Suitability of Fourier transform infrared microscopy for the diagnosis of cystic echinococcosis in human tissue sections

Cystic echinococcosis (CE) is a global health concern caused by cestodes, posing diagnostic challenges due to nonspecific symptoms and inconclusive radiographic results. Diagnosis relies on histopathological evaluation of affected tissue, demanding comprehensive tools. In this retrospective case study, Fourier transform infrared microscopy was explored for detecting and identifying CE through biochemical changes in human tissue sections. Tissue samples from 11 confirmed CE patients were analyzed. Archived FFPE blocks were cut and stained, and then CE-positive unstained sections were examined using Fourier transform infrared microscopy post-deparaffinization. Results revealed the method's ability to distinguish echinococcus elements from human tissue, irrespective of organ type. This research showcases the potential of mid-infrared microscopy as a valuable diagnostic tool for CE, offering promise in enhancing diagnostic precision in the face of the disease's complexities.

Deep learning analysis of mid-infrared microscopic imaging data for the diagnosis and classification of human lymphomas

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.

Visible- and near-infrared hyperspectral imaging for the quantitative analysis of PD-L1+ cells in human lymphomas: Comparison with fluorescent multiplex immunohistochemistry

INTRODUCTION

We analyzed the expression of PD-L1 in human lymphomas using hyperspectral imaging (HSI) compared to visual assessment (VA) and conventional digital image analysis (DIA) to strengthen further the value of HSI as a tool for the evaluation of brightfield-based immunohistochemistry (IHC). In addition, fluorescent multiplex immunohistochemistry (mIHC) was used as a second detection method to analyze the impact of a different detection method.

MATERIAL AND METHODS

18 cases (6 follicular lymphomas and 12 diffuse large B-cell lymphomas) were stained for PD-L1 by IHC and for PD-L1, CD3, and CD8 by fluorescent mIHC. The percentage of positively stained cells was evaluated with VA, HSI, and DIA for IHC and VA and DIA for mIHC. Results were compared between the different methods of detection and analysis.

RESULTS

An overall high concordance was found between VA, HSI, and DIA in IHC (Cohens Kappa = 0.810^VA/HSI, 0.710 ^VA/DIA, and 0.516 ^HSI/DIA) and for VA^mIHCversus DIA^mIHC (Cohens Kappa = 0.894). Comparing IHC and mIHC general agreement differed depending on the methods compared but reached at most a moderate agreement (Coheńs Kappa between 0.250 and 0.483). This is reflected by the significantly higher percentage of PD-L1+ cells found with mIHC (p^Friedman = 0.014).

CONCLUSION

Our study shows a good concordance for the different analysis methods. Compared to VA and DIA, HSI proved to be a reliable tool for assessing IHC. Understanding the regulation of PD-L1 expression will further enlighten the role of PD-L1 as a biomarker. Therefore it is necessary to develop an instrument, such as HSI, which can offer a reliable and objective evaluation of PD-L1 expression.

Raman microscopic spectroscopy as a diagnostic tool to detect Staphylococcus epidermidis in bone grafts

INTRODUCTION

Raman microscopic spectroscopyis a new approach for further characterization and detection of molecular features in many pathological processes. This technique has been successfully applied to scrutinize the spatial distribution of small molecules and proteins within biological systems by in situ analysis. This study uses Raman microscopic spectroscopyto identify any in-depth benefits and drawbacks in diagnosing Staphylococcus epidermidis in human bone grafts.

MATERIAL AND METHODS

40 non-infected human bone samples and 10 human bone samples infected with Staphylococcus epidermidis were analyzed using Raman microscopic spectroscopy. Reflectance data were collected between 200 cm^-1 and 3600 cm^-1 with a spectral resolution of 4 cm^-1 using a Senterra II microscope (Bruker, Ettlingen, Germany). The acquired spectral information was used for spectral and unsupervised classification, such as principal component analysis.

