1
|
Zelger P, Brunner A, Zelger B, Willenbacher E, Unterberger SH, Stalder R, Huck CW, Willenbacher W, Pallua JD. Deep learning analysis of mid-infrared microscopic imaging data for the diagnosis and classification of human lymphomas. J Biophotonics 2023; 16:e202300015. [PMID: 37578837 DOI: 10.1002/jbio.202300015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 01/18/2023] [Revised: 07/19/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The present study presents an alternative analytical workflow that combines mid-infrared (MIR) microscopic imaging and deep learning to diagnose human lymphoma and differentiate between small and large cell lymphoma. We could show that using a deep learning approach to analyze MIR hyperspectral data obtained from benign and malignant lymph node pathology results in high accuracy for correct classification, learning the distinct region of 3900 to 850 cm-1 . The accuracy is above 95% for every pair of malignant lymphoid tissue and still above 90% for the distinction between benign and malignant lymphoid tissue for binary classification. These results demonstrate that a preliminary diagnosis and subtyping of human lymphoma could be streamlined by applying a deep learning approach to analyze MIR spectroscopic data.
Collapse
Affiliation(s)
- P Zelger
- University Hospital of Hearing, Voice and Speech Disorders, Medical University of Innsbruck, Innsbruck, Austria
| | - A Brunner
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - B Zelger
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - E Willenbacher
- University Hospital of Internal Medicine V, Hematology & Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - S H Unterberger
- Institute of Material-Technology, Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - R Stalder
- Institute of Mineralogy and Petrography, Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - C W Huck
- Institute of Analytical Chemistry and Radiochemistry, Innsbruck, Austria
| | - W Willenbacher
- University Hospital of Internal Medicine V, Hematology & Oncology, Medical University of Innsbruck, Innsbruck, Austria
- Oncotyrol, Centre for Personalized Cancer Medicine, Innsbruck, Austria
| | - J D Pallua
- University Hospital for Orthopedics and Traumatology, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
2
|
Kümmel T, van Marwick B, Rittel M, Ramallo Guevara C, Wühler F, Teumer T, Wängler B, Hopf C, Rädle M. Rapid brain structure and tumour margin detection on whole frozen tissue sections by fast multiphotometric mid-infrared scanning. Sci Rep 2021; 11:11307. [PMID: 34050224 DOI: 10.1038/s41598-021-90777-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/17/2021] [Indexed: 01/31/2023] Open
Abstract
Frozen section analysis is a frequently used method for examination of tissue samples, especially for tumour detection. In the majority of cases, the aim is to identify characteristic tissue morphologies or tumour margins. Depending on the type of tissue, a high number of misdiagnoses are associated with this process. In this work, a fast spectroscopic measurement device and workflow was developed that significantly improves the speed of whole frozen tissue section analyses and provides sufficient information to visualize tissue structures and tumour margins, dependent on their lipid and protein molecular vibrations. That optical and non-destructive method is based on selected wavenumbers in the mid-infrared (MIR) range. We present a measuring system that substantially outperforms a commercially available Fourier Transform Infrared (FT-IR) Imaging system, since it enables acquisition of reduced spectral information at a scan field of 1 cm2 in 3 s, with a spatial resolution of 20 µm. This allows fast visualization of segmented structure areas with little computational effort. For the first time, this multiphotometric MIR system is applied to biomedical tissue sections. We are referencing our novel MIR scanner on cryopreserved murine sagittal and coronal brain sections, especially focusing on the hippocampus, and show its usability for rapid identification of primary hepatocellular carcinoma (HCC) in mouse liver.
Collapse
|
3
|
Taskin MB, Ahmad T, Wistlich L, Meinel L, Schmitz M, Rossi A, Groll J. Bioactive Electrospun Fibers: Fabrication Strategies and a Critical Review of Surface-Sensitive Characterization and Quantification. Chem Rev 2021; 121:11194-11237. [DOI: 10.1021/acs.chemrev.0c00816] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mehmet Berat Taskin
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Taufiq Ahmad
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Laura Wistlich
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry and Helmholtz Institute for RNA Based Infection Research, 97074 Würzburg, Germany
| | - Michael Schmitz
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Angela Rossi
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Jürgen Groll
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| |
Collapse
|
4
|
Cologna SM, Rosenhouse-Dantsker A. Insights into the Molecular Mechanisms of Cholesterol Binding to the NPC1 and NPC2 Proteins. Adv Exp Med Biol 2019; 1135:139-60. [PMID: 31098815 DOI: 10.1007/978-3-030-14265-0_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years, a growing number of studies have implicated the coordinated action of NPC1 and NPC2 in intralysosomal transport and efflux of cholesterol. Our current understanding of this process developed with just over two decades of research. Since the cloning of the genes encoding the NPC1 and NPC2 proteins, studies of the biochemical defects observed when either gene is mutated along with computational and structural studies have unraveled key steps in the underlying mechanism. Here, we summarize the major contributions to our understanding of the proposed cholesterol transport controlled by NPC1 and NPC2, and briefly discuss recent findings of cholesterol binding and transport proteins beyond NPC1 and NPC2. We conclude with key questions and major challenges for future research on cholesterol transport by the NPC1 and NPC2 proteins.
