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Yong MP, Hum YC, Lai KW, Lee YL, Goh CH, Yap WS, Tee YK. Histopathological Gastric Cancer Detection on GasHisSDB Dataset Using Deep Ensemble Learning. Diagnostics (Basel) 2023; 13:diagnostics13101793. [PMID: 37238277 DOI: 10.3390/diagnostics13101793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/08/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] [Imported: 08/29/2023] Open
Abstract
Gastric cancer is a leading cause of cancer-related deaths worldwide, underscoring the need for early detection to improve patient survival rates. The current clinical gold standard for detection is histopathological image analysis, but this process is manual, laborious, and time-consuming. As a result, there has been growing interest in developing computer-aided diagnosis to assist pathologists. Deep learning has shown promise in this regard, but each model can only extract a limited number of image features for classification. To overcome this limitation and improve classification performance, this study proposes ensemble models that combine the decisions of several deep learning models. To evaluate the effectiveness of the proposed models, we tested their performance on the publicly available gastric cancer dataset, Gastric Histopathology Sub-size Image Database. Our experimental results showed that the top 5 ensemble model achieved state-of-the-art detection accuracy in all sub-databases, with the highest detection accuracy of 99.20% in the 160 × 160 pixels sub-database. These results demonstrated that ensemble models could extract important features from smaller patch sizes and achieve promising performance. Overall, our proposed work could assist pathologists in detecting gastric cancer through histopathological image analysis and contribute to early gastric cancer detection to improve patient survival rates.
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Affiliation(s)
- Ming Ping Yong
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Yan Chai Hum
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Khin Wee Lai
- Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Ying Loong Lee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Choon-Hian Goh
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Wun-She Yap
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Yee Kai Tee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
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Larkin JR, Foo LS, Sutherland BA, Khrapitchev A, Tee YK. Magnetic Resonance pH Imaging in Stroke – Combining the Old With the New. Front Physiol 2022; 12:793741. [PMID: 35185600 PMCID: PMC8852727 DOI: 10.3389/fphys.2021.793741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] [Imported: 08/29/2023] Open
Abstract
The study of stroke has historically made use of traditional spectroscopy techniques to provide the ground truth for parameters like pH. However, techniques like 31P spectroscopy have limitations, in particular poor temporal and spatial resolution, coupled with a need for a high field strength and specialized coils. More modern magnetic resonance spectroscopy (MRS)-based imaging techniques like chemical exchange saturation transfer (CEST) have been developed to counter some of these limitations but lack the definitive gold standard for pH that 31P spectroscopy provides. In this perspective, both the traditional (31P spectroscopy) and emerging (CEST) techniques in the measurement of pH for ischemic imaging will be discussed. Although each has its own advantages and limitations, it is likely that CEST may be preferable simply due to the hardware, acquisition time and image resolution advantages. However, more experiments on CEST are needed to determine the specificity of endogenous CEST to absolute pH, and 31P MRS can be used to calibrate CEST for pH measurement in the preclinical model to enhance our understanding of the relationship between CEST and pH. Combining the two imaging techniques, one old and one new, we may be able to obtain new insights into stroke physiology that would not be possible otherwise with either alone.
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Affiliation(s)
- James R. Larkin
- Department of Oncology, Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
- *Correspondence: James R. Larkin,
| | - Lee Sze Foo
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Brad A. Sutherland
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Alexandre Khrapitchev
- Department of Oncology, Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Yee Kai Tee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
- Yee Kai Tee,
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Foo LS, Harston G, Mehndiratta A, Yap WS, Hum YC, Lai KW, Mohamed Mukari SA, Mohd Zaki F, Tee YK. Clinical translation of amide proton transfer (APT) MRI for ischemic stroke: a systematic review (2003-2020). Quant Imaging Med Surg 2021; 11:3797-3811. [PMID: 34341751 DOI: 10.21037/qims-20-1339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/22/2021] [Indexed: 12/15/2022] [Imported: 08/29/2023]
Abstract
Amide proton transfer (APT) magnetic resonance imaging (MRI) is a pH-sensitive imaging technique that can potentially complement existing clinical imaging protocol for the assessment of ischemic stroke. This review aims to summarize the developments in the clinical research of APT imaging of ischemic stroke after 17 years of progress since its first preclinical study in 2003. Three electronic databases: PubMed, Scopus, and Cochrane Library were systematically searched for articles reporting clinical studies on APT imaging of ischemic stroke. Only articles in English published between 2003 to 2020 that involved patients presenting ischemic stroke-like symptoms that underwent APT MRI were included. Of 1,093 articles screened, 14 articles met the inclusion criteria with a total of 282 patients that had been scanned using APT imaging. Generally, the clinical studies agreed APT effect to be hypointense in ischemic tissue compared to healthy tissue, allowing for the detection of ischemic stroke. Other uses of APT imaging have also been investigated in the studies, including penumbra identification, predicting long term clinical outcome, and serving as a biomarker for supportive treatment monitoring. The published results demonstrated the potential of APT imaging in these applications, but further investigations and larger trials are needed for conclusive evidence. Future studies are recommended to report the result of asymmetry analysis at 3.5 ppm along with the findings of the study to reduce this contribution to the heterogeneity of experimental methods observed and to facilitate effective comparison of results between studies and centers. In addition, it is important to focus on the development of fast 3D imaging for full volumetric ischemic tissue assessment for clinical translation.
