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Peng W, Chen S, Kong D, Zhou X, Lu X, Chang C. Grade classification of human glioma using a convolutional neural network based on mid-infrared spectroscopy mapping. JOURNAL OF BIOPHOTONICS 2022; 15:e202100313. [PMID: 34931464 DOI: 10.1002/jbio.202100313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/15/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
This study proposes a convolutional neural network (CNN)-based computer-aided diagnosis (CAD) system for the grade classification of human glioma by using mid-infrared (MIR) spectroscopic mappings. Through data augmentation of pixels recombination, the mappings in the training set increased almost 161 times relative to the original mappings. The pixels of the recombined mappings in the training set came from all of the one-dimensional (1D) vibrational spectroscopy of 62 (almost 80% of all 77 patients) patients at specific bands. Compared with the performance of the CNN-CAD system based on the 1D vibrational spectroscopy, we found that the mean diagnostic accuracy of the recombined MIR spectroscopic mappings at peaks of 2917 cm-1 , 1539 cm-1 and 1234 cm-1 on the test set performed higher and the model also had more stable patterns. This research demonstrates that two-dimensional MIR mapping at a single frequency can be used by the CNN-CAD system for diagnosis and the research also gives a prompt that the mapping collection process can be replaced by a single-frequency IR imaging system, which is cheaper and more portable than a Fourier transform infrared microscopy and thus may be widely utilized in hospitals to provide meaningful assistance for pathologists in clinics.
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Affiliation(s)
- Wenyu Peng
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, China
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing, China
| | - Shuo Chen
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing, China
| | - Dongsheng Kong
- Department of Neurosurgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Xiaojie Zhou
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Xiaoyun Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, China
| | - Chao Chang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, China
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing, China
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2
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Derruau S, Gobinet C, Untereiner V, Sockalingum GD, Nassif A, Viguier M, Piot O, Lorimier S. New insights into hidradenitis suppurativa diagnosis via salivary infrared biosignatures: A pilot study. JOURNAL OF BIOPHOTONICS 2021; 14:e202000327. [PMID: 33231348 DOI: 10.1002/jbio.202000327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 06/11/2023]
Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease which can lead to a prolonged physical disability. HS diagnosis is exclusively clinical with the absence of biomarkers. Our study aims at assessing the HS-diagnostic potential of infrared spectroscopy from saliva, as a biofluid reflecting the body's pathophysiological state. Infrared spectra from 127 patients (57 HS and 70 non-HS) were processed by multivariate methods: principal component analysis coupled with Kruskal-Wallis or Mann-Whitney tests to identify discriminant spectral wavenumbers and linear discriminant analysis to evaluate the performances of HS-diagnostic approach. Infrared features, mainly in the 1300 cm-1 -1600 cm-1 region, were identified as discriminant for HS and prediction models revealed diagnostic performances of about 80%. Tobacco and obesity, two main HS risk factors, do not seem to alter the infrared diagnosis. This pilot study shows the potential of salivary "liquid biopsy" associated to vibrational spectroscopy to develop a personalized medical approach for HS patients' management.
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Affiliation(s)
- Stéphane Derruau
- Université de Reims Champagne-Ardenne, BioSpect EA 7506, UFR de Pharmacie, Reims, France
- Université de Reims Champagne-Ardenne, UFR Odontologie, Département de Biologie Orale, Reims, France
- Centre Hospitalier Universitaire de Reims, Pôle de Médecine Bucco-dentaire, Reims, France
| | - Cyril Gobinet
- Université de Reims Champagne-Ardenne, BioSpect EA 7506, UFR de Pharmacie, Reims, France
| | | | - Ganesh D Sockalingum
- Université de Reims Champagne-Ardenne, BioSpect EA 7506, UFR de Pharmacie, Reims, France
| | - Aude Nassif
- Service de Pathologie Infectieuse et Tropicale, Institut Pasteur, Centre Médical, Paris, France
| | - Manuelle Viguier
- Centre Hospitalier Universitaire de Reims, Service de Dermatologie -Vénéréologie, Reims, France
| | - Olivier Piot
- Université de Reims Champagne-Ardenne, BioSpect EA 7506, UFR de Pharmacie, Reims, France
- Université de Reims Champagne-Ardenne, PICT, Reims, France
| | - Sandrine Lorimier
- Université de Reims Champagne-Ardenne, UFR Odontologie, Département de Biologie Orale, Reims, France
- Centre Hospitalier Universitaire de Reims, Pôle de Médecine Bucco-dentaire, Reims, France
- Université de Reims Champagne-Ardenne, GRESPI EA-4694, UFR Sciences Exactes et Naturelles, Reims, France
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3
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Pereira TM, Diem M, Bachmann L, Bird B, Miljković M, Zezell DM. Evaluating biochemical differences in thyroglobulin from normal and goiter tissues by infrared spectral imaging. Analyst 2021; 145:7907-7915. [PMID: 33016272 DOI: 10.1039/d0an00700e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Thyroglobulin is a glycoiodoprotein that is produced by thyroid follicular cells; it is stored in follicles in structures known as colloids. The main function of this protein is to stock the hormones triiodothyronine (T3) and thyroxine (T4) until the body requires them. This study aims to demonstrate that infrared spectral imaging with appropriate multivariate analysis can reveal biochemical changes in this glycoprotein. The results achieved herein point out biochemical differences in the colloid samples obtained from normal and goiter patients including glycosylation and changes in the secondary conformational structure. We have presented the first spectral histopathology-based method to detect biochemical differences in thyroid colloids, such as TG iodination, glycosylation, and changes in the secondary structure in normal and goiter patients. The observed changes in the colloids were mainly due to the alterations in amide I and amide II (secondary conformation of proteins) and there is a correlation with different glycosylation between normal and goiter tissues.
