Infrared spectral histopathology (SHP): a novel diagnostic tool for the accurate classification of lung cancer

Applications of machine learning in time-domain fluorescence lifetime imaging: a review

Many medical imaging modalities have benefited from recent advances in Machine Learning (ML), specifically in deep learning, such as neural networks. Computers can be trained to investigate and enhance medical imaging methods without using valuable human resources. In recent years, Fluorescence Lifetime Imaging (FLIm) has received increasing attention from the ML community. FLIm goes beyond conventional spectral imaging, providing additional lifetime information, and could lead to optical histopathology supporting real-time diagnostics. However, most current studies do not use the full potential of machine/deep learning models. As a developing image modality, FLIm data are not easily obtainable, which, coupled with an absence of standardisation, is pushing back the research to develop models which could advance automated diagnosis and help promote FLIm. In this paper, we describe recent developments that improve FLIm image quality, specifically time-domain systems, and we summarise sensing, signal-to-noise analysis and the advances in registration and low-level tracking. We review the two main applications of ML for FLIm: lifetime estimation and image analysis through classification and segmentation. We suggest a course of action to improve the quality of ML studies applied to FLIm. Our final goal is to promote FLIm and attract more ML practitioners to explore the potential of lifetime imaging.

A biospectroscopic approach toward colorectal cancer diagnosis from bodily fluid samples via ATR-MIR spectroscopy combined with multivariate data analysis

In this study, a biospectroscopic approach was reported for the detection of spectral changes and biomarkers for the diagnosis of colorectal cancer (CC) cases from different bodily fluids (blood plasma, blood serum, saliva and colonoscopy disinfection/wash fluids) by using attenuated total reflection-mid infrared (ATR-MIR) spectroscopy. To recognize the molecular level changes in the spectral characteristics of CC and their healthy/control (CH) groups, different multivariate data analyses (HCA, LDA, PCA and SIMCA) were successfully performed over the data of ATR-MIR spectroscopy. Two hundred specimens were characterized in detail over the data of spectral regions (4000-650 cm-1 and regions V-XXII). The findings revealed that significant changes were clearly observed in the concentrations of lipid, protein, nucleic acid and carbohydrate biomolecules for cancer cases based upon their necessity to overcome energy requirements. Supervised multivariate data methodology SIMCA, presented an excellent classification for the studied groups; similarly 100% of the specimens from different bodily fluids were correctly classified by supervised methodology LDA. As a result, the developed ATR-MIR methodology for the classification of CC and their healthy groups highlighted a rapid cancer diagnosis approach from different bodily fluids; therefore, it could be guide to make well decision before histopathological assessment and to screen CC populations existing in society.

Roadmap on optical sensors

Optical sensors and sensing technologies are playing a more and more important role in our modern world. From micro-probes to large devices used in such diverse areas like medical diagnosis, defence, monitoring of industrial and environmental conditions, optics can be used in a variety of ways to achieve compact, low cost, stand-off sensing with extreme sensitivity and selectivity. Actually, the challenges to the design and functioning of an optical sensor for a particular application requires intimate knowledge of the optical, material, and environmental properties that can affect its performance. This roadmap on optical sensors addresses different technologies and application areas. It is constituted by twelve contributions authored by world-leading experts, providing insight into the current state-of-the-art and the challenges their respective fields face. Two articles address the area of optical fibre sensors, encompassing both conventional and specialty optical fibres. Several other articles are dedicated to laser-based sensors, micro- and nano-engineered sensors, whispering-gallery mode and plasmonic sensors. The use of optical sensors in chemical, biological and biomedical areas is discussed in some other papers. Different approaches required to satisfy applications at visible, infrared and THz spectral regions are also discussed.

Digital Histopathology by Infrared Spectroscopic Imaging

Infrared (IR) spectroscopic imaging records spatially resolved molecular vibrational spectra, enabling a comprehensive measurement of the chemical makeup and heterogeneity of biological tissues. Combining this novel contrast mechanism in microscopy with the use of artificial intelligence can transform the practice of histopathology, which currently relies largely on human examination of morphologic patterns within stained tissue. First, this review summarizes IR imaging instrumentation especially suited to histopathology, analyses of its performance, and major trends. Second, an overview of data processing methods and application of machine learning is given, with an emphasis on the emerging use of deep learning. Third, a discussion on workflows in pathology is provided, with four categories proposed based on the complexity of methods and the analytical performance needed. Last, a set of guidelines, termed experimental and analytical specifications for spectroscopic imaging in histopathology, are proposed to help standardize the diversity of approaches in this emerging area.

Non-Invasive Disease Specific Biomarker Detection Using Infrared Spectroscopy: A Review

Many life-threatening diseases remain obscure in their early disease stages. Symptoms appear only at the advanced stage when the survival rate is poor. A non-invasive diagnostic tool may be able to identify disease even at the asymptotic stage and save lives. Volatile metabolites-based diagnostics hold a lot of promise to fulfil this demand. Many experimental techniques are being developed to establish a reliable non-invasive diagnostic tool; however, none of them are yet able to fulfil clinicians' demands. Infrared spectroscopy-based gaseous biofluid analysis demonstrated promising results to fulfil clinicians' expectations. The recent development of the standard operating procedure (SOP), sample measurement, and data analysis techniques for infrared spectroscopy are summarized in this review article. It has also outlined the applicability of infrared spectroscopy to identify the specific biomarkers for diseases such as diabetes, acute gastritis caused by bacterial infection, cerebral palsy, and prostate cancer.

Cell Phase Identification in a Three-Dimensional Engineered Tumor Model by Infrared Spectroscopic Imaging

Cell cycle progression plays a vital role in regulating proliferation, metabolism, and apoptosis. Three-dimensional (3D) cell cultures have emerged as an important class of in vitro disease models, and incorporating the variation occurring from cell cycle progression in these systems is critical. Here, we report the use of Fourier transform infrared (FT-IR) spectroscopic imaging to identify subtle biochemical changes within cells, indicative of the G1/S and G2/M phases of the cell cycle. Following previous studies, we first synchronized samples from two-dimensional (2D) cell cultures, confirmed their states by flow cytometry and DNA quantification, and recorded spectra. We determined two critical wavenumbers (1059 and 1219 cm^-1) as spectral indicators of the cell cycle for a set of isogenic breast cancer cell lines (MCF10AT series). These two simple spectral markers were then applied to distinguish cell cycle stages in a 3D cell culture model using four cell lines that represent the main stages of cancer progression from normal cells to metastatic disease. Temporal dependence of spectral biomarkers during acini maturation validated the hypothesis that the cells are more proliferative in the early stages of acini development; later stages of the culture showed stability in the overall composition but unique spatial differences in cells in the two phases. Altogether, this study presents a computational and quantitative approach for cell phase analysis in tissue-like 3D structures without any biomarker staining and provides a means to characterize the impact of the cell cycle on 3D biological systems and disease diagnostic studies using IR imaging.