Collapse
|
5
|
Abstract
The Niemann-Pick family of diseases was poorly understood until Roscoe Brady and his colleagues began their investigations in the 1960s. Following Brady's discovery of the defect in acid sphingomyelinase in Niemann-Pick disease, types A and B, Peter Pentchev, a senior scientist in the group, launched a series of investigations of an unusual lipid storage disease in a spontaneous mouse model. These led initially to identification of the cholesterol trafficking defect in the mouse, and then in human Niemann-Pick disease, type C (NPC). This discovery formed the basis of the standard diagnostic test for NPC for the next three decades. Subsequently, an international collaboration was established, based at the Brady lab at NIH, which culminated in discovery of the NPC1 gene. Roscoe Brady, Peter Pentchev and their colleagues defined and refined the clinical biochemical and pathological phenotypes of NPC in a series of elegant parallel studies. They also identified abnormal oxysterols in NPC; later work has proved such compounds to be sensitive biomarkers of the disease. The dedication of the Brady lab to NPC, and the discoveries that flowed therefrom, provided critical foundations for the current explosion of progress in this disease.
Collapse
Affiliation(s)
- Marc C Patterson
- Department of Neurology, Mayo Clinic Children's Center, RO_MA_16_03ECON, 200 First Street SW, Rochester, MN 55905, United States; Department of Pediatrics and Medical Genetics, Mayo Clinic Children's Center, RO_MA_16_03ECON, 200 First Street SW, Rochester, MN 55905, United States.
| | - Steven U Walkley
- Department of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, New York, NY, United States.
| |
Collapse
|
6
|
Zhang Y, Wang Q, Li B, Wang Z, Li C, Yao Y, Huang P, Wang Z. Changes in Attenuated Total Reflection Fourier Transform Infrared Spectra as Blood Dries Out. J Forensic Sci 2016; 62:761-767. [DOI: 10.1111/1556-4029.13324] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 07/07/2016] [Accepted: 08/07/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Yinming Zhang
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| | - Qi Wang
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| | - Bing Li
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| | - Zhijun Wang
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| | - Chengzhi Li
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| | - Yao Yao
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| | - Ping Huang
- Department of Forensic Pathology; Institute of Forensic Science; Ministry of Justice; Shanghai 200063 PR China
| | - Zhenyuan Wang
- Department of Forensic Medicine; School of Medicine; Xi'an Jiaotong University; Xi'an 710061 PR China
| |
Collapse
|
7
|
Steiner G, Küchler S, Hermann A, Koch E, Salzer R, Schackert G, Kirsch M. Rapid and label-free classification of human glioma cells by infrared spectroscopic imaging. Cytometry A 2008; 73A:1158-64. [DOI: 10.1002/cyto.a.20639] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
8
|
Abstract
The capability of Fourier transform infrared (FTIR) spectroscopic imaging to provide detailed images of unprocessed latent fingerprints while also preserving important trace evidence is demonstrated. Unprocessed fingerprints were developed on various porous and nonporous substrates. Data-processing methods used to extract the latent fingerprint ridge pattern from the background material included basic infrared spectroscopic band intensities, addition and subtraction of band intensity measurements, principal components analysis (PCA) and calculation of second derivative band intensities, as well as combinations of these various techniques. Additionally, trace evidence within the fingerprints was recovered and identified.
