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Kuş Z, Aydin M. MedSegBench: A comprehensive benchmark for medical image segmentation in diverse data modalities. Sci Data 2024; 11:1283. [PMID: 39587124 PMCID: PMC11589128 DOI: 10.1038/s41597-024-04159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 11/19/2024] [Indexed: 11/27/2024] Open
Abstract
MedSegBench is a comprehensive benchmark designed to evaluate deep learning models for medical image segmentation across a wide range of modalities. It covers a wide range of modalities, including 35 datasets with over 60,000 images from ultrasound, MRI, and X-ray. The benchmark addresses challenges in medical imaging by providing standardized datasets with train/validation/test splits, considering variability in image quality and dataset imbalances. The benchmark supports binary and multi-class segmentation tasks with up to 19 classes and uses the U-Net architecture with various encoder/decoder networks such as ResNets, EfficientNet, and DenseNet for evaluations. MedSegBench is a valuable resource for developing robust and flexible segmentation algorithms and allows for fair comparisons across different models, promoting the development of universal models for medical tasks. It is the most comprehensive study among medical segmentation datasets. The datasets and source code are publicly available, encouraging further research and development in medical image analysis.
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Affiliation(s)
- Zeki Kuş
- Fatih Sultan Mehmet Vakif University, Computer Engineering, İstanbul, 34445, Türkiye.
| | - Musa Aydin
- Fatih Sultan Mehmet Vakif University, Computer Engineering, İstanbul, 34445, Türkiye
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Wang Q, Han X, Song L, Zhang X, Zhang B, Gu Z, Jiang B, Li C, Li X, Yu Y. Automatic quality assessment of knee radiographs using knowledge graphs and convolutional neural networks. Med Phys 2024; 51:7464-7478. [PMID: 39016559 DOI: 10.1002/mp.17316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND X-ray radiography is a widely used imaging technique worldwide, and its image quality directly affects diagnostic accuracy. Therefore, X-ray image quality control (QC) is essential. However, subjectively assessing image quality is inefficient and inconsistent, especially when large amounts of image data are being evaluated. Thus, subjective assessment cannot meet current QC needs. PURPOSE To meet current QC needs and improve the efficiency of image quality assessment, a complete set of quality assessment criteria must be established and implemented using artificial intelligence (AI) technology. Therefore, we proposed a multi-criteria AI system for automatically assessing the image quality of knee radiographs. METHODS A knee radiograph QC knowledge graph containing 16 "acquisition technique" labels representing 16 image quality defects and five "clarity" labels representing five grades of clarity were developed. Ten radiographic technologists conducted three rounds of QC based on this graph. The single-person QC results were denoted as QC1 and QC2, and the multi-person QC results were denoted as QC3. Each technologist labeled each image only once. The ResNet model structure was then used to simultaneously perform classification (detection of image quality defects) and regression (output of a clarity score) tasks to construct an image QC system. The QC3 results, comprising 4324 anteroposterior and lateral knee radiographs, were used for model training (70% of the images), validation (10%), and testing (20%). The 865 test set data were used to evaluate the effectiveness of the AI model, and an AI QC result, QC4, was automatically generated by the model after training. Finally, using a double-blind method, the senior QC expert reviewed the final QC results of the test set with reference to the results QC3 and QC4 and used them as a reference standard to evaluate the performance of the model. The precision and mean absolute error (MAE) were used to evaluate the quality of all the labels in relation to the reference standard. RESULTS For the 16 "acquisition technique" features, QC4 exhibited the highest weighted average precision (98.42% ± 0.81%), followed by QC3 (91.39% ± 1.35%), QC2 (87.84% ± 1.68%), and QC1 (87.35% ± 1.71%). For the image clarity features, the MAEs between QC1, QC2, QC3, and QC4 and the reference standard were 0.508 ± 0.021, 0.475 ± 0.019, 0.237 ± 0.016, and 0.303 ± 0.018, respectively. CONCLUSIONS The experimental results show that our automated quality assessment system performed well in classifying the acquisition technique used for knee radiographs. The image clarity quality evaluation accuracy of the model must be further improved but is generally close to that of radiographic technologists. Intelligent QC methods using knowledge graphs and convolutional neural networks have the potential for clinical applications.