Automatic optical biopsy for colorectal cancer using hyperspectral imaging and artificial neural networks

BACKGROUND

Intraoperative identification of cancerous tissue is fundamental during oncological surgical or endoscopic procedures. This relies on visual assessment supported by histopathological evaluation, implying a longer operative time. Hyperspectral imaging (HSI), a contrast-free and contactless imaging technology, provides spatially resolved spectroscopic analysis, with the potential to differentiate tissue at a cellular level. However, HSI produces "big data", which is impossible to directly interpret by clinicians. We hypothesize that advanced machine learning algorithms (convolutional neural networks-CNNs) can accurately detect colorectal cancer in HSI data.

METHODS

In 34 patients undergoing colorectal resections for cancer, immediately after extraction, the specimen was opened, the tumor-bearing section was exposed and imaged using HSI. Cancer and normal mucosa were categorized from histopathology. A state-of-the-art CNN was developed to automatically detect regions of colorectal cancer in a hyperspectral image. Accuracy was validated with three levels of cross-validation (twofold, fivefold, and 15-fold).

RESULTS

32 patients had colorectal adenocarcinomas confirmed by histopathology (9 left, 11 right, 4 transverse colon, and 9 rectum). 6 patients had a local initial stage (T1-2) and 26 had a local advanced stage (T3-4). The cancer detection performance of the CNN using 15-fold cross-validation showed high sensitivity and specificity (87% and 90%, respectively) and a ROC-AUC score of 0.95 (considered outstanding). In the T1-2 group, the sensitivity and specificity were 89% and 90%, respectively, and in the T3-4 group, the sensitivity and specificity were 81% and 93%, respectively.

CONCLUSIONS

Automatic colorectal cancer detection on fresh specimens using HSI, using a properly trained CNN is feasible and accurate, even with small datasets, regardless of the local tumor extension. In the near future, this approach may become a useful intraoperative tool during oncological endoscopic and surgical procedures, and may result in precise and non-destructive optical biopsies to support objective and consistent tumor-free resection margins.

Deep learning-assisted co-registration of full-spectral autofluorescence lifetime microscopic images with H&E-stained histology images

Autofluorescence lifetime images reveal unique characteristics of endogenous fluorescence in biological samples. Comprehensive understanding and clinical diagnosis rely on co-registration with the gold standard, histology images, which is extremely challenging due to the difference of both images. Here, we show an unsupervised image-to-image translation network that significantly improves the success of the co-registration using a conventional optimisation-based regression network, applicable to autofluorescence lifetime images at different emission wavelengths. A preliminary blind comparison by experienced researchers shows the superiority of our method on co-registration. The results also indicate that the approach is applicable to various image formats, like fluorescence in-tensity images. With the registration, stitching outcomes illustrate the distinct differences of the spectral lifetime across an unstained tissue, enabling macro-level rapid visual identification of lung cancer and cellular-level characterisation of cell variants and common types. The approach could be effortlessly extended to lifetime images beyond this range and other staining technologies.

Clinical Spectroscopy: Lost in Translation?

This Focal Point Review paper discusses the developments of biomedical Raman and infrared spectroscopy, and the recent strive towards these technologies being regarded as reliable clinical tools. The promise of vibrational spectroscopy in the field of biomedical science, alongside the development of computational methods for spectral analysis, has driven a plethora of proof-of-concept studies which convey the potential of various spectroscopic approaches. Here we report a brief review of the literature published over the past few decades, with a focus on the current technical, clinical, and economic barriers to translation, namely the limitations of many of the early studies, and the lack of understanding of clinical pathways, health technology assessments, regulatory approval, clinical feasibility, and funding applications. The field of biomedical vibrational spectroscopy must acknowledge and overcome these hurdles in order to achieve clinical efficacy. Current prospects have been overviewed with comment on the advised future direction of spectroscopic technologies, with the aspiration that many of these innovative approaches can ultimately reach the frontier of medical diagnostics and many clinical applications.

High-Resolution Fourier Transform Infrared (FT-IR) Spectroscopic Imaging for Detection of Lung Structures and Cancer-Related Abnormalities in a Murine Model

Label-free molecular imaging is a promising utility to study tissues in terms of the identification of their compartments as well as chemical features and alterations induced by disease. The aim of this work was to assess if higher magnification of optics in the Fourier transform infrared (FT-IR) microscope coupled with the focal plane detector resulted in better resolution of lung structures and if the histopathological features correlated with clustering of spectral images. FT-IR spectroscopic imaging was performed on paraffinized lung tissue sections from mice with optics providing a total magnification of 61× and 36×. Then, IR images were subjected to unsupervised cluster analysis and, subsequently, cluster maps were compared with hematoxylin and eosin staining of the same tissue section. Based on these results, we observed minute features such as cellular compartments in single alveoli and bronchiole, blood cells and megakaryocytes in a vessel as well as atelectasis of the lung. In the case of the latter, differences in composition were also noted between the tissue from the non-cancerous and cancerous specimen. This study demonstrated the ability of high-definition FT-IR imaging to evaluate the chemical features of well-resolved lung structures that could complement the histological examination widely used in animal models of disease.

A rapid diagnostic approach for gastric and colon cancers via Fourier transform mid-infrared spectroscopy coupled with chemometrics from paraffin-embedded tissues

This paper describes the feasibility of Attenuated total reflection-Fourier transform mid-infrared (ATR-MIR) spectroscopy method coupled with chemometrics for the rapid diagnostic approach and screening spectral changes for gastric and colon cancers from paraffin-embedded tissues. A total number of 82 tissue samples were analyzed by a simple ATR-MIR method combined with PCA, HCA, SIMCA and LDA methodologies. Spectral analyses showed significant differences for the molecular contents particularly about the lipid, nucleic acid, protein and other biomolecules in the samples of gastric cancer (GC) and colon cancer (CC) groups from their control/healthy groups. Significant changes in the characteristic of these molecules were only observed for cancer groups based upon the increment in their biosynthesis, and they could be utilized as diagnostic spectral biomarkers. Under the optimum conditions, SIMCA provided excellent classification for diseased and control groups, with 5% significance level. As well, 97.75% of the studied tissue samples were correctly discriminated on the basis of their origin by LDA. Consequently, the findings of this study highlighted the rapid diagnosis of gastric and colon cancer cases from paraffin-embedded tissues via ATR-MIR spectroscopy complemented with chemometrics.