Collapse
Affiliation(s)
- Nicole J Crane
- Oak Ridge Institute for Science Education, FBI Laboratory, Counterterrorism and Forensic Science Research Unit, FBI Academy, Quantico, VA 22135, USA
| | | | | | | |
Collapse
|
9
|
Kazarian SG, Chan KLA. Applications of ATR-FTIR spectroscopic imaging to biomedical samples. Biochimica et Biophysica Acta (BBA) - Biomembranes 2006; 1758:858-67. [PMID: 16566893 DOI: 10.1016/j.bbamem.2006.02.011] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 02/11/2006] [Indexed: 11/26/2022]
Abstract
FTIR spectroscopic imaging in ATR (Attenuated Total Reflection) mode is a powerful tool for studying biomedical samples. This paper summarises recent advances in the applications of ATR-FTIR imaging to dissolution of pharmaceutical formulations and drug release. The use of two different ATR accessories to obtain chemical images of formulations in contact with water as a function of time is demonstrated. The innovative use of the diamond ATR accessory allowed in situ imaging of tablet compaction and dissolution. ATR-FTIR imaging was also applied to obtain images of the surface of skin and the spatial distribution of protein and lipid rich domains was obtained. Chemical images of cross-section of rabbit aorta were obtained using a diamond ATR accessory and the possibility of in situ imaging of arterial samples in contact with aqueous solution was demonstrated for the first time. This experiment opens an opportunity to image arterial samples in contact with solutions containing drug molecules. This approach may help in understanding the mechanisms of treatment of atherosclerosis.
Collapse
Affiliation(s)
- S G Kazarian
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | | |
Collapse
|
10
|
Cakmak G, Togan I, Severcan F. 17Beta-estradiol induced compositional, structural and functional changes in rainbow trout liver, revealed by FT-IR spectroscopy: a comparative study with nonylphenol. Aquat Toxicol 2006; 77:53-63. [PMID: 16325934 DOI: 10.1016/j.aquatox.2005.10.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 10/20/2005] [Accepted: 10/27/2005] [Indexed: 05/05/2023]
Abstract
Steroidal hormones produced by humans and animals are constantly being excreted into the environment. It has been demonstrated that sewage effluent discharged to surface water contains natural estrogens and synthetic estrogenic chemicals. As estrogen levels continuously increase in the aquatic environment, it is very important to have a detailed understanding of estrogens' effects on fish. In the present study, juvenile rainbow trout (Oncorhynchus mykiss) were exposed to 17beta-estradiol (E2) for 3 weeks and the effects of E2 on rainbow trout livers were investigated at the molecular level using Fourier transform infrared spectroscopy. The results revealed that E2 induced significant alterations in the liver tissues. A decrease in glycogen levels and protein concentration, and an increase in both the population of hepatic lipids, especially triglycerides, as well as the relative content of nucleic acids was observed in the E2 treated liver. In addition, a decrease in the membrane fluidity and an increase in lipid order were found in the cells of treated samples. In order to compare the effect of E2 with that of NP at molecular level, the fish were also treated with an estrogenic compound, nonylphenol (NP). The NP-treated fish liver spectra were found to be quite similar to those of E2-treated fish confirming that NP mimics the effect of E2 in immature rainbow trout.
Collapse
Affiliation(s)
- Gulgun Cakmak
- Department of Biological Sciences, Middle East Technical University, 06531 Ankara, Turkey
| | | | | |
Collapse
|
11
|
Lee E, Kidder LH, Kalasinsky VF, Schoppelrei JW, Lewis EN. Forensic visualization of foreign matter in human tissue by near-infrared spectral imaging: Methodology and data mining strategies. Cytometry A 2006; 69:888-96. [PMID: 16969809 DOI: 10.1002/cyto.a.20277] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Rapidity of data acquisition, high image fidelity and large field of view are of tremendous value when looking for chemical contaminants or for the proverbial "needle in the haystack" - in this case foreign inclusions in histologic sections of biopsy or autopsy tissues. Near infrared chemical imaging is one of three chemical imaging techniques (NIR, MIR and Raman) based on vibrational spectroscopy, and provides distinct technical advantages for this application. METHODS We have chosen to utilize and evaluate near infrared (NIR) imaging for studies of foreign materials in tissue because the experimental configuration is relatively simple, data collection is rapid, and large sample areas can be screened with high image fidelity and spatial resolution. RESULTS We have shown that NIR imaging can readily find and identify silicone gel inclusions in biological tissue samples. Additionally, preliminary results indicate that spectral signatures in the data set are also potentially sensitive to structural changes in the surrounding tissue that may be induced by the foreign body. CONCLUSIONS NIR chemical imaging is a powerful, non-destructive tool for localization and identifying foreign contaminants in biological tissue. Preliminary results indicate that NIR imaging is also sensitive enough to differentiate tissue types (perhaps based on collagen structural differences), and provide data on the spatial localization of these components.