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Affiliation(s)
- Qian Wang
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiao Han
- College of Medical Information Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Liangliang Song
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xin Zhang
- College of Computer Science and Technology, Anhui University, Hefei, China
| | - Biao Zhang
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Artificial Intelligence Research Institute, Hefei Comprehensive National Science Center, Hefei, China
| | - Zongyun Gu
- College of Medical Information Engineering, Anhui University of Chinese Medicine, Hefei, China
- Artificial Intelligence Research Institute, Hefei Comprehensive National Science Center, Hefei, China
| | - Bo Jiang
- College of Computer Science and Technology, Anhui University, Hefei, China
| | - Chuanfu Li
- College of Medical Information Engineering, Anhui University of Chinese Medicine, Hefei, China
- Artificial Intelligence Research Institute, Hefei Comprehensive National Science Center, Hefei, China
- Anhui Provincial Imaging Diagnosis Quality Control Center, Anhui Provincial Health Commission, Hefei, China
| | - Xiaohu Li
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Provincial Imaging Diagnosis Quality Control Center, Anhui Provincial Health Commission, Hefei, China
| | - Yongqiang Yu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Provincial Imaging Diagnosis Quality Control Center, Anhui Provincial Health Commission, Hefei, China
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Singh SB, Sarrami AH, Gatidis S, Varniab ZS, Chaudhari A, Daldrup-Link HE. Applications of Artificial Intelligence for Pediatric Cancer Imaging. AJR Am J Roentgenol 2024; 223:e2431076. [PMID: 38809123 PMCID: PMC11874589 DOI: 10.2214/ajr.24.31076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Artificial intelligence (AI) is transforming the medical imaging of adult patients. However, its utilization in pediatric oncology imaging remains constrained, in part due to the inherent scarcity of data associated with childhood cancers. Pediatric cancers are rare, and imaging technologies are evolving rapidly, leading to insufficient data of a particular type to effectively train these algorithms. The small market size of pediatric patients compared with adult patients could also contribute to this challenge, as market size is a driver of commercialization. This review provides an overview of the current state of AI applications for pediatric cancer imaging, including applications for medical image acquisition, processing, reconstruction, segmentation, diagnosis, staging, and treatment response monitoring. Although current developments are promising, impediments due to the diverse anatomies of growing children and nonstandardized imaging protocols have led to limited clinical translation thus far. Opportunities include leveraging reconstruction algorithms to achieve accelerated low-dose imaging and automating the generation of metric-based staging and treatment monitoring scores. Transfer learning of adult-based AI models to pediatric cancers, multiinstitutional data sharing, and ethical data privacy practices for pediatric patients with rare cancers will be keys to unlocking the full potential of AI for clinical translation and improving outcomes for these young patients.
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Affiliation(s)
- Shashi B. Singh
- Department of Radiology, Division of Pediatric Radiology, Stanford University School of Medicine, 1201 Welch Rd, Stanford, CA 94305
| | - Amir H. Sarrami
- Department of Radiology, Division of Pediatric Radiology, Stanford University School of Medicine, 1201 Welch Rd, Stanford, CA 94305
| | - Sergios Gatidis
- Department of Radiology, Division of Pediatric Radiology, Stanford University School of Medicine, 1201 Welch Rd, Stanford, CA 94305
| | - Zahra S. Varniab
- Department of Radiology, Division of Pediatric Radiology, Stanford University School of Medicine, 1201 Welch Rd, Stanford, CA 94305
| | - Akshay Chaudhari
- Department of Radiology, Integrative Biomedical Imaging Informatics (IBIIS), Stanford University School of Medicine, Stanford University, Stanford, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford University, Stanford, CA
| | - Heike E. Daldrup-Link
- Department of Radiology, Division of Pediatric Radiology, Stanford University School of Medicine, 1201 Welch Rd, Stanford, CA 94305
- Department of Pediatrics, Pediatric Hematology-Oncology, Lucile Packard Children’s Hospital, Stanford University, Stanford, CA
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Hopson JB, Neji R, Dunn JT, McGinnity CJ, Flaus A, Reader AJ, Hammers A. Pre-training via Transfer Learning and Pretext Learning a Convolutional Neural Network for Automated Assessments of Clinical PET Image Quality. IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES 2023; 7:372-381. [PMID: 37051163 PMCID: PMC7614424 DOI: 10.1109/trpms.2022.3231702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Positron emission tomography (PET) using a fraction of the usual injected dose would reduce the amount of radioligand needed, as well as the radiation dose to patients and staff, but would compromise reconstructed image quality. For performing the same clinical tasks with such images, a clinical (rather than numerical) image quality assessment is essential. This process can be automated with convolutional neural networks (CNNs). However, the scarcity of clinical quality readings is a challenge. We hypothesise that exploiting easily available quantitative information in pretext learning tasks or using established pre-trained networks could improve CNN performance for predicting clinical assessments with limited data. CNNs were pre-trained to predict injected dose from image patches extracted from eight real patient datasets, reconstructed using between 0.5%-100% of the available data. Transfer learning with seven different patients was used to predict three clinically-scored quality metrics ranging from 0-3: global quality rating, pattern recognition and diagnostic confidence. This was compared to pre-training via a VGG16 network at varying pre-training levels. Pre-training improved test performance for this task: the mean absolute error of 0.53 (compared to 0.87 without pre-training), was within clinical scoring uncertainty. Future work may include using the CNN for novel reconstruction methods performance assessment.