Breast cancer or surrounding normal tissue? A successful discrimination by FTIR or Raman microspectroscopy

Breast cancer is a type of cancer with the highest incidence worldwide in 2021, with early diagnosis and rapid treatment intervention being the reasons for the decreasing mortality rate associated with the disease.

Infrared Spectroscopic Analysis in the Differentiation of Epithelial Misplacement From Adenocarcinoma in Sigmoid Colonic Adenomatous Polyps

Purpose

The differential diagnosis of epithelial misplacement from invasive cancer in the colon is a challenging endeavour, augmented by the introduction of bowel cancer population screening. The main aim of the work is to test, as a proof-of concept study, the ability of the infrared spectroscopic imaging approach to differentiate epithelial misplacement from adenocarcinoma in sigmoid colonic adenomatous polyps.

Methods

Ten samples from each of the four diagnostic groups, normal colonic mucosa, adenomatous polyps with low grade dysplasia, epithelial misplacement in adenomatous polyps and adenocarcinoma, were analysed using IR spectroscopic imaging and data processing methods. IR spectral images were subjected to data pre-processing and cluster analysis based segmentation to identify epithelial, connective tissue and stromal regions. Statistical analysis was carried out using principal component analysis and linear discriminant analysis based cross validation, to classify spectral features according to the pathology, and the diagnostic attributes were compared.

Results

The combined 4-group classification model on an average showed a sensitivity of 64%, a specificity of 88% and an accuracy of 76% for prediction based on a 'single spectrum', whilst a 'majority-vote' prediction on an average showed a sensitivity of 73%, a specificity of 90% and an accuracy of 82%. The 2-group model, for the differential diagnosis of epithelial misplacement versus adenocarcinoma, showed an average sensitivity and specificity of 82.5% for prediction based on a 'single spectrum' whilst a 'majority-vote' classification showed an average sensitivity and specificity of 90%. A 92% area under the curve (AUC) value was obtained when evaluating the classifier using the Receiver Operating Characteristics (ROC) curves.

Conclusions

IR spectroscopy shows promise in its ability to differentiate epithelial misplacement from adenocarcinoma in tissue sections, considered as one of the most challenging endeavours in population-wide diagnostic histopathology. Further studies with larger series, including cases with challenging diagnostic features are required to ascertain the capability of this modern digital pathology approach. In the long-term, IR spectroscopy based pathology which is relatively low-cost and rapid, could be a promising endeavour to consider for integration into the existing histopathology pathway, in particular for population based screening programmes where large number of samples are scrutinised.

Infrared micro-spectroscopy coupled with multivariate and machine learning techniques for cancer classification in tissue: a comparison of classification method, performance, and pre-processing technique

A meta-analysis of various multivariate/Machine Learning (ML) classifiers trained on IR Micro-spectroscopy tissue datasets for cancer classification are directly compared using a calculated F1-Score metric alongside study pre-processing techniques.

Advances in Digital Pathology: From Artificial Intelligence to Label-Free Imaging

BACKGROUND

Digital pathology, in its primary meaning, describes the utilization of computer screens to view scanned histology slides. Digitized tissue sections can be easily shared for a second opinion. In addition, it allows tissue image analysis using specialized software to identify and measure events previously observed by a human observer. These tissue-based readouts were highly reproducible and precise. Digital pathology has developed over the years through new technologies. Currently, the most discussed development is the application of artificial intelligence to automatically analyze tissue images. However, even new label-free imaging technologies are being developed to allow imaging of tissues by means of their molecular composition.

SUMMARY

This review provides a summary of the current state-of-the-art and future digital pathologies. Developments in the last few years have been presented and discussed. In particular, the review provides an outlook on interesting new technologies (e.g., infrared imaging), which would allow for deeper understanding and analysis of tissue thin sections beyond conventional histopathology.

KEY MESSAGES

In digital pathology, mathematical methods are used to analyze images and draw conclusions about diseases and their progression. New innovative methods and techniques (e.g., label-free infrared imaging) will bring significant changes in the field in the coming years.

Infrared-spectroscopic, dynamic near-field microscopy of living cells and nanoparticles in water

Infrared fingerprint spectra can reveal the chemical nature of materials down to 20-nm detail, far below the diffraction limit, when probed by scattering-type scanning near-field optical microscopy (s-SNOM). But this was impossible with living cells or aqueous processes as in corrosion, due to water-related absorption and tip contamination. Here, we demonstrate infrared s-SNOM of water-suspended objects by probing them through a 10-nm thick SiN membrane. This separator stretches freely over up to 250 µm, providing an upper, stable surface to the scanning tip, while its lower surface is in contact with the liquid and localises adhering objects. We present its proof-of-principle applicability in biology by observing simply drop-casted, living E. coli in nutrient medium, as well as living A549 cancer cells, as they divide, move and develop rich sub-cellular morphology and adhesion patterns, at 150 nm resolution. Their infrared spectra reveal the local abundances of water, proteins, and lipids within a depth of ca. 100 nm below the SiN membrane, as we verify by analysing well-defined, suspended polymer spheres and through model calculations. SiN-membrane based s-SNOM thus establishes a novel tool of live cell nano-imaging that returns structure, dynamics and chemical composition. This method should benefit the nanoscale analysis of any aqueous system, from physics to medicine.

A New Look into Cancer-A Review on the Contribution of Vibrational Spectroscopy on Early Diagnosis and Surgery Guidance

Simple Summary

Cancer is a leading cause of death worldwide, with the detection of the disease in its early stages, as well as a correct assessment of the tumour margins, being paramount for a successful recovery. While breast cancer is one of most common types of cancer, head and neck cancer is one of the types of cancer with a lower prognosis and poor aesthetic results. Vibrational spectroscopy detects molecular vibrations, being sensitive to different sample compositions, even when the difference was slight. The use of spectroscopy in biomedicine has been extensively explored, since it allows a broader assessment of the biochemical fingerprint of several diseases. This literature review covers the most recent advances in breast and head and neck cancer early diagnosis and intraoperative margin assessment, through Raman and Fourier transform infrared spectroscopies. The rising field of spectral histopathology was also approached. The authors aimed at expounding in a more concise and simple way the challenges faced by clinicians and how vibrational spectroscopy has evolved to respond to those needs for the two types of cancer with the highest potential for improvement regarding an early diagnosis, surgical margin assessment and histopathology.

