing through the graphical user interface. GloFinder employs CircleNet, an anchor-free detection framework utilizing circle representations for precise object localization, with models trained on approximately 160,000 manually annotated glomeruli. To further enhance accuracy, the plugin incorporates weighted circle fusion-an ensemble method that combines confidence scores from multiple CircleNet models to produce refined predictions, achieving superior performance in glomerular detection. GloFinder enables direct visualization and editing of results in QuPath, facilitating seamless interaction for clinicians and providing a powerful tool for nephropathology research and clinical practice.

Computational pathology: A survey review and the way forward

Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.

Intracranial aneurysm detection: an object detection perspective

PURPOSE

Intracranial aneurysm detection from 3D Time-Of-Flight Magnetic Resonance Angiography images is a problem of increasing clinical importance. Recently, a streak of methods have shown promising performance by using segmentation neural networks. However, these methods may be less relevant in a clinical settings where diagnostic decisions rely on detecting objects rather than their segmentation.

METHODS

We introduce a 3D single-stage object detection method tailored for small object detection such as aneurysms. Our anchor-free method incorporates fast data annotation, adapted data sampling and generation to address class imbalance problem, and spherical representations for improved detection.

RESULTS

A comprehensive evaluation was conducted, comparing our method with the state-of-the-art SCPM-Net, nnDetection and nnUNet baselines, using two datasets comprising 402 subjects. The evaluation used adapted object detection metrics. Our method exhibited comparable or superior performance, with an average precision of 78.96%, sensitivity of 86.78%, and 0.53 false positives per case.

CONCLUSION

Our method significantly reduces the detection complexity compared to existing methods and highlights the advantages of object detection over segmentation-based approaches for aneurysm detection. It also holds potential for application to other small object detection problems.

CRDet: A circle representation detector for lung granulomas based on multi-scale attention features with center point calibration

Lung granuloma is a very common lung disease, and its specific diagnosis is important for determining the exact cause of the disease as well as the prognosis of the patient. And, an effective lung granuloma detection model based on computer-aided diagnostics (CAD) can help pathologists to localize granulomas, thereby improving the efficiency of the specific diagnosis. However, for lung granuloma detection models based on CAD, the significant size differences between granulomas and how to better utilize the morphological features of granulomas are both critical challenges to be addressed. In this paper, we propose an automatic method CRDet to localize granulomas in histopathological images and deal with these challenges. We first introduce the multi-scale feature extraction network with self-attention to extract features at different scales at the same time. Then, the features will be converted to circle representations of granulomas by circle representation detection heads to achieve the alignment of features and ground truth. In this way, we can also more effectively use the circular morphological features of granulomas. Finally, we propose a center point calibration method at the inference stage to further optimize the circle representation. For model evaluation, we built a lung granuloma circle representation dataset named LGCR, including 288 images from 50 subjects. Our method yielded 0.316 mAP and 0.571 mAR, outperforming the state-of-the-art object detection methods on our proposed LGCR.

Development and Validation of a Deep-Learning Network for Detecting Congenital Heart Disease from Multi-View Multi-Modal Transthoracic Echocardiograms

Early detection and treatment of congenital heart disease (CHD) can significantly improve the prognosis of children. However, inexperienced sonographers often face difficulties in recognizing CHD through transthoracic echocardiogram (TTE) images. In this study, 2-dimensional (2D) and Doppler TTEs of children collected from 2 clinical groups from Beijing Children's Hospital between 2018 and 2022 were analyzed, including views of apical 4 chamber, subxiphoid long-axis view of 2 atria, parasternal long-axis view of the left ventricle, parasternal short-axis view of aorta, and suprasternal long-axis view. A deep learning (DL) framework was developed to identify cardiac views, integrate information from various views and modalities, visualize the high-risk region, and predict the probability of the subject being normal or having an atrial septal defect (ASD) or a ventricular septaldefect (VSD). A total of 1,932 children (1,255 healthy controls, 292 ASDs, and 385 VSDs) were collected from 2 clinical groups. For view classification, the DL model reached a mean [SD] accuracy of 0.989 [0.001]. For CHD screening, the model using both 2D and Doppler TTEs with 5 views achieved a mean [SD] area under the receiver operating characteristic curve (AUC) of 0.996 [0.000] and an accuracy of 0.994 [0.002] for within-center evaluation while reaching a mean [SD] AUC of 0.990 [0.003] and an accuracy of 0.993 [0.001] for cross-center test set. For the classification of healthy, ASD, and VSD, the model reached the mean [SD] accuracy of 0.991 [0.002] and 0.986 [0.001] for within- and cross-center evaluation, respectively. The DL models aggregating TTEs with more modalities and scanning views attained superior performance to approximate that of experienced sonographers. The incorporation of multiple views and modalities of TTEs in the model enables accurate identification of children with CHD in a noninvasive manner, suggesting the potential to enhance CHD detection performance and simplify the screening process.