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Affiliation(s)
| | | | - Joel T Dunn
- King's College London & Guy's and St Thomas' PET Centre, King's College London
| | - Colm J McGinnity
- King's College London & Guy's and St Thomas' PET Centre, King's College London
| | - Anthime Flaus
- King's College London & Guy's and St Thomas' PET Centre, King's College London
| | | | - Alexander Hammers
- King's College London & Guy's and St Thomas' PET Centre, King's College London
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Hu J, Zhang C, Zhou K, Gao S. Chest X-Ray Diagnostic Quality Assessment: How Much Is Pixel-Wise Supervision Needed? IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:1711-1723. [PMID: 35120002 DOI: 10.1109/tmi.2022.3149171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chest X-ray is an important imaging method for the diagnosis of chest diseases. Chest radiograph diagnostic quality assessment is vital for the diagnosis of the disease because unqualified radiographs have negative impacts on doctors' diagnosis and thus increase the burden on patients due to the re-acquirement of the radiographs. So far no algorithms and public data sets have been developed for chest radiograph diagnostic quality assessment. Towards effective chest X-ray diagnostic quality assessment, we analyze the image characteristics of four main chest radiograph diagnostic quality issues, i.e. Scapula Overlapping Lung, Artifact, Lung Field Loss, and Clavicle Unflatness. Our experiments show that general image classification methods are not competent for the task because the detailed information used for quality assessment by radiologists cannot be fully exploited by deep CNNs and image-level annotations. Then we propose to leverage a multi-label semantic segmentation framework to find the problematic regions, and then classify the quality issues based on the results of segmentation. However, subsequent classification is often negatively affected by certain small segmentation errors. Therefore, we propose to estimate a distance map that measures the distance from a pixel to its nearest segment, and use it to force the prediction of semantic segmentation more holistic and suitable for classification. Extensive experiments validate the effectiveness of our semantic-segmentation-based solution for chest X-ray diagnostic quality assessment. However, general segmentation-based algorithms requires fine pixel-wise annotations in the era of deep learning. In order to reduce reliance on fine annotations and further validate how important pixel-wise annotations are, weak supervision for segmentation is applied, and demonstrates its ability close to that of full supervision. Finally, we present ChestX-rayQuality, a chest radiograph data set, which comprises 480 frontal-view chest radiographs with semantic segmentation annotations and four labels of quality issue. Also, other 1212 chest radiographs with limited annotations are imported to validate our algorithms and arguments on larger data set. These two data set will be made publicly available.
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Lim A, Lo J, Wagner MW, Ertl-Wagner B, Sussman D. Automatic Artifact Detection Algorithm in Fetal MRI. Front Artif Intell 2022; 5:861791. [PMID: 35783351 PMCID: PMC9244144 DOI: 10.3389/frai.2022.861791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Fetal MR imaging is subject to artifacts including motion, chemical shift, and radiofrequency artifacts. Currently, such artifacts are detected by the MRI operator, a process which is subjective, time consuming, and prone to errors. We propose a novel algorithm, RISE-Net, that can consistently, automatically, and objectively detect artifacts in 3D fetal MRI. It makes use of a CNN ensemble approach where the first CNN aims to identify and classify any artifacts in the image, and the second CNN uses regression to determine the severity of the detected artifacts. The main mechanism in RISE-Net is the stacked Residual, Inception, Squeeze and Excitation (RISE) blocks. This classification network achieved an accuracy of 90.34% and a F1 score of 90.39% and outperformed other state-of-the-art architectures, such as VGG-16, Inception, ResNet-50, ReNet-Inception, SE-ResNet, and SE-Inception. The severity regression network had an MSE of 0.083 across all classes. The presented algorithm facilitates rapid and accurate fetal MRI quality assurance that can be implemented into clinical use.