Abstract

In 2020, approximately 10 million people died of cancer, rendering this disease the second leading cause of death worldwide. Detecting cancer in its early stages is paramount for patients’ prognosis and survival. Hence, the scientific and medical communities are engaged in improving both therapeutic strategies and diagnostic methodologies, beyond prevention. Optical vibrational spectroscopy has been shown to be an ideal diagnostic method for early cancer diagnosis and surgical margins assessment, as a complement to histopathological analysis. Being highly sensitive, non-invasive and capable of real-time molecular imaging, Raman and Fourier transform infrared (FTIR) spectroscopies give information on the biochemical profile of the tissue under analysis, detecting the metabolic differences between healthy and cancerous portions of the same sample. This constitutes tremendous progress in the field, since the cancer-prompted morphological alterations often occur after the biochemical imbalances in the oncogenic process. Therefore, the early cancer-associated metabolic changes are unnoticed by the histopathologist. Additionally, Raman and FTIR spectroscopies significantly reduce the subjectivity linked to cancer diagnosis. This review focuses on breast and head and neck cancers, their clinical needs and the progress made to date using vibrational spectroscopy as a diagnostic technique prior to surgical intervention and intraoperative margin assessment.

Molecular Origin of Blood-Based Infrared Spectroscopic Fingerprints*

Infrared spectroscopy of liquid biopsies is a time- and cost-effective approach that may advance biomedical diagnostics. However, the molecular nature of disease-related changes of infrared molecular fingerprints (IMFs) remains poorly understood, impeding the method's applicability. Here we probe 148 human blood sera and reveal the origin of the variations in their IMFs. To that end, we supplemented infrared spectroscopy with biochemical fractionation and proteomic profiling, providing molecular information about serum composition. Using lung cancer as an example of a medical condition, we demonstrate that the disease-related differences in IMFs are dominated by contributions from twelve highly abundant proteins-that, if used as a pattern, may be instrumental for detecting malignancy. Tying proteomic to spectral information and machine learning advances our understanding of the infrared spectra of liquid biopsies, a framework that could be applied to probing of any disease.

Distinguishing Non-Small Cell Lung Cancer Subtypes in Fine Needle Aspiration Biopsies by Desorption Electrospray Ionization Mass Spectrometry Imaging

BACKGROUND

Distinguishing adenocarcinoma and squamous cell carcinoma subtypes of non-small cell lung cancers is critical to patient care. Preoperative minimally-invasive biopsy techniques, such as fine needle aspiration (FNA), are increasingly used for lung cancer diagnosis and subtyping. Yet, histologic distinction of lung cancer subtypes in FNA material can be challenging. Here, we evaluated the usefulness of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) to diagnose and differentiate lung cancer subtypes in tissues and FNA samples.

METHODS

DESI-MSI was used to analyze 22 normal, 26 adenocarcinoma, and 25 squamous cell carcinoma lung tissues. Mass spectra obtained from the tissue sections were used to generate and validate statistical classifiers for lung cancer diagnosis and subtyping. Classifiers were then tested on DESI-MSI data collected from 16 clinical FNA samples prospectively collected from 8 patients undergoing interventional radiology guided FNA.

RESULTS

Various metabolites and lipid species were detected in the mass spectra obtained from lung tissues. The classifiers generated from tissue sections yielded 100% accuracy, 100% sensitivity, and 100% specificity for lung cancer diagnosis, and 73.5% accuracy for lung cancer subtyping for the training set of tissues, per-patient. On the validation set of tissues, 100% accuracy for lung cancer diagnosis and 94.1% accuracy for lung cancer subtyping were achieved. When tested on the FNA samples, 100% diagnostic accuracy and 87.5% accuracy on subtyping were achieved per-slide.

CONCLUSIONS

DESI-MSI can be useful as an ancillary technique to conventional cytopathology for diagnosis and subtyping of non-small cell lung cancers.

Perspective on Multimodal Imaging Techniques Coupling Mass Spectrometry and Vibrational Spectroscopy: Picturing the Best of Both Worlds

Studies on complex biological phenomena often combine two or more imaging techniques to collect high-quality comprehensive data directly in situ, preserving the biological context. Mass spectrometry imaging (MSI) and vibrational spectroscopy imaging (VSI) complement each other in terms of spatial resolution and molecular information. In the past decade, several combinations of such multimodal strategies arose in research fields as diverse as microbiology, cancer, and forensics, overcoming many challenges toward the unification of these techniques. Here we focus on presenting the advantages and challenges of multimodal imaging from the point of view of studying biological samples as well as giving a perspective on the upcoming trends regarding this topic. The latest efforts in the field are discussed, highlighting the purpose of the technique for clinical applications.

Perspectives on infrared spectroscopic imaging from cancer diagnostics to process analysis

This perspective paper discusses the recent and potential developments in the application of infrared spectroscopic imaging, with a focus on Fourier transform infrared (FTIR) spectroscopic imaging. The current state-of-the-art has been briefly reported, that includes recent trends and advances in applications of FTIR spectroscopic imaging to biomedical systems. Here, some new opportunities for research in the biomedical field, particularly for cancer diagnostics, and also in the engineering field of process analysis; as well as challenges in FTIR spectroscopic imaging are discussed. Current and future prospects that will bring spectroscopic imaging technologies to the frontier of advanced medical diagnostics and to process analytics in engineering applications will be outlined in this opinion paper.

A representation learning approach for recovering scatter-corrected spectra from Fourier-transform infrared spectra of tissue samples

Infrared spectra obtained from cell or tissue specimen have commonly been observed to involve a significant degree of scattering effects, often Mie scattering, which probably overshadows biochemically relevant spectral information by a nonlinear, nonadditive spectral component in Fourier transform infrared (FTIR) spectroscopic measurements. Correspondingly, many successful machine learning approaches for FTIR spectra have relied on preprocessing procedures that computationally remove the scattering components from an infrared spectrum. We propose an approach to approximate this complex preprocessing function using deep neural networks. As we demonstrate, the resulting model is not just several orders of magnitudes faster, which is important for real-time clinical applications, but also generalizes strongly across different tissue types. Using Bayesian machine learning approaches, our approach unveils model uncertainty that coincides with a band shift in the amide I region that occurs when scattering is removed computationally based on an established physical model. Furthermore, our proposed method overcomes the trade-off between computation time and the corrected spectrum being biased towards an artificial reference spectrum.

