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Liberda D, Koziol P, Wrobel TP. Comprehensive Histopathology Imaging in Pancreatic Biopsies: High Definition Infrared Imaging with Machine Learning Approach. Int J Biol Sci 2023; 19:3200-3208. [PMID: 37416783 PMCID: PMC10321284 DOI: 10.7150/ijbs.83068] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/05/2023] [Indexed: 07/08/2023] Open
Abstract
Infrared (IR) based histopathology offers a new paradigm in looking at tissues and can provide a complimentary information source for more classical histopathology, which makes it a noteworthy tool given possible clinical application. This study aims to build a robust, pixel level machine learning model for pancreatic cancer detection using IR imaging. In this article, we report a pancreatic cancer classification model based on data from over 600 biopsies (coming from 250 patients) imaged with IR diffraction-limited spatial resolution. To fully research model's classification ability, we measured tissues using two optical setups, resulting in Standard and High Definitions data. This forms one of the largest IR datasets analyzed up to now, with almost 700 million spectra of different tissue types. The first six-class model created for comprehensive histopathology achieved pixel (tissue) level AUC values above 0.95, giving a successful technique for digital staining with biochemical information extracted from IR spectra.
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Affiliation(s)
- Danuta Liberda
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Prof. St. Łojasiewicza 11, PL30348, Cracow, Poland
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
| | - Paulina Koziol
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
- Institute of Physics, Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland
| | - Tomasz P. Wrobel
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
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Koziol P, Kosowska K, Liberda D, Borondics F, Wrobel TP. Super-Resolved 3D Mapping of Molecular Orientation Using Vibrational Techniques. J Am Chem Soc 2022; 144:14278-14287. [PMID: 35881536 PMCID: PMC9376951 DOI: 10.1021/jacs.2c05306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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When a sample has an anisotropic structure, it is possible
to obtain
additional information controlling the polarization of incident light.
With their straightforward instrumentation approaches, infrared (IR)
and Raman spectroscopies are widely popular in this area. Single-band-based
determination of molecular in-plane orientation, typically used in
materials science, is here extended by the concurrent use of two vibration
bands, revealing the orientational ordering in three dimension. The
concurrent analysis was applied to IR spectromicroscopic data to obtain
orientation angles of a model polycaprolactone spherulite sample.
The applicability of this method spans from high-resolution, diffraction-limited
Fourier transform infrared (FT-IR) and Raman imaging to super-resolved
optical photothermal infrared (O-PTIR) imaging. Due to the nontomographic
experimental approach, no image distortion is visible and nanometer
scale orientation domains can be observed. Three-dimensional (3D)
bond orientation maps enable in-depth characterization and consequently
precise control of the sample’s physicochemical properties
and functions.
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Affiliation(s)
- Paulina Koziol
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392 Krakow, Poland.,Institute of Physics, Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland
| | - Karolina Kosowska
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392 Krakow, Poland
| | - Danuta Liberda
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392 Krakow, Poland
| | - Ferenc Borondics
- Synchrotron SOLEIL, L'Orme Des Merisiers, Saint-Aubin - BP 48, 91192 Gif-Sur-Yvette, France
| | - Tomasz P Wrobel
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392 Krakow, Poland
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Liberda D, Pięta E, Pogoda K, Piergies N, Roman M, Koziol P, Wrobel TP, Paluszkiewicz C, Kwiatek WM. The Impact of Preprocessing Methods for a Successful Prostate Cell Lines Discrimination Using Partial Least Squares Regression and Discriminant Analysis Based on Fourier Transform Infrared Imaging. Cells 2021; 10:cells10040953. [PMID: 33924045 PMCID: PMC8073124 DOI: 10.3390/cells10040953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/30/2022] Open
Abstract
Fourier transform infrared spectroscopy (FT-IR) is widely used in the analysis of the chemical composition of biological materials and has the potential to reveal new aspects of the molecular basis of diseases, including different types of cancer. The potential of FT-IR in cancer research lies in its capability of monitoring the biochemical status of cells, which undergo malignant transformation and further examination of spectral features that differentiate normal and cancerous ones using proper mathematical approaches. Such examination can be performed with the use of chemometric tools, such as partial least squares discriminant analysis (PLS-DA) classification and partial least squares regression (PLSR), and proper application of preprocessing methods and their correct sequence is crucial for success. Here, we performed a comparison of several state-of-the-art methods commonly used in infrared biospectroscopy (denoising, baseline correction, and normalization) with the addition of methods not previously used in infrared biospectroscopy classification problems: Mie extinction extended multiplicative signal correction, Eiler’s smoothing, and probabilistic quotient normalization. We compared all of these approaches and their effect on the data structure, classification, and regression capability on experimental FT-IR spectra collected from five different prostate normal and cancerous cell lines. Additionally, we tested the influence of added spectral noise. Overall, we concluded that in the case of the data analyzed here, the biggest impact on data structure and performance of PLS-DA and PLSR was caused by the baseline correction; therefore, much attention should be given, especially to this step of data preprocessing.
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Affiliation(s)
- Danuta Liberda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
| | - Ewa Pięta
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
| | - Katarzyna Pogoda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: (K.P.); (T.P.W.)
| | - Natalia Piergies
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
| | - Maciej Roman
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
| | - Paulina Koziol
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
| | - Tomasz P. Wrobel
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
- Correspondence: (K.P.); (T.P.W.)
| | - Czeslawa Paluszkiewicz
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
| | - Wojciech M. Kwiatek
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland; (D.L.); (E.P.); (N.P.); (M.R.); (P.K.); (C.P.); (W.M.K.)