From WSI-level to patch-level: Structure prior-guided binuclear cell fine-grained detection

Accurate and quick binuclear cell (BC) detection plays a significant role in predicting the risk of leukemia and other malignant tumors. However, manual counting of BCs using microscope images is time consuming and subjective. Moreover, traditional image processing approaches perform poorly due to the limitations in staining quality and the diversity of morphological features in binuclear cell (BC) microscopy whole-slide images (WSIs). To overcome this challenge, we propose a multi-task method inspired by the structure prior of BCs based on deep learning, which cascades to implement BC coarse detection at the WSI level and fine-grained classification at the patch level. The coarse detection network is a multitask detection framework based on circular bounding boxes for cell detection and central key points for nucleus detection. Circle representation reduces the degrees of freedom, mitigates the effect of surrounding impurities compared to usual rectangular boxes and can be rotation invariant in WSIs. Detecting key points in the nucleus can assist in network perception and be used for unsupervised color layer segmentation in later fine-grained classification. The fine classification network consists of a background region suppression module based on color layer mask supervision and a key region selection module based on a transformer due to its global modeling capability. Additionally, an unsupervised and unpaired cytoplasm generator network is first proposed to expand the long-tailed distribution dataset. Finally, experiments are performed on BC multicenter datasets. The proposed BC fine detection method outperforms other benchmarks in almost all evaluation criteria, providing clarification and support for tasks such as cancer screenings.

Inflating 2D convolution weights for efficient generation of 3D medical images

BACKGROUND AND OBJECTIVE

The generation of three-dimensional (3D) medical images has great application potential since it takes into account the 3D anatomical structure. Two problems prevent effective training of a 3D medical generative model: (1) 3D medical images are expensive to acquire and annotate, resulting in an insufficient number of training images, and (2) a large number of parameters are involved in 3D convolution.

METHODS

We propose a novel GAN model called 3D Split&Shuffle-GAN. To address the 3D data scarcity issue, we first pre-train a two-dimensional (2D) GAN model using abundant image slices and inflate the 2D convolution weights to improve the initialization of the 3D GAN. Novel 3D network architectures are proposed for both the generator and discriminator of the GAN model to significantly reduce the number of parameters while maintaining the quality of image generation. Several weight inflation strategies and parameter-efficient 3D architectures are investigated.

RESULTS

Experiments on both heart (Stanford AIMI Coronary Calcium) and brain (Alzheimer's Disease Neuroimaging Initiative) datasets show that our method leads to improved 3D image generation quality (14.7 improvements on Frchet inception distance) with significantly fewer parameters (only 48.5% of the baseline method).

CONCLUSIONS

We built a parameter-efficient 3D medical image generation model. Due to the efficiency and effectiveness, it has the potential to generate high-quality 3D brain and heart images for real use cases.

A Fast Circle Detection Algorithm Based on Circular Arc Feature Screening

Circle detection is a crucial problem in computer vision and pattern recognition. In this paper, we propose a fast circle detection algorithm based on circular arc feature screening. In order to solve the invalid sampling and time consumption of the traditional circle detection algorithms, we improve the fuzzy inference edge detection algorithm by adding main contour edge screening, edge refinement, and arc-like determination to enhance edge positioning accuracy and remove unnecessary contour edges. Then, we strengthen the arc features with step-wise sampling on two feature matrices and set auxiliary points for defective circles. Finally, we built a square verification support region to further find the true circle with the complete circle and defective circle constraints. Extensive experiments were conducted on complex images, including defective, blurred-edge, and interfering images from four diverse datasets (three publicly available and one we built). The experimental results show that our method can remove up to 89.03% of invalid edge points by arc feature filtering and is superior to RHT, RCD, Jiang, Wang, and CACD in terms of speed, accuracy, and robustness.

An Anti-Noise Fast Circle Detection Method Using Five-Quadrant Segmentation

Extracting circle information from images has always been a basic problem in computer vision. Common circle detection algorithms have some defects, such as poor noise resistance and slow computation speed. In this paper, we propose an anti-noise fast circle detection algorithm. In order to improve the anti-noise of the algorithm, we first perform curve thinning and connection on the image after edge extraction, then suppress noise interference by the irregularity of noise edges and extract circular arcs by directional filtering. In order to reduce the invalid fitting and speed up the running speed, we propose a circle fitting algorithm with five quadrants, and improve the efficiency of the algorithm by the idea of "divide and conquer". We compare the algorithm with RCD, CACD, WANG and AS on two open datasets. The results show that we have the best performance under noise while keeping the speed of the algorithm.