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Affiliation(s)
- Adam Lim
- Department of Electrical, Computer and Biomedical Engineering, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, Canada
- Institute for Biomedical Engineering, Science and Technology (iBEST), Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, Canada
| | - Justin Lo
- Department of Electrical, Computer and Biomedical Engineering, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, Canada
- Institute for Biomedical Engineering, Science and Technology (iBEST), Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, Canada
| | - Matthias W. Wagner
- Division of Neuroradiology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Birgit Ertl-Wagner
- Division of Neuroradiology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Imaging, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Dafna Sussman
- Department of Electrical, Computer and Biomedical Engineering, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, Canada
- Institute for Biomedical Engineering, Science and Technology (iBEST), Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- *Correspondence: Dafna Sussman
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Sagawa H, Itagaki K, Matsushita T, Miyati T. Evaluation of motion artifacts in brain magnetic resonance images using convolutional neural network-based prediction of full-reference image quality assessment metrics. J Med Imaging (Bellingham) 2022; 9:015502. [PMID: 35106324 PMCID: PMC8782596 DOI: 10.1117/1.jmi.9.1.015502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/03/2022] [Indexed: 01/23/2023] Open
Abstract
Purpose: Motion artifacts in magnetic resonance (MR) images mostly undergo subjective evaluation, which is poorly reproducible, time consuming, and costly. Recently, full-reference image quality assessment (FR-IQA) metrics, such as structural similarity (SSIM), have been used, but they require a reference image and hence cannot be used to evaluate clinical images. We developed a convolutional neural network (CNN) model to quantify motion artifacts without using reference images. Approach: The brain MR images were obtained from an open dataset. The motion-corrupted images were generated retrospectively, and the peak signal-to-noise ratio, cross-correlation coefficient, and SSIM were calculated. The CNN was trained using these images and their FR-IQA metrics to predict the FR-IQA metrics without reference images. Receiver operating characteristic (ROC) curves were created for binary classification, with artifact scores < 4 indicating the need for rescanning. ROC curve analysis was performed on the binary classification of the real motion images. Results: The predicted FR-IQA metric having the highest correlation with the subjective evaluation was SSIM, which was able to classify images requiring rescanning with a sensitivity of 89.5%, specificity of 78.2%, and area under the ROC curve (AUC) of 0.930. The real motion artifacts were classified with the AUC of 0.928. Conclusions: Our CNN model predicts FR-IQA metrics with high accuracy, which enables quantitative assessment of motion artifacts in MR images without reference images. It enables classification of images requiring rescanning with a high AUC, which can improve the workflow of MR imaging examinations.
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Affiliation(s)
- Hajime Sagawa
- Kyoto University Hospital, Division of Clinical Radiology Service, Kyoto, Japan,Kanazawa University, Graduate School of Medical Sciences, Division of Health Sciences, Kanazawa, Japan,Address all correspondence to Hajime Sagawa,
| | - Koji Itagaki
- Kyoto University Hospital, Division of Clinical Radiology Service, Kyoto, Japan
| | - Tatsuhiko Matsushita
- Kyoto University Hospital, Division of Clinical Radiology Service, Kyoto, Japan,Kanazawa University, Pharmaceutical and Health Sciences, Institute of Medical, Faculty of Health Sciences, Kanazawa, Japan
| | - Tosiaki Miyati
- Kanazawa University, Graduate School of Medical Sciences, Division of Health Sciences, Kanazawa, Japan,Kanazawa University, Pharmaceutical and Health Sciences, Institute of Medical, Faculty of Health Sciences, Kanazawa, Japan
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Kalra MK, Rehani MM. Five-star rating system for acceptable quality and dose in CT. Eur Radiol 2021; 31:9161-9163. [PMID: 34114057 DOI: 10.1007/s00330-021-08112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 11/24/2022]
Abstract
KEY POINTS • Recent papers have shown examples of the methodology involved in integrating image quality with radiation dose and assessing acceptable quality dose (AQD).• As a further step in that direction, translating a 5-point score into a 5-star rating shall be helpful for wider and uniform application and shall be in line with the popular use of the 5-star rating.
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Affiliation(s)
- Mannudeep K Kalra
- Massachusetts General Hospital, 55 Fruit Str, Boston, MA, 02114, USA
| | - Madan M Rehani
- Massachusetts General Hospital, 55 Fruit Str, Boston, MA, 02114, USA. .,Radiology Department, Massachusetts General Hospital, 175 Cambridge Str., Suite 244, Boston, MA, 02114, USA.
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