RESULTS

Raman measurements produced distinct diagnostic spectra that were used to distinguish between non-infected human bone samples and Staphylococcus epidermidis infected human bone samples by spectral and principal component analyses. A substantial loss in bone quality and protein conformation was detected by human bone samples co-cultured with Staphylococcus epidermidis. The mineral-to-matrix ratio using the phosphate/Amide I ratio (p = 0.030) and carbonate/phosphate ratio (p = 0.001) indicates that the loss of relative mineral content in bones upon bacterial infection is higher than in non-infected human bones. Also, an increase of alterations in the collagen network (p = 0.048) and a decrease in the structural organization and relative collagen in infected human bone could be detected. Subsequent principal component analyses identified Staphylococcus epidermidis in different spectral regions, respectively, originating mainly from CH₂ deformation (wagging) of protein (at 1450 cm^-1) and bending and stretching modes of C-H groups (∼2800-3000 cm^-1).

CONCLUSION

Raman microscopic spectroscopyis presented as a promising diagnostic tool to detect Staphylococcus epidermidis in human bone grafts. Further studies in human tissues are warranted.

Tissue characterization of the medical fungus Hericium coralloides by focus-variation microscopy

In this study, the potential of focus-variation microscopic imaging was evaluated in a study of morphological patterns of the potential medicinal fungus Hericium coralloides (Basidiomycota). We created three-dimensional reconstructions and visualizations using the imaging technique on a fresh H. coralloides basidioma. The aim was to approximate the spore dispersal efficiency of this basidiomata type regarding the investment of tissue biomass and its reproductive output (production of basidiospores). Results were correlated with published data gained from magnetic resonance imaging and micro-computed tomography. It is demonstrated that focus-variation microscopic imaging results in a more distinct picture of the morphology of the edible and potentially medicinal H. coralloides basidiomata. However, a direct measurement of spore production was not possible. Spore production could only be estimated in combination with a mathematical model because the surface was not directly measurable due to the cellular heterogeneity. However, focus-variation microscopic imaging allows a better and faster estimation of spore production compared with the published methods. Furthermore, it was found that a scanning resolution of 5× is sufficient for determining the fungal surface precisely because at a higher resolution artifacts occur, resulting in adulteration of the image.

The future of pathology is digital

Information, archives, and intelligent artificial systems are part of everyday life in modern medicine. They already support medical staff by mapping their workflows with shared availability of cases' referral information, as needed for example, by the pathologist, and this support will be increased in the future even more. In radiology, established standards define information models, data transmission mechanisms, and workflows. Other disciplines, such as pathology, cardiology, and radiation therapy, now define further demands in addition to these established standards. Pathology may have the highest technical demands on the systems, with very complex workflows, and the digitization of slides generating enormous amounts of data up to Gigabytes per biopsy. This requires enormous amounts of data to be generated per biopsy, up to the gigabyte range. Digital pathology allows a change from classical histopathological diagnosis with microscopes and glass slides to virtual microscopy on the computer, with multiple tools using artificial intelligence and machine learning to support pathologists in their future work.

Comparison of structure and composition of a fossil Champsosaurus vertebra with modern Crocodylidae vertebrae: A multi-instrumental approach

Information on the adaptation of bone structures during evolution is rare since histological data are limited. Micro- and nano-computed tomography of a fossilized vertebra from Champsosaurus sp., which has an estimated age of 70-73 million years, revealed lower porosity and higher bone density compared to modern Crocodylidae vertebrae. Mid-infrared reflectance and energy dispersive X-ray mapping excluded a petrification process, and demonstrated a typical carbonate apatite distribution, confirming histology in light- and electron microscopy of the preserved vertebra. As a consequence of this evolutionary process, the two vertebrae of modern Crocodylidae show reduced overall stiffness in the finite element analysis simulation compared to the fossilized Champsosaurus sp. vertebra, with predominant stiffness along the longitudinal z-axes.

Clinical infrared microscopic imaging: An overview

New developments in Mid-infrared microscopic imaging instrumentation and data analysis have turned this method into a conventional technique. This imaging method offers a global analysis of samples, with a resolution close to the cellular level enabling the acquisition of local molecular expression profiles. It is possible to get chemo-morphological information about the tissue status, which represents an essential benefit for future analytical interpretation of pathological changes of tissue. In this review, we give an overview of Mid-infrared microscopic imaging and its applications in clinical research.

Application of mid-infrared (MIR) microscopy imaging for discrimination between follicular hyperplasia and follicular lymphoma in transgenic mice

Mid-infrared (MIR) microscopy imaging is a vibrational spectroscopic technique that