Collapse
Affiliation(s)
- Eunah Lee
- Spectral Dimensions Inc, Olney, MD USA
| | | | | | | | | |
Collapse
|
12
|
Abstract
The recent development of Fourier transform infrared (FTIR) spectroscopic imaging has enhanced our capability to examine, on a microscopic scale, the spatial distribution of vibrational spectroscopic signatures of materials spanning the physical and biomedical disciplines. Recent activity in this emerging area has concentrated on instrumentation development, theoretical analyses to provide guidelines for imaging practice, novel data processing algorithms, and the introduction of the technique to new fields. To illustrate the impact and promise of this spectroscopic imaging methodology, we present fundamental principles of the technique in the context of FTIR spectroscopy and review new applications in various venues ranging from the physical chemistry of macromolecular systems to the detection of human disease.
Collapse
Affiliation(s)
- Ira W Levin
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| | | |
Collapse
|
13
|
Ouyang H, Sherman PJ, Paschalis EP, Boskey AL, Mendelsohn R. Fourier transform infrared microscopic imaging: effects of estrogen and estrogen deficiency on fracture healing in rat femurs. Appl Spectrosc 2004; 58:1-9. [PMID: 14727714 DOI: 10.1366/000370204322729405] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Infrared spectroscopic imaging with 6-10 microm spatial resolution was used to characterize the changes in fracture callus mineral content, carbonate content, mineral crystallinity, and collagen maturity in femurs of 3-month-old ovariectomized rats treated with estrogen (estrogen sufficiency) or vehicle (estrogen deficiency). Comparisons were also made in these animals to cortical bone at a distance from the callus. Analyses at 4, 8, and 12 weeks post fracture demonstrated that healing was accelerated in the estrogen-sufficient animals as demonstrated by increasing mineral content and collagen maturity and decreasing carbonate incorporation.
Collapse
Affiliation(s)
- Hao Ouyang
- Rutgers University, Department of Chemistry, Newark, New Jersey 07102, USA
| | | | | | | | | |
Collapse
|
14
|
Abstract
Nonylphenol (NP) is a biodegradation product of nonylphenol ethoxylates (NPEs) belonging to the alkylphenol ethoxylates (APEs) group. APEs are widely used nonionic surfactants in detergents, herbicides, pesticides, paints, and cosmetics. The present work investigates the effects of NP on rainbow trout (Oncorhynchus mykiss) livers at the molecular level using Fourier transform infrared (FT-IR) spectroscopy. The FT-IR spectra revealed dramatic differences between the NP-treated and control tissues, which mainly indicated that the level of triglycerides increased, the lipid order increased, and the protein concentration decreased in the treated samples. Moreover, it was also found that glycogen levels significantly decreased and the relative content of nucleic acids increased in NP-treated fish. The 17beta-Estradiol-treated fish liver spectra were found to be quite similar to those of NP-treated fish. All these results implied that rainbow trout may offer considerable promise to be used as a bioindicator for NP in the future.
Collapse
Affiliation(s)
- Gülgün Cakmak
- Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey
| | | | | | | |
Collapse
|
15
|
Zhang L, Small GW, Haka AS, Kidder LH, Lewis EN. Classification of Fourier transform infrared microscopic imaging data of human breast cells by cluster analysis and artificial neural networks. Appl Spectrosc 2003; 57:14-22. [PMID: 14610931 DOI: 10.1366/000370203321165151] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cluster analysis and artificial neural networks (ANNs) are applied to the automated assessment of disease state in Fourier transform infrared microscopic imaging measurements of normal and carcinomatous immortalized human breast cell lines. K-means clustering is used to implement an automated algorithm for the assignment of pixels in the image to cell and non-cell categories. Cell pixels are subsequently classified into carcinoma and normal categories through the use of a feed-forward ANN computed with the Broyden-Fletcher-Goldfarb-Shanno training algorithm. Inputs to the ANN consist of principal component scores computed from Fourier filtered absorbance data. A grid search optimization procedure is used to identify the optimal network architecture and filter frequency response. Data from three images corresponding to normal cells, carcinoma cells, and a mixture of normal and carcinoma cells are used to build and test the classification methodology. A successful classifier is developed through this work, although differences in the spectral backgrounds between the three images are observed to complicate the classification problem. The robustness of the final classifier is improved through the use of a rejection threshold procedure to prevent classification of outlying pixels.
Collapse
Affiliation(s)
- Lin Zhang
- Ohio University, Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Clippinger Laboratories, Athens, Ohio 45701, USA
| | | | | | | | | |
Collapse
|