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Affiliation(s)
- Lee Sze Foo
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | | | - Amit Mehndiratta
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India.,Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, India
| | - Wun-She Yap
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Yan Chai Hum
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Khin Wee Lai
- Faculty of Engineering, Department of Biomedical Engineering, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Faizah Mohd Zaki
- Department of Radiology, Universiti Kebangsaan Malaysia Medical Center (UKMMC), Kuala Lumpur, Malaysia
| | - Yee Kai Tee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
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Foo LS, Larkin JR, Sutherland BA, Ray KJ, Yap WS, Hum YC, Lai KW, Manan HA, Sibson NR, Tee YK. Study of common quantification methods of amide proton transfer magnetic resonance imaging for ischemic stroke detection. Magn Reson Med 2021; 85:2188-2200. [PMID: 33107119 DOI: 10.1002/mrm.28565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022] [Imported: 08/29/2023]
Abstract
PURPOSE To assess the correlation and differences between common amide proton transfer (APT) quantification methods in the diagnosis of ischemic stroke. METHODS Five APT quantification methods, including asymmetry analysis and its variants as well as two Lorentzian model-based methods, were applied to data acquired from six rats that underwent middle cerebral artery occlusion scanned at 9.4T. Diffusion and perfusion-weighted images, and water relaxation time maps were also acquired to study the relationship of these conventional imaging modalities with the different APT quantification methods. RESULTS The APT ischemic area estimates had varying sizes (Jaccard index: 0.544 ≤ J ≤ 0.971) and had varying correlations in their distributions (Pearson correlation coefficient: 0.104 ≤ r ≤ 0.995), revealing discrepancies in the quantified ischemic areas. The Lorentzian methods produced the highest contrast-to-noise ratios (CNRs; 1.427 ≤ CNR ≤ 2.002), but generated APT ischemic areas that were comparable in size to the cerebral blood flow (CBF) deficit areas; asymmetry analysis and its variants produced APT ischemic areas that were smaller than the CBF deficit areas but larger than the apparent diffusion coefficient deficit areas, though having lower CNRs (0.561 ≤ CNR ≤ 1.083). CONCLUSION There is a need to further investigate the accuracy and correlation of each quantification method with the pathophysiology using a larger scale multi-imaging modality and multi-time-point clinical study. Future studies should include the magnetization transfer ratio asymmetry results alongside the findings of the study to facilitate the comparison of results between different centers and also the published literature.
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Affiliation(s)
- Lee Sze Foo
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - James R Larkin
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Brad A Sutherland
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kevin J Ray
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Wun-She Yap
- Department of Electrical and Electronic Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - Yan Chai Hum
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - Khin Wee Lai
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Jalan Universiti, Kuala Lumpur, Malaysia
| | - Hanani Abdul Manan
- Department of Radiology, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Nicola R Sibson
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Yee Kai Tee
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
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Foo LS, Yap WS, Hum YC, Manan HA, Tee YK. Analysis of model-based and model-free CEST effect quantification methods for different medical applications. J Magn Reson 2020; 310:106648. [PMID: 31760147 DOI: 10.1016/j.jmr.2019.106648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023] [Imported: 08/29/2023]
Abstract
Chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) holds great potential to provide new metabolic information for clinical applications such as tumor, stroke and Parkinson's Disease diagnosis. Many active research and developments have been conducted to translate this emerging MRI technique for routine clinical applications. In general, there are two CEST quantification techniques: (i) model-free and (ii) model-based techniques. The reliability of these quantification techniques depends heavily on the experimental conditions and quality of the collected data. Errors such as noise may lead to misleading quantification results and thus inaccurate diagnosis when CEST imaging becomes a standard or routine imaging scan in the future. This paper investigates the accuracy and robustness of these quantification techniques under different signal-to-noise (SNR) levels and magnetic field strengths. The quantified CEST effect before and after adding random Gaussian White Noise using model-free and model-based quantification techniques were compared. It was found that the model-free technique consistently yielded larger average percentage error across all tested parameters compared to its model-based counterpart, and that the model-based technique could withstand SNR of about 3 times lower than the model-free technique. When applied on noisy brain tumor, ischemic stroke, and Parkinson's Disease clinical data, the model-free technique failed to produce significant differences between normal and abnormal tissue whereas the model-based technique consistently generated significant differences. Although the model-free technique was less accurate and robust, its simplicity and thus speed would still make it a good approximate when the SNR was high (>50) or when the CEST effect was large and well-defined. For more accurate CEST quantification, model-based techniques should be considered. When SNR was low (<50) and the CEST effect was small such as those acquired from clinical field strength scanners, which are generally 3T and below, model-based techniques should be considered over model-free counterpart to maintain an average percentage error of less than 44% even under very noisy condition as tested in this work.