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Affiliation(s)
- Thiago Martini Pereira
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, Rua Talim, 330-12231-280 - São José dos Campos, Brazil.
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Derruau S, Robinet J, Untereiner V, Piot O, Sockalingum GD, Lorimier S. Vibrational Spectroscopy Saliva Profiling as Biometric Tool for Disease Diagnostics: A Systematic Literature. Molecules 2020; 25:molecules25184142. [PMID: 32927716 PMCID: PMC7570680 DOI: 10.3390/molecules25184142] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/05/2020] [Accepted: 09/05/2020] [Indexed: 02/07/2023] Open
Abstract
Saliva is a biofluid that can be considered as a “mirror” reflecting our body’s health status. Vibrational spectroscopy, Raman and infrared, can provide a detailed salivary fingerprint that can be used for disease biomarker discovery. We propose a systematic literature review based on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to evaluate the potential of vibrational spectroscopy to diagnose oral and general diseases using saliva as a biological specimen. Literature searches were recently conducted in May 2020 through MEDLINE-PubMed and Scopus databases, without date limitation. Finally, over a period of 10 years, 18 publications were included reporting on 10 diseases (three oral and seven general diseases), with very high diagnostic performance rates in terms of sensitivity, specificity, and accuracy. Thirteen articles were related to six different cancers of the following anatomical sites: mouth, nasopharynx, lung, esophagus, stomach, and breast. The other diseases investigated and included in this review were periodontitis, Sjögren’s syndrome, diabetes, and myocardial infarction. Moreover, most articles focused on Raman spectroscopy (n = 16/18) and more specifically surface-enhanced Raman spectroscopy (n = 12/18). Interestingly, vibrational spectroscopy appears promising as a rapid, label-free, and non-invasive diagnostic salivary biometric tool. Furthermore, it could be adapted to investigate subclinical diseases—even if developmental studies are required.
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Affiliation(s)
- Stéphane Derruau
- Université de Reims Champagne-Ardenne, Département de Biologie Orale, UFR Odontologie, 2 rue du Général Koenig, 51100 Reims, France; (S.D.); (J.R.)
- Pôle de Médecine Bucco-dentaire, Centre Hospitalier Universitaire de Reims, 45 rue Cognacq-Jay, 51092 Reims, France
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51 rue Cognacq-Jay, 51097 Reims, France; (O.P.); (G.D.S.)
| | - Julien Robinet
- Université de Reims Champagne-Ardenne, Département de Biologie Orale, UFR Odontologie, 2 rue du Général Koenig, 51100 Reims, France; (S.D.); (J.R.)
| | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, PICT, 51 rue Cognacq-Jay, 51097 Reims, France;
| | - Olivier Piot
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51 rue Cognacq-Jay, 51097 Reims, France; (O.P.); (G.D.S.)
- Université de Reims Champagne-Ardenne, PICT, 51 rue Cognacq-Jay, 51097 Reims, France;
| | - Ganesh D. Sockalingum
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51 rue Cognacq-Jay, 51097 Reims, France; (O.P.); (G.D.S.)
| | - Sandrine Lorimier
- Université de Reims Champagne-Ardenne, Département de Biologie Orale, UFR Odontologie, 2 rue du Général Koenig, 51100 Reims, France; (S.D.); (J.R.)