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Liberda D, Koziol P, Raczkowska MK, Kwiatek WM, Wrobel TP. Influence of interference effects on the spectral quality and histological classification by FT-IR imaging in transflection geometry. Analyst 2020; 146:646-654. [PMID: 33206067 DOI: 10.1039/d0an01565b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Infrared (IR) imaging can be used for fast, accurate and non-destructive pathology recognition of biopsies when supported by machine learning algorithms. Transflection mode of measurements has the potential to be translated into the clinic due to economic reasons of large-scale imaging with the need for inexpensive substrates. Unfortunately, in this mode spectral distortions originating from light interference appear. Due to this fact transmission measurement mode is more frequently used in pathology recognition. Nevertheless, this measurement mode also is not devoid of spectral distortion effects like scattering. However, this effect is better understood and there are preprocessing algorithms to minimize it. In this work, we investigated the influence of interference effects on spectral quality of pancreatic tissues measured in transmission and transflection mode with Fourier tranform IR (FT-IR) microscopy using samples embedded with and without paraffin. The removal of paraffin leads to an altered magnitude of interference in transflection and provides a platform for a detailed analysis of its effect on the spectra of biological material, since the same sample is measured with different interference conditions. Moreover, the potential of transflection mode measurements in histological classification of analyzed samples was investigated and compared with classification results for transmission mode.
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Affiliation(s)
- Danuta Liberda
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392 Krakow, Poland.
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Abstract
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Fourier
transform infrared spectroscopy has emerged as a powerful
tool for tissue specimen investigation. Its nondestructive and label-free
character enables direct determination of biochemical composition
of samples. Furthermore, the introduction of polarization enriches
this technique by the possibility of molecular orientation study apart
from purely quantitative analysis. Most of the molecular orientation
studies focused on polymer samples with a well-defined molecular axis.
Here, a four-polarization approach for Herman’s in-plane orientation
function and azimuthal angle determination was applied to a human
tissue sample investigation for the first time. Attention was focused
on fibrous tissues rich in collagen because of their cylindrical shape
and established amide bond vibrations. Despite the fact that the tissue
specimen contains a variety of molecules, the presented results of
molecular ordering and orientation agree with the theoretical prediction
based on sample composition and vibration directions.
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Affiliation(s)
- Paulina Koziol
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, Krakow 30-392, Poland
- Institute of Nuclear Physics, Polish Academy of Sciences, Krakow PL-31342, Poland
| | - Danuta Liberda
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, Krakow 30-392, Poland
- Institute of Nuclear Physics, Polish Academy of Sciences, Krakow PL-31342, Poland
| | - Wojciech M. Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences, Krakow PL-31342, Poland
| | - Tomasz P. Wrobel
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, Krakow 30-392, Poland
- Institute of Nuclear Physics, Polish Academy of Sciences, Krakow PL-31342, Poland
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Liberda D, Hermes M, Koziol P, Stone N, Wrobel TP. Translation of an esophagus histopathological FT-IR imaging model to a fast quantum cascade laser modality. J Biophotonics 2020; 13:e202000122. [PMID: 32406973 DOI: 10.1002/jbio.202000122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/02/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
The technical progress in fast quantum cascade laser (QCL) microscopy offers a platform where chemical imaging becomes feasible for clinical diagnostics. QCL systems allow the integration of previously developed FT-IR-based pathology recognition models in a faster workflow. The translation of such models requires a systematic approach, focusing only on the spectral frequencies that carry crucial information for discrimination of pathologic features. In this study, we optimize an FT-IR-based histopathological method for esophageal cancer detection to work with a QCL system. We explore whether the classifier's performance is affected by paraffin presence from tissue blocks compared to removing it chemically. Working with paraffin-embedded samples reduces preprocessing time in the lab and allows samples to be archived after analysis. Moreover, we test, whether the creation of a QCL model requires a preestablished FTIR model or can be optimized using solely QCL measurements.
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Affiliation(s)
- Danuta Liberda
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
| | - Michael Hermes
- School of Physics and Astronomy, University of Exeter, Exeter, UK
| | - Paulina Koziol
- Institute of Nuclear Physics Polish Academy of Sciences, Krakow, Poland
| | - Nick Stone
- School of Physics and Astronomy, University of Exeter, Exeter, UK
| | - Tomasz P Wrobel
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Wrobel TP, Koziol P, Raczkowska MK, Liberda D, Paluszkiewicz C, Kwiatek WM. Noise-free simulation of an FT-IR imaging hyperspectral dataset of pancreatic biopsy core bound by experiment. Sci Data 2019; 6:239. [PMID: 31664041 PMCID: PMC6820761 DOI: 10.1038/s41597-019-0260-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/27/2019] [Indexed: 12/23/2022] Open
Abstract
A noise-free hyperspectral FT-IR imaging dataset of a pancreatic tissue core was simulated based on experimental data that allows to test the performance of various data analysis and processing algorithms. A set of experimental noise levels was also added and used for denoising approaches comparison, which due to the noise-free reference signal enables to truly observe signal distortion caused by different approaches.
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Affiliation(s)
- Tomasz P Wrobel
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342, Krakow, Poland.
| | - Paulina Koziol
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342, Krakow, Poland
| | - Magda K Raczkowska
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342, Krakow, Poland.,Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, Krakow, Poland
| | - Danuta Liberda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342, Krakow, Poland
| | | | - Wojciech M Kwiatek
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342, Krakow, Poland
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