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Affiliation(s)
- Lee Sze Foo
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Malaysia
| | - Wun-She Yap
- Department of Electrical and Electronic Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Malaysia
| | - Yan Chai Hum
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Malaysia
| | - Hanani Abdul Manan
- Department of Radiology, Universiti Kebangsaan Malaysia Medical Centre, Malaysia
| | - Yee Kai Tee
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Malaysia.
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Tee YK, Harston GWJ, Blockley N, Okell TW, Levman J, Sheerin F, Cellerini M, Jezzard P, Kennedy J, Payne SJ, Chappell MA. Comparing different analysis methods for quantifying the MRI amide proton transfer (APT) effect in hyperacute stroke patients. NMR Biomed 2014; 27:1019-29. [PMID: 24913989 PMCID: PMC4737232 DOI: 10.1002/nbm.3147] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 05/06/2014] [Accepted: 05/07/2014] [Indexed: 05/08/2023] [Imported: 08/29/2023]
Abstract
Amide proton transfer (APT) imaging is a pH mapping method based on the chemical exchange saturation transfer phenomenon that has potential for penumbra identification following stroke. The majority of the literature thus far has focused on generating pH-weighted contrast using magnetization transfer ratio asymmetry analysis instead of quantitative pH mapping. In this study, the widely used asymmetry analysis and a model-based analysis were both assessed on APT data collected from healthy subjects (n = 2) and hyperacute stroke patients (n = 6, median imaging time after onset = 2 hours 59 minutes). It was found that the model-based approach was able to quantify the APT effect with the lowest variation in grey and white matter (≤ 13.8 %) and the smallest average contrast between these two tissue types (3.48 %) in the healthy volunteers. The model-based approach also performed quantitatively better than the other measures in the hyperacute stroke patient APT data, where the quantified APT effect in the infarct core was consistently lower than in the contralateral normal appearing tissue for all the patients recruited, with the group average of the quantified APT effect being 1.5 ± 0.3 % (infarct core) and 1.9 ± 0.4 % (contralateral). Based on the fitted parameters from the model-based analysis and a previously published pH and amide proton exchange rate relationship, quantitative pH maps for hyperacute stroke patients were generated, for the first time, using APT imaging.
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Affiliation(s)
- Y. K. Tee
- Institute of Biomedical Engineering, Department of Engineering ScienceUniversity of OxfordOxfordUK
- Centre for Doctoral Training in Healthcare InnovationUniversity of OxfordOxfordUK
| | | | - N. Blockley
- Oxford Centre of Functional MRI of the Brain, Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Thomas W. Okell
- Oxford Centre of Functional MRI of the Brain, Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - J. Levman
- Institute of Biomedical Engineering, Department of Engineering ScienceUniversity of OxfordOxfordUK
| | - F. Sheerin
- Department of NeuroradiologyOxford University Hospitals NHS TrustOxfordUK
| | - M. Cellerini
- Department of NeuroradiologyOxford University Hospitals NHS TrustOxfordUK
| | - P. Jezzard
- Oxford Centre of Functional MRI of the Brain, Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - J. Kennedy
- Acute Stroke ProgrammeRadcliffe Department of MedicineOxfordUK
| | - S. J. Payne
- Institute of Biomedical Engineering, Department of Engineering ScienceUniversity of OxfordOxfordUK
| | - M. A. Chappell
- Institute of Biomedical Engineering, Department of Engineering ScienceUniversity of OxfordOxfordUK
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Tee YK, Donahue MJ, Harston GWJ, Payne SJ, Chappell MA. Quantification of amide proton transfer effect pre- and post-gadolinium contrast agent administration. J Magn Reson Imaging 2013; 40:832-8. [PMID: 24214526 DOI: 10.1002/jmri.24441] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/10/2013] [Indexed: 12/30/2022] [Imported: 08/29/2023] Open
Abstract
PURPOSE To compare quantification of the amide proton transfer (APT) effect pre- and post-gadolinium contrast agent (Gd) administration in order to establish to what extent Gd alters quantification of the APT effect. MATERIALS AND METHODS Four patients with internal carotid stenosis were recruited. APT imaging was acquired pre- and post-contrast in two sessions (before and after surgery) to assess the extent of relaxation time, T1 , change on APT effect calculated using magnetization transfer ratio asymmetry analysis at offsets of ±3.5 ppm relative to water resonance. Statistical and modeling evaluations were performed on the pre- and post-contrast APT effect to study the sensitivity to contrast administration. RESULTS Before surgery, the post-contrast T1 was estimated to drop <10% of the pre-value for the majority of the patients. After surgery, higher post-contrast T1 reductions were observed in all the patients (maximum decrease was about 20% of the pre-value). Consistent differences between pre- and post-contrast were seen in the APT effect quantified using the asymmetry measure in most regions of the brain, with significant differences found in the white matter at the group level and in 25% of the individual patient results. CONCLUSION APT imaging should be performed prior to Gd administration to avoid potential misinterpretation of the APT effect.
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Affiliation(s)
- Yee Kai Tee
- Institute of Biomedical Engineering Department of Engineering Science, University of Oxford, UK; Centre for Doctoral Training in Healthcare Innovation, University of Oxford, UK
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