Simultaneous Characterization of Implant Wear and Tribocorrosion Debris within Its Corresponding Tissue Response Using Infrared Chemical Imaging

Biotribology is one of the key branches in the field of artificial joint development. Wear and corrosion are among fundamental processes which cause material loss in a joint biotribological system; the characteristics of wear and corrosion debris are central to determining the in vivo bioreactivity. Much effort has been made elucidating the debris-induced tissue responses. However, due to the complexity of the biological environment of the artificial joint, as well as a lack of effective imaging tools, there is still very little understanding of the size, composition, and concentration of the particles needed to trigger adverse local tissue reactions, including periprosthetic osteolysis. Fourier transform infrared spectroscopic imaging (FTIR-I) provides fast biochemical composition analysis in the direct context of underlying physiological conditions with micron-level spatial resolution, and minimal additional sample preparation in conjunction with the standard histopathological analysis workflow. In this study, we have demonstrated that FTIR-I can be utilized to accurately identify fine polyethylene debris accumulation in macrophages that is not achievable using conventional or polarized light microscope with histological staining. Further, a major tribocorrosion product, chromium phosphate, can be characterized within its histological milieu, while simultaneously identifying the involved immune cell such as macrophages and lymphocytes. In addition, we have shown the different spectral features of particle-laden macrophages through image clustering analysis. The presence of particle composition variance inside macrophages could shed light on debris evolution after detachment from the implant surface. The success of applying FTIR-I in the characterization of prosthetic debris within their biological context may very well open a new avenue of research in the orthopedics community.

Interrogation of IDH1 Status in Gliomas by Fourier Transform Infrared Spectroscopy

Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are found in a high proportion of diffuse gliomas. The presence of the IDH1 mutation is a valuable diagnostic, prognostic and predictive biomarker for the management of patients with glial tumours. Techniques involving vibrational spectroscopy, e.g., Fourier transform infrared (FTIR) spectroscopy, have previously demonstrated analytical capabilities for cancer detection, and have the potential to contribute to diagnostics. The implementation of FTIR microspectroscopy during surgical biopsy could present a fast, label-free method for molecular genetic classification. For example, the rapid determination of IDH1 status in a patient with a glioma diagnosis could inform intra-operative decision-making between alternative surgical strategies. In this study, we utilized synchrotron-based FTIR microanalysis to probe tissue microarray sections from 79 glioma patients, and distinguished the positive class (IDH1-mutated) from the IDH1-wildtype glioma, with a sensitivity and specificity of 82.4% and 83.4%, respectively. We also examined the ability of attenuated total reflection (ATR)-FTIR spectroscopy in detecting the biomolecular events and global epigenetic and metabolic changes associated with mutations in the IDH1 enzyme, in blood serum samples collected from an additional 72 brain tumour patients. Centrifugal filtration enhanced the diagnostic ability of the classification models, with balanced accuracies up to ~69%. Identification of the molecular status from blood serum prior to biopsy could further direct some patients to alternative treatment strategies.

Synergy Effect of Combined Near and Mid-Infrared Fibre Spectroscopy for Diagnostics of Abdominal Cancer

Cancers of the abdominal cavity comprise one of the most prevalent forms of cancers, with the highest contribution from colon and rectal cancers (12% of the human population), followed by stomach cancers (4%). Surgery, as the preferred choice of treatment, includes the selection of adequate resection margins to avoid local recurrences due to minimal residual disease. The presence of functionally vital structures can complicate the choice of resection margins. Spectral analysis of tissue samples in combination with chemometric models constitutes a promising approach for more efficient and precise tumour margin identification. Additionally, this technique provides a real-time tumour identification approach not only for intraoperative application but also during endoscopic diagnosis of tumours in hollow organs. The combination of near-infrared and mid-infrared spectroscopy has advantages compared to individual methods for the clinical implementation of this technique as a diagnostic tool.

Vibrational Spectroscopy for Identification of Metabolites in Biologic Samples

Vibrational spectroscopy (mid-infrared (IR) and Raman) and its fingerprinting capabilities offer rapid, high-throughput, and non-destructive analysis of a wide range of sample types producing a characteristic chemical "fingerprint" with a unique signature profile. Nuclear magnetic resonance (NMR) spectroscopy and an array of mass spectrometry (MS) techniques provide selectivity and specificity for screening metabolites, but demand costly instrumentation, complex sample pretreatment, are labor-intensive, require well-trained technicians to operate the instrumentation, and are less amenable for implementation in clinics. The potential for vibration spectroscopy techniques to be brought to the bedside gives hope for huge cost savings and potential revolutionary advances in diagnostics in the clinic. We discuss the utilization of current vibrational spectroscopy methodologies on biologic samples as an avenue towards rapid cost saving diagnostics.

Developing infrared spectroscopic detection for stratifying brain tumour patients: glioblastoma multiforme vs. lymphoma

Over a third of brain tumour patients visit their general practitioner more than five times prior to diagnosis in the UK, leading to 62% of patients being diagnosed as emergency presentations. Unfortunately, symptoms are non-specific to brain tumours, and the majority of these patients complain of headaches on multiple occasions before being referred to a neurologist. As there are currently no methods in place for the early detection of brain cancer, the affected patients' average life expectancy is reduced by 20 years. These statistics indicate that the current pathway is ineffective, and there is a vast need for a rapid diagnostic test. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy is sensitive to the hallmarks of cancer, as it analyses the full range of macromolecular classes. The combination of serum spectroscopy and advanced data analysis has previously been shown to rapidly and objectively distinguish brain tumour severity. Recently, a novel high-throughput ATR accessory has been developed, which could be cost-effective to the National Health Service in the UK, and valuable for clinical translation. In this study, 765 blood serum samples have been collected from healthy controls and patients diagnosed with various types of brain cancer, contributing to one of the largest spectroscopic studies to date. Three robust machine learning techniques - random forest, partial least squares-discriminant analysis and support vector machine - have all provided promising results. The novel high-throughput technology has been validated by separating brain cancer and non-cancer with balanced accuracies of 90% which is comparable to the traditional fixed diamond crystal methodology. Furthermore, the differentiation of brain tumour type could be useful for neurologists, as some are difficult to distinguish through medical imaging alone. For example, the highly aggressive glioblastoma multiforme and primary cerebral lymphoma can appear similar on magnetic resonance imaging (MRI) scans, thus are often misdiagnosed. Here, we report the ability of infrared spectroscopy to distinguish between glioblastoma and lymphoma patients, at a sensitivity and specificity of 90.1% and 86.3%, respectively. A reliable serum diagnostic test could avoid the need for surgery and speed up time to definitive chemotherapy and radiotherapy.

