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Wu Y, Qiu S, Groot ML, Zhang Z. Self-Supervised Image Denoising of Third Harmonic Generation Microscopic Images of Human Glioma Tissue by Transformer-Based Blind Spot (TBS) Network. IEEE J Biomed Health Inform 2024; 28:4688-4700. [PMID: 38801682 DOI: 10.1109/jbhi.2024.3405562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Third harmonic generation (THG) microscopy shows great potential for instant pathology of brain tumor tissue during surgery. However, due to the maximal permitted exposure of laser intensity and inherent noise of the imaging system, the noise level of THG images is relatively high, which affects subsequent feature extraction analysis. Denoising THG images is challenging for modern deep-learning based methods because of the rich morphologies contained and the difficulty in obtaining the noise-free counterparts. To address this, in this work, we propose an unsupervised deep-learning network for denoising of THG images which combines a self-supervised blind spot method and a U-shape Transformer using a dynamic sparse attention mechanism. The experimental results on THG images of human glioma tissue show that our approach exhibits superior denoising performance qualitatively and quantitatively compared with previous methods. Our model achieves an improvement of 2.47-9.50 dB in SNR and 0.37-7.40 dB in CNR, compared to six recent state-of-the-art unsupervised learning models including Neighbor2Neighbor, Blind2Unblind, Self2Self+, ZS-N2N, Noise2Info and SDAP. To achieve an objective evaluation of our model, we also validate our model on public datasets including natural and microscopic images, and our model shows a better denoising performance than several recent unsupervised models such as Neighbor2Neighbor, Blind2Unblind and ZS-N2N. In addition, our model is nearly instant in denoising a THG image, which has the potential for real-time applications of THG microscopy.
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Cicchi R, Baria E, Mari M, Filippidis G, Chorvat D. Extraction of collagen morphological features from second-harmonic generation microscopy images via GLCM and CT analyses: A cross-laboratory study. JOURNAL OF BIOPHOTONICS 2024:e202400090. [PMID: 38937995 DOI: 10.1002/jbio.202400090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/29/2024]
Abstract
Second-harmonic generation (SHG) microscopy provides a high-resolution label-free approach for noninvasively detecting collagen organization and its pathological alterations. Up to date, several imaging analysis algorithms for extracting collagen morphological features from SHG images-such as fiber size and length, order and anisotropy-have been developed. However, the dependence of extracted features on experimental setting represents a significant obstacle for translating the methodology in the clinical practice. We tackled this problem by acquiring SHG images of the same kind of collagenous sample in various laboratories using different experimental setups and imaging conditions. The acquired images were analyzed by commonly used algorithms, such as gray-level co-occurrence matrix or curvelet transform; the extracted morphological features were compared, finding that they strongly depend on some experimental parameters, whereas they are almost independent from others. We conclude with useful suggestions for comparing results obtained in different labs using different experimental setups and conditions.
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Affiliation(s)
- R Cicchi
- National Institute of Optics, National Research Council, Florence, Italy
- European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy
| | - E Baria
- European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - M Mari
- Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology-Hellas (FORTH), Crete, Greece
| | - G Filippidis
- Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology-Hellas (FORTH), Crete, Greece
| | - D Chorvat
- Department of Biophotonics, International Laser Centre (ILC), Slovak Centre of Scientific and Technical Information (SCSTI), Bratislava, Slovakia
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Mukherjee S, Dhar R, Jonnalagadda S, Gorai S, Nag S, Kar R, Mukerjee N, Mukherjee D, Vatsa R, Arikketh D, Krishnan A, Gundamaraju R, Jha SK, Alexiou A, Papadakis M. Exosomal miRNAs and breast cancer: a complex theranostics interlink with clinical significance. Biomarkers 2023; 28:502-518. [PMID: 37352015 DOI: 10.1080/1354750x.2023.2229537] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
Breast cancer (BC) remains the most challenging global health crisis of the current decade, impacting a large population of females annually. In the field of cancer research, the discovery of extracellular vesicles (EVs), specifically exosomes (a subpopulation of EVs), has marked a significant milestone. In general, exosomes are released from all active cells but tumour cell-derived exosomes (TDXs) have a great impact (TDXs miRNAs, proteins, lipid molecules) on cancer development and progression. TDXs regulate multiple events in breast cancer such as tumour microenvironment remodelling, immune cell suppression, angiogenesis, metastasis (EMT-epithelial mesenchymal transition, organ-specific metastasis), and therapeutic resistance. In BC, early detection is the most challenging event, exosome-based BC screening solved the problem. Exosome-based BC treatment is a sign of the transforming era of liquid biopsy, it is also a promising therapeutic tool for breast cancer. Exosome research goes to closer precision oncology via a single exosome profiling approach. Our hope is that this review will serve as motivation for researchers to explore the field of exosomes and develop an efficient, and affordable theranostics approach for breast cancer.