- Pôle de Médecine Bucco-dentaire, Centre Hospitalier Universitaire de Reims, 45 rue Cognacq-Jay, 51092 Reims, France
- Université de Reims Champagne-Ardenne, GRESPI-EA4694, UFR Sciences Exactes et Naturelles, 51687 Reims, France
- Correspondence: ; Tel.: +33-612162282
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Kontsek E, Pesti A, Björnstedt M, Üveges T, Szabó E, Garay T, Gordon P, Gergely S, Kiss A. Mid-Infrared Imaging Is Able to Characterize and Separate Cancer Cell Lines. Pathol Oncol Res 2020; 26:2401-2407. [PMID: 32556889 PMCID: PMC7471106 DOI: 10.1007/s12253-020-00825-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022]
Abstract
Malignancies are still responsible for a large share of lethalities. Macroscopical evaluation of the surgical resection margins is uncertain. Big data based imaging approaches have emerged in the recent decade (mass spectrometry, two-photon microscopy, infrared and Raman spectroscopy). Indocianine green labelled MS is the most common approach, however, label free mid-infrared imaging is more promising for future practical application. We aimed to identify and separate different transformed (A-375, HT-29) and non-transformed (CCD986SK) cell lines by a label-free infrared spectroscopy method. Our approach applied a novel set-up for label-free mid-infrared range classification method. Transflection spectroscopy was used on aluminium coated glass slides. Both whole range spectra (4000-648 cm-1) and hypersensitive fingerprint regions (1800-648 cm-1) were tested on the imaged areas of cell lines fixed in ethanol. Non-cell spectra were possible to be excluded based on mean transmission values being above 90%. Feasibility of a mean transmission based spectra filtering method with principal component analysis and linear discriminant analysis was shown to separate cell lines representing different tissue types. Fingerprint region resulted the best separation of cell lines spectra with accuracy of 99.84% at 70-75 mean transmittance range. Our approach in vitro was able to separate unique cell lines representing different tissues of origin. Proper data handling and spectra processing are key steps to achieve the adaptation of this dye-free technique for intraoperative surgery. Further studies are urgently needed to test this novel, marker-free approach.
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Affiliation(s)
- E Kontsek
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary.
| | - A Pesti
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - M Björnstedt
- Laboratory for Clinical Pathology and Cytology, Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - T Üveges
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - E Szabó
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - T Garay
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - P Gordon
- Department of Electronics Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - S Gergely
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - A Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
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Féré M, Gobinet C, Liu LH, Beljebbar A, Untereiner V, Gheldof D, Chollat M, Klossa J, Chatelain B, Piot O. Implementation of a classification strategy of Raman data collected in different clinical conditions: application to the diagnosis of chronic lymphocytic leukemia. Anal Bioanal Chem 2019; 412:949-962. [PMID: 31853604 DOI: 10.1007/s00216-019-02321-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/31/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023]
Abstract
The literature is rich in proof of concept studies demonstrating the potential of Raman spectroscopy for disease diagnosis. However, few studies are conducted in a clinical context to demonstrate its applicability in current clinical practice and workflow. Indeed, this translational research remains far from the patient's bedside for several reasons. First, samples are often cultured cell lines. Second, they are prepared on non-standard substrates for clinical routine. Third, a unique supervised classification model is usually constructed using inadequate cross-validation strategy. Finally, the implemented models maximize classification accuracy without taking into account the clinician's needs. In this paper, we address these issues through a diagnosis problem in real clinical conditions, i.e., the diagnosis of chronic lymphocytic leukemia from fresh unstained blood smears spread on glass slides. From Raman data acquired in different experimental conditions, a repeated double cross-validation strategy was combined with different cross-validation approaches, a consensus label strategy and adaptive thresholds able to adapt to the clinician's needs. Combined with validation at the patient level, classification results were improved compared to traditional strategies.
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Affiliation(s)
- M Féré
- BioSpecT EA 7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France
| | - C Gobinet
- BioSpecT EA 7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France.
| | - L H Liu
- BioSpecT EA 7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France
| | - A Beljebbar
- BioSpecT EA 7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France
| | - V Untereiner
- Cellular and Tissular Imaging Platform PICT, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France
| | - D Gheldof
- CHU UCL Namur, Namur Thrombosis and Hemostasis Center, Hematology Laboratory, Rue Dr Gaston Therasse, Catholic University of Louvain, 5530, Yvoir, Belgium
| | - M Chollat
- TRIBVN, 39 Rue Louveau, 92320, Châtillon, France
| | - J Klossa
- TRIBVN, 39 Rue Louveau, 92320, Châtillon, France
| | - B Chatelain
- CHU UCL Namur, Namur Thrombosis and Hemostasis Center, Hematology Laboratory, Rue Dr Gaston Therasse, Catholic University of Louvain, 5530, Yvoir, Belgium
| | - O Piot
- BioSpecT EA 7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France.,Cellular and Tissular Imaging Platform PICT, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims, France
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Gaydou V, Polette M, Gobinet C, Kileztky C, Angiboust JF, Birembaut P, Vuiblet V, Piot O. New insights into spectral histopathology: infrared-based scoring of tumour aggressiveness of squamous cell lung carcinomas. Chem Sci 2019; 10:4246-4258. [PMID: 31057753 PMCID: PMC6471539 DOI: 10.1039/c8sc04320e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/01/2019] [Indexed: 12/25/2022] Open
Abstract
Spectral histopathology, based on infrared interrogation of tissue sections, proved a promising tool for helping pathologists in characterizing histological structures in a quantitative and automatic manner.