All-digital histopathology by infrared-optical hybrid microscopy

Optical microscopy for biomedical samples requires expertise in staining to visualize structure and composition. Midinfrared (mid-IR) spectroscopic imaging offers label-free molecular recording and virtual staining by probing fundamental vibrational modes of molecular components. This quantitative signal can be combined with machine learning to enable microscopy in diverse fields from cancer diagnoses to forensics. However, absorption of IR light by common optical imaging components makes mid-IR light incompatible with modern optical microscopy and almost all biomedical research and clinical workflows. Here we conceptualize an IR-optical hybrid (IR-OH) approach that sensitively measures molecular composition based on an optical microscope with wide-field interferometric detection of absorption-induced sample expansion. We demonstrate that IR-OH exceeds state-of-the-art IR microscopy in coverage (10-fold), spatial resolution (fourfold), and spectral consistency (by mitigating the effects of scattering). The combined impact of these advances allows full slide infrared absorption images of unstained breast tissue sections on a visible microscope platform. We further show that automated histopathologic segmentation and generation of computationally stained (stainless) images is possible, resolving morphological features in both color and spatial detail comparable to current pathology protocols but without stains or human interpretation. IR-OH is compatible with clinical and research pathology practice and could make for a cost-effective alternative to conventional stain-based protocols for stainless, all-digital pathology.

Is Infrared Spectroscopy Ready for the Clinic?

Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.

Spectral histopathology of the lung: A review of two large studies

This paper summarizes results from two large lung cancer studies comprising over 700 samples that demonstrate the ability of spectral histopathology (SHP) to distinguish cancerous tissue regions from normal tissue, to differentiate benign lesions from normal tissue and cancerous lesions, and to classify lung cancer types. Furthermore, malignancy-associated changes can be identified in cancer-adjacent normal tissue. The ability to differentiate a multitude of normal cells and tissue types allow SHP to identify tumor margins and immune cell infiltration. Finally, SHP easily distinguishes small cell lung cancer (SCLC) from non-SCLC (NSCLC) and provides a further differentiation of NSCLC into adenocarcinomas and squamous cell carcinomas with an accuracy comparable of classical histopathology combined with immunohistochemistry. Case studies are presented that demonstrates that SHP can resolve interobserver discrepancies in standard histopathology.

Improved infrared spectroscopic discrimination between gall bladder (GB) polyps and GB cancer using component-descriptive spectral features of separated phases from bile

This study demonstrates a unique strategy for enhancing infrared (IR) spectroscopic discrimination between gall bladder (GB) polyps and cancer. This strategy includes the separation of raw bile juice into three sections of organic, aqueous, and amphiphilic phases and a cooperative combination of all IR spectral features of each separated phase for the discrimination. Raw bile juice is viscous and complex in composition because it contains fatty acids, cholesterol, proteins, phospholipids, bilirubin, and other components; therefore, the acquisition of IR spectra providing more component-discernible information is fundamental for improving discrimination. For this purpose, raw bile juice was separated into an aqueous phase, mostly containing bile salts, an organic phase with isolated lipids, and an amphiphilic phase, mainly containing proteins. The subsequent IR spectra of each separated phase were mutually characteristic and complementary to each other. When all the IR spectral features were combined, the discrimination was improved compared to that using the spectra of raw bile juice with no separation. The cooperative integration of more component-specific spectra obtained from each separated phase enhanced the discrimination. In addition, the IR spectra of the major constituents in bile juice, such as bile acids, conjugated bile salts, lecithin, and cholesterol, were recorded to explain the IR features of each separated phase.

An Innovative Platform Merging Elemental Analysis and Ftir Imaging for Breast Tissue Analysis

Histopathology and immunohistology remain the gold standard for breast cancer diagnostic. Yet, these approaches do not usually provide a sufficiently detailed characterization of the pathology. The purpose of this work is to demonstrate for the first time that elemental analysis and Fourier transform infrared spectroscopy microscopic examination of breast tissue sections can be merged into one dataset to provide a single set of markers based on both organic molecules and inorganic trace elements. For illustrating the method, 6 mammary tissue sections were used. Fourier transform infrared (FTIR) spectroscopy images reported a fingerprint of the organic molecules present in the tissue section and laser ablation elemental analysis (LA-ICP-MS) images brought inorganic element profiles. The 6 tissue sections provided 31 10⁶ and 150,000 spectra for FTIR and LA-ICP-MS spectra respectively. The results bring the proof of concept that breast tissue can be analyzed simultaneously by FTIR spectroscopy and laser ablation elemental analysis (LA-ICP-MS) to provide in both case reasonably high resolution images. We show how to bring the images obtained by the two methods to a same spatial resolution and how to use image registration to analyze the data originating from both techniques as one block of data. We finally demonstrates the elemental analysis is orthogonal to all FTIR markers as no significant correlation is found between FTIR and LA-ICP-MS data. Combining FTIR and LA-ICP-MS imaging becomes possible, providing two orthogonal methods which can bring an unprecedented diversity of information on the tissue. This opens a new avenue of tissue section analyses providing unprecedented diagnostic potential.

Qualitative and quantitative analysis of therapeutic solutions using Raman and infrared spectroscopy

Anticancer drugs are prescribed and administrated to an increasing number of patients on a daily basis. As a consequence, a number of concerns have been raised about the patient health and safety in the case that the drugs administered are not at the required concentration or even worse not the correct ones. Quality control of therapeutic solutions has therefore been extensively implemented in hospital environments, in order to avoid any failure in the intense workflow faced by administering pharmacists. In the present study, infrared (IR) and Raman spectroscopy have been employed for the analysis of 3 commercially available therapeutic solutions TEVA®, MYLAN®, CERUBIDINE®, respectively containing doxorubicin, epirubicin and daunorubicin. They perfectly illustrate the analytical difficulties encountered, as these 3 chemotherapeutic drugs are isomers, hardly distinguishable with conventional approaches such as UV/VIS spectrometry. Any analytical failure to identify these molecules can lead to delays in patient treatment. While Partial Least Squares Regression analysis demonstrates that both Raman and IR can deliver satisfactory quantitative analysis in the clinical range, with respective Root Mean Square Error of Cross Validation (RMSECV) between 0.0127 - 0.0220 g·L^-1 and 0.0573 - 0.0759 g·L^-1, the identification rate between the 2 techniques differs substantially. Indeed, Principal Component Analysis - Factorial Discriminant Analysis (PCA-FDA) highlights that, depending on the data preprocessing applied to Raman spectra, the discrimination between the 3 drugs is decreased, with in some cases specificity and sensitivity below 50%. However, IR analysis displays encouraging results with an overall specificity and sensitivity between 99 and 100%, suggesting that reliable validation of the therapeutic solution for administration to patients can be achieved. IR and Raman spectroscopy could assist and support quality control of chemotherapeutic solutions prepared in personalised concentrations for each patient. The effective and reliable characterisation of therapeutic solutions could have a lot to offer to improve current practices in a near future.