Artificial intelligence for early detection of renal cancer in computed tomography: A review

Renal cancer is responsible for over 100,000 yearly deaths and is principally discovered in computed tomography (CT) scans of the abdomen. CT screening would likely increase the rate of early renal cancer detection, and improve general survival rates, but it is expected to have a prohibitively high financial cost. Given recent advances in artificial intelligence (AI), it may be possible to reduce the cost of CT analysis and enable CT screening by automating the radiological tasks that constitute the early renal cancer detection pipeline. This review seeks to facilitate further interdisciplinary research in early renal cancer detection by summarising our current knowledge across AI, radiology, and oncology and suggesting useful directions for future novel work. Initially, this review discusses existing approaches in automated renal cancer diagnosis, and methods across broader AI research, to summarise the existing state of AI cancer analysis. Then, this review matches these methods to the unique constraints of early renal cancer detection and proposes promising directions for future research that may enable AI-based early renal cancer detection via CT screening. The primary targets of this review are clinicians with an interest in AI and data scientists with an interest in the early detection of cancer.

CroReLU: Cross-Crossing Space-Based Visual Activation Function for Lung Cancer Pathology Image Recognition

Lung cancer is one of the most common malignant tumors in human beings. It is highly fatal, as its early symptoms are not obvious. In clinical medicine, physicians rely on the information provided by pathology tests as an important reference for the final diagnosis of many diseases. Therefore, pathology diagnosis is known as the gold standard for disease diagnosis. However, the complexity of the information contained in pathology images and the increase in the number of patients far outpace the number of pathologists, especially for the treatment of lung cancer in less developed countries. To address this problem, we propose a plug-and-play visual activation function (AF), CroReLU, based on a priori knowledge of pathology, which makes it possible to use deep learning models for precision medicine. To the best of our knowledge, this work is the first to optimize deep learning models for pathology image diagnosis from the perspective of AFs. By adopting a unique crossover window design for the activation layer of the neural network, CroReLU is equipped with the ability to model spatial information and capture histological morphological features of lung cancer such as papillary, micropapillary, and tubular alveoli. To test the effectiveness of this design, 776 lung cancer pathology images were collected as experimental data. When CroReLU was inserted into the SeNet network (SeNet_CroReLU), the diagnostic accuracy reached 98.33%, which was significantly better than that of common neural network models at this stage. The generalization ability of the proposed method was validated on the LC25000 dataset with completely different data distribution and recognition tasks in the face of practical clinical needs. The experimental results show that CroReLU has the ability to recognize inter- and intra-class differences in cancer pathology images, and that the recognition accuracy exceeds the extant research work on the complex design of network layers.

Glo-In-One: holistic glomerular detection, segmentation, and lesion characterization with large-scale web image mining

Purpose: The quantitative detection, segmentation, and characterization of glomeruli from high-resolution whole slide imaging (WSI) play essential roles in the computer-assisted diagnosis and scientific research in digital renal pathology. Historically, such comprehensive quantification requires extensive programming skills to be able to handle heterogeneous and customized computational tools. To bridge the gap of performing glomerular quantification for non-technical users, we develop the Glo-In-One toolkit to achieve holistic glomerular detection, segmentation, and characterization via a single line of command. Additionally, we release a large-scale collection of 30,000 unlabeled glomerular images to further facilitate the algorithmic development of self-supervised deep learning. Approach: The inputs of the Glo-In-One toolkit are WSIs, while the outputs are (1) WSI-level multi-class circle glomerular detection results (which can be directly manipulated with ImageScope), (2) glomerular image patches with segmentation masks, and (3) different lesion types. In the current version, the fine-grained global glomerulosclerosis (GGS) characterization is provided, including assessed-solidified-GSS (associated with hypertension-related injury), disappearing-GSS (a further end result of the SGGS becoming contiguous with fibrotic interstitium), and obsolescent-GSS (nonspecific GGS increasing with aging) glomeruli. To leverage the performance of the Glo-In-One toolkit, we introduce self-supervised deep learning to glomerular quantification via large-scale web image mining. Results: The GGS fine-grained classification model achieved a decent performance compared with baseline supervised methods while only using 10% of the annotated data. The glomerular detection achieved an average precision of 0.627 with circle representations, while the glomerular segmentation achieved a 0.955 patch-wise Dice dimilarity coefficient. Conclusion: We develop and release an open-source Glo-In-One toolkit, a software with holistic glomerular detection, segmentation, and lesion characterization. This toolkit is user-friendly to non-technical users via a single line of command. The toolbox and the 30,000 web mined glomerular images have been made publicly available at https://github.com/hrlblab/Glo-In-One.