Spectral histopathology, based on infrared interrogation of tissue sections, proved a promising tool for helping pathologists in characterizing histological structures in a quantitative and automatic manner. In cancer diagnosis, the use of chemometric methods permits establishing numerical models able to detect cancer cells and to characterize their tissular environment. In this study, we focused on exploiting multivariate infrared data to score the tumour aggressiveness in preneoplastic lesions and squamous cell lung carcinomas. These lesions present a wide range of aggressive phenotypes; it is also possible to encounter cases with various degrees of aggressiveness within the same lesion. Implementing an infrared-based approach for a more precise histological determination of the tumour aggressiveness should arouse interest among pathologists with direct benefits for patient care. In this study, the methodology was developed from a set of samples including all degrees of tumour aggressiveness and by constructing a chain of data processing steps for an automated analysis of tissues currently manipulated in routine histopathology.
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Affiliation(s)
- Vincent Gaydou
- BioSpecT Unit , EA 7506 , University of Reims Champagne-Ardenne , Pharmacy Department , 51 rue Cognacq-Jay , 51096 Reims , France .
| | - Myriam Polette
- INSERM UMR-S 1250 , University of Reims Champagne-Ardenne , 45, rue Cognacq-Jay , 51092 Reims , France.,Biopathology Laboratory , Centre Hospitalier et Universitaire de Reims , 45 Rue Cognacq-Jay , 51092 Reims , France
| | - Cyril Gobinet
- BioSpecT Unit , EA 7506 , University of Reims Champagne-Ardenne , Pharmacy Department , 51 rue Cognacq-Jay , 51096 Reims , France .
| | - Claire Kileztky
- INSERM UMR-S 1250 , University of Reims Champagne-Ardenne , 45, rue Cognacq-Jay , 51092 Reims , France
| | - Jean-François Angiboust
- BioSpecT Unit , EA 7506 , University of Reims Champagne-Ardenne , Pharmacy Department , 51 rue Cognacq-Jay , 51096 Reims , France .
| | - Philippe Birembaut
- INSERM UMR-S 1250 , University of Reims Champagne-Ardenne , 45, rue Cognacq-Jay , 51092 Reims , France.,Biopathology Laboratory , Centre Hospitalier et Universitaire de Reims , 45 Rue Cognacq-Jay , 51092 Reims , France
| | - Vincent Vuiblet
- BioSpecT Unit , EA 7506 , University of Reims Champagne-Ardenne , Pharmacy Department , 51 rue Cognacq-Jay , 51096 Reims , France . .,Biopathology Laboratory , Centre Hospitalier et Universitaire de Reims , 45 Rue Cognacq-Jay , 51092 Reims , France
| | - Olivier Piot
- BioSpecT Unit , EA 7506 , University of Reims Champagne-Ardenne , Pharmacy Department , 51 rue Cognacq-Jay , 51096 Reims , France . .,Platform of Cellular and Tissular Imaging (PICT) , University of Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims , France
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de Lima FA, Gobinet C, Sockalingum G, Garcia SB, Manfait M, Untereiner V, Piot O, Bachmann L. Digital de-waxing on FTIR images. Analyst 2018; 142:1358-1370. [PMID: 28001153 DOI: 10.1039/c6an01975g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents a procedure that digitally neutralizes the contribution of paraffin to FTIR hyperspectral images. A brief mathematical derivation of the procedure is demonstrated and applied on one normal human colon sample to exemplify the de-waxing procedure. The proposed method includes construction of a paraffin model based on PCA, EMSC normalization and application of two techniques for spectral quality control. We discuss every step in which the researcher needs to take a subjective decision during the de-waxing procedure, and we explain how to make an adequate choice of parameters involved. Application of this procedure to 71 hyperspectral images collected from 55 human colon biopsies (20 normal, 17 ulcerative colitis, and 18 adenocarcinoma) showed that paraffin was appropriately neutralized, which made the de-waxed images adequate for analysis by pattern-recognition techniques such as k-means clustering or PCA-LDA.
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Wrobel TP, Bhargava R. Infrared Spectroscopic Imaging Advances as an Analytical Technology for Biomedical Sciences. Anal Chem 2018; 90:1444-1463. [PMID: 29281255 PMCID: PMC6421863 DOI: 10.1021/acs.analchem.7b05330] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Tomasz P. Wrobel
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
- Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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