Deep representation learning for domain adaptable classification of infrared spectral imaging data

Motivation

Applying infrared microscopy in the context of tissue diagnostics heavily relies on computationally preprocessing the infrared pixel spectra that constitute an infrared microscopic image. Existing approaches involve physical models, which are non-linear in nature and lead to classifiers that do not generalize well, e.g. across different types of tissue preparation. Furthermore, existing preprocessing approaches involve iterative procedures that are computationally demanding, so that computation time required for preprocessing does not keep pace with recent progress in infrared microscopes which can capture whole-slide images within minutes.

Results

We investigate the application of stacked contractive autoencoders as an unsupervised approach to preprocess infrared microscopic pixel spectra, followed by supervised fine-tuning to obtain neural networks that can reliably resolve tissue structure. To validate the robustness of the resulting classifier, we demonstrate that a network trained on embedded tissue can be transferred to classify fresh frozen tissue. The features obtained from unsupervised pretraining thus generalize across the large spectral differences between embedded and fresh frozen tissue, where under previous approaches separate classifiers had to be trained from scratch.

Availability and implementation

Our implementation can be downloaded from https://github.com/arnrau/SCAE_IR_Spectral_Imaging.

Supplementary information

Supplementary data are available at Bioinformatics online.

Fourier transform infrared spectroscopic imaging of wear and corrosion products within joint capsule tissue from total hip replacements patients

Implant debris generated by wear and corrosion is a prominent cause of joint replacement failure. This study utilized Fourier transform infrared spectroscopic imaging (FTIR-I) to gain a better understanding of the chemical structure of implant debris and its impact on the surrounding biological environment. Therefore, retrieved joint capsule tissue from five total hip replacement patients was analyzed. All five cases presented different implant designs and histopathological patterns. All tissue samples were formalin-fixed and paraffin-embedded. Unstained, 5 μm thick sections were prepared. The unstained sections were placed on BaF₂ windows and deparaffinized with xylene prior to analysis. FTIR-I data were collected at a spectral resolution of 4 cm^-1 using an Agilent Cary 670 spectrometer coupled with Cary 620 FTIR microscope. The results of study demonstrated that FTIR-I is a powerful tool that can be used complimentary to the existing histopathological evaluation of tissue. FTIR-I was able to distinguish areas with different cell types (macrophages, lymphocytes). Small, but distinct differences could be detected depending on the state of cells (viable, necrotic) and depending on what type of debris was present (polyethylene [PE], suture material, and metal oxides). Although, metal oxides were mainly below the measurable range of FTIR-I, the infrared spectra of tissues exhibited noticeable difference in their presence. Tens of micrometer sized polyethylene particles could be easily imaged, but also accumulations of submicron particles could be detected within macrophages. FTIR-I was also able to distinguish between PE debris, and other birefringent materials such as suture. Chromium-phosphate particles originating from corrosion processes within modular taper junctions of hip implants could be identified and easily distinguished from other phosphorous materials such as bone. In conclusion, this study successfully demonstrated that FTIR-I is a useful tool that can image and determine the biochemical information of retrieved tissue samples over tens of square millimeters in a completely label free, nondestructive, and objective manner. The resulting chemical images provide a deeper understanding of the chemical nature of implant debris and their impact on chemical changes of the tissue within which they are embedded.

New insights into spectral histopathology: infrared-based scoring of tumour aggressiveness of squamous cell lung carcinomas

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.

Spectroscopic Analysis of Human Tracheal Tissue during Decellularization

OBJECTIVE

To use mid-infrared (IR) spectroscopy to assess changes in the cartilaginous framework of human trachea during decellularization.

STUDY DESIGN

Laboratory-based study.

SETTING

Research laboratory.

METHODS

Six cadaveric human tracheas were decellularized using a detergent enzymatic method (DEM). Tissue samples were obtained from each specimen after 0, 1, 10, and 25 DEM cycles for histologic and spectroscopic analysis. Decellularization was confirmed using hematoxylin and eosin (H&E) and 2-(4-amidinophenyl)-1H-indole-6-carboxamidine (DAPI) staining. Changes in cartilaginous framework were examined using Fourier transform infrared imaging spectroscopy (FT-IRIS) and an attenuated total reflectance (ATR) probe in the mid-IR frequencies. Results were statistically analyzed using 1-way analysis of variance (ANOVA) and principal component analysis (PCA).

RESULTS

Six decellularized tracheal scaffolds were successfully created using a DEM protocol. Histologic examination showed near-complete nuclear loss following 25 DEM cycles. As observed with FT-IRIS analysis, the collagen absorbance signal (1336 cm-1) was predominantly in the perichondria and remained stable after 25 DEM cycles ( P = .132), while the absorbance from sugar rings in proteoglycans and nucleic acids in hyaline cartilage (1080 cm-1) showed a significant decrease after 1 DEM cycle ( P = .0007). Examination of the luminal surface of the trachea with an ATR probe showed raw mid-IR spectra consistent with cartilage. PCA showed significant separation of spectra corresponding to treatment cycle along the principal components 1 and 2.

CONCLUSION

Mid-IR spectroscopy is a viable method of monitoring changes in extracellular matrix components during the decellularization of human trachea.

Resolving Interobserver Discrepancies in Lung Cancer Diagnoses by Spectral Histopathology

This paper reports the results of a collaborative lung cancer study between City of Hope Cancer Center (Duarte, California) and CIRECA, LLC (Cambridge, Massachusetts), comprising 328 samples from 249 patients, that used an optical technique known as spectral histopathology (SHP) for tissue classification. Because SHP is based on a physical measurement, it renders diagnoses on a more objective and reproducible basis than methods based on assessing cell morphology and tissue architecture. This report demonstrates that SHP provides distinction of adenocarcinomas from squamous cell carcinomas of the lung with an accuracy comparable to that of immunohistochemistry and highly reliable classification of adenosquamous carcinoma. Furthermore, this report shows that SHP can be used to resolve interobserver differences in lung pathology. Spectral histopathology is based on the detection of changes in biochemical composition, rather than morphologic features, and is therefore more akin to methods such as matrix-assisted laser desorption ionization time-of-flight mass spectrometry imaging. Both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and SHP imaging modalities demonstrate that changes in tissue morphologic features observed in classical pathology are accompanied by, and may be correlated to, changes in the biochemical composition at the cellular level. Thus, these imaging methods provide novel insight into biochemical changes due to disease.

High definition infrared chemical imaging of colorectal tissue using a Spero QCL microscope

Mid-infrared microscopy has become a key technique in the field of biomedical science and spectroscopy. This label-free, non-destructive technique permits the visualisation of a wide range of intrinsic biochemical markers in tissues, cells and biofluids by detection of the vibrational modes of the constituent molecules. Together, infrared microscopy and chemometrics is a widely accepted method that can distinguish healthy and diseased states with high accuracy. However, despite the exponential growth of the field and its research world-wide, several barriers currently exist for its full translation into the clinical sphere, namely sample throughput and data management. The advent and incorporation of quantum cascade lasers (QCLs) into infrared microscopes could help propel the field over these remaining hurdles. Such systems offer several advantages over their FT-IR counterparts, a simpler instrument architecture, improved photon flux, use of room temperature camera systems, and the flexibility of a tunable illumination source. In this current study we explore the use of a QCL infrared microscope to produce high definition, high throughput chemical images useful for the screening of biopsied colorectal tissue.

Virtual staining of colon cancer tissue by label-free Raman micro-spectroscopy

The great capability of the label-free classification of tissue via vibrational spectroscopy, like Raman or infrared imaging, is shown in numerous publications (review: Diem et al., J. Biophotonics, 2013, 6, 855-886). Herein, we present a new approach, virtual staining, that improves the Raman spectral histopathology (SHP) images of colorectal cancer tissue by combining the integrated Raman intensity image in the C-H stretching region (2800-3050 cm^-1) with the pseudo-colour Raman image. This allows the display of fine structures such as the filamentous composition of muscle tissue. The morphology of the virtually stained images is in agreement with the gold standard in medical diagnosis, the haematoxylin-eosin staining. The virtual staining image also represents the whole biochemical fingerprint, and several tissue components including carcinoma were identified automatically with high sensitivity and specificity. For fast tissue classifications, a similar approach was applied on coherent anti-Stokes Raman scattering (CARS) spectral data that is faster and therefore potentially more suitable for clinical applications.

Advancing Raman microspectroscopy for cellular and subcellular analysis: towards in vitro high-content spectralomic analysis

In the confocal mode, Raman microspectroscopy can profile the biochemical content of biological cells at a subcellular level, and any changes to it by exogenous agents, such as therapeutic drugs or toxicants. As an exploration of the potential of the technique as a high-content, label-free analysis technique, this report reviews work to monitor the spectroscopic signatures associated with the uptake and response pathways of commercial chemotherapeutic agents and polymeric nanoparticles by human lung cells. It is demonstrated that the signatures are reproducible and characteristic of the cellular event, and can be used, for example, to identify the mode of action of the agent as well as the subsequent cell death pathway, and even mechanisms of cellular resistance. Data mining approaches are discussed and a spectralomics approach is proposed.

Compositional Assessment of Human Tracheal Cartilage by Infrared Spectroscopy

Objectives To assess the potential of infrared fiber-optic spectroscopy to evaluate the compositional properties of human tracheal cartilage. Study Design Laboratory-based study. Methods Twenty human cadaveric distal tracheas were harvested (age range 20-78 years; 6 females, 14 males) for compositional analysis. Histologic staining, Fourier transform infrared imaging spectroscopy data on collagen and proteoglycan (PG) content, and near-infrared (NIR) fiber-optic probe spectroscopic data that reflect protein and water content were evaluated. NIR fiber-optic probe data were also obtained from the proximal trachea in 4 human cadavers (age range 51-65 years; 2 females, 2 males) in situ for comparison to distal trachea spectral data. Results In the distal trachea cohort, the spectroscopic-determined ratio of PG/amide I, indicative of the relative amount of PG, was significantly higher in the tissues from the younger group compared to the older group (0.37 ± 0.08 vs 0.32 ± 0.05, P = .05). A principal component analysis of the NIR spectral data enabled separation of spectra based on tracheal location, likely due to differences in both protein and water content. The NIR-determined water content based on the 5200-cm-1 peak was significantly higher in the distal trachea compared to the proximal trachea ( P < .001). Conclusions Establishment of normative compositional values and further elucidating differences between the segments of trachea will enable more directed research toward appropriate compositional end points in regenerative medicine for tracheal repair.

Biofluid spectroscopic disease diagnostics: A review on the processes and spectral impact of drying

The complex patterns observed from evaporated liquid drops have been examined extensively over the last 20 years. Complete understanding of drop deposition is vital in many medical processes, and one which is essential to the translation of biofluid spectroscopic disease diagnostics. The promising use of spectroscopy in disease diagnosis has been hindered by the complicated patterns left by dried biological fluids which may inhibit the clinical translation of this technology. Coffee-ring formation, cracking and gelation patterns have all been observed in biofluid drops, and with surface homogeneity being a key element to many spectroscopic techniques, experimental issues have been found to arise. A better understanding of the fundamental processes involved in a drying droplet could allow efficient progression in this research field, and ultimately benefit the population with the development of a reliable cancer diagnostic.

Infrared micro-spectroscopy of human tissue: principles and future promises

This article summarizes the methods employed, and the progress achieved over the past two decades in applying vibrational (Raman and IR) micro-spectroscopy to problems of medical diagnostics and cellular biology. During this time, several research groups have verified the enormous information contained in vibrational spectra; in fact, information on protein, lipid and metabolic composition of cells and tissues can be deduced by decoding the observed vibrational spectra. This decoding process is aided by the availability of computer workstations and advanced algorithms for data analysis. Furthermore, commercial instrumentation for the fast collection of both Raman and infrared micro-spectral data has enabled the collection of images of cells and tissues based solely on vibrational spectroscopic data. The progress in the field has been manifested by a steady increase in the number and quality of publications submitted by established and new research groups in vibrational spectroscopy in the biological and biomedical arenas.

Miniature diamond-anvil cells for FTIR-microspectroscopy of small quantities of biosamples

A small amount of biosample is mounted on a diamond anvil cell and spectra registered using simple 15× infrared objective instead of being grown on a diamond and measured by FTIR-ATR.