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Affiliation(s)
- Sayantanee Mukherjee
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Rajib Dhar
- Department of Genetic Engineering, Cancer and Stem Cell Biology Laboratory, SRM Institute of Science and Technology, Kattankulathur, India
| | | | - Sukhamoy Gorai
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Sagnik Nag
- Department of Biotechnology, School of Biosciences & Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - Rishav Kar
- Department of Medical Biotechnology, Ramakrishna Mission Vivekananda Educational and Research Institute, Belur Math,India
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Australia
| | | | - Rishabh Vatsa
- Department of Microbiology, Vels Institute of Science, Technology and Advanced Studies, Chennai, India
| | - Devi Arikketh
- Department of Genetic Engineering, Cancer and Stem Cell Biology Laboratory, SRM Institute of Science and Technology, Kattankulathur, India
| | - Anand Krishnan
- Department of Chemical Pathology, School of Pathology, University of the Free State, Bloemfontein, South Africa
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Laboratory, School of Health Sciences, University of Tasmania, Launceston, Australia
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, Australia
- AFNP Med, Wien, Austria
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Wuppertal, Germany
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Yu D, Zhang X, Lin J, Cao T, Chen Y. SECS: An Effective CNN Joint Construction Strategy for Breast Cancer Histopathological Image Classification. JOURNAL OF KING SAUD UNIVERSITY - COMPUTER AND INFORMATION SCIENCES 2023. [DOI: 10.1016/j.jksuci.2023.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Chen W, Li Z, Deng P, Li Z, Xu Y, Li H, Su W, Qin J. Advances of Exosomal miRNAs in Breast Cancer Progression and Diagnosis. Diagnostics (Basel) 2021; 11:diagnostics11112151. [PMID: 34829498 PMCID: PMC8622700 DOI: 10.3390/diagnostics11112151] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Breast cancer is one of the most commonly diagnosed malignancies and the leading cause of cancer death in women worldwide. Although many factors associated with breast cancer have been identified, the definite etiology of breast cancer is still unclear. In addition, early diagnosis of breast cancer remains challenging. Exosomes are membrane-bound nanovesicles secreted by most types of cells and contain a series of biologically important molecules, such as lipids, proteins, and miRNAs, etc. Emerging evidence shows that exosomes can affect the status of cells by transmitting substances and messages among cells and are involved in various physiological and pathological processes. In breast cancer, exosomes play a significant role in breast tumorigenesis and progression through transfer miRNAs which can be potential biomarkers for early diagnosis of breast cancer. This review discusses the potential utility of exosomal miRNAs in breast cancer progression such as tumorigenesis, metastasis, immune regulation and drug resistance, and further in breast cancer diagnosis.
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Affiliation(s)
- Wenwen Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (W.C.); (P.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongyu Li
- College of Life Science, Dalian Minzu University, Dalian 116600, China;
| | - Pengwei Deng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (W.C.); (P.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengnan Li
- Clinical Laboratory, Dalian University Affiliated Xinhua Hospital, Dalian 116021, China;
| | - Yuhai Xu
- First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (Y.X.); (H.L.)
| | - Hongjing Li
- First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (Y.X.); (H.L.)
| | - Wentao Su
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- Correspondence: (W.S.); (J.Q.)
| | - Jianhua Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (W.C.); (P.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100049, China
- CAS Centre for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (W.S.); (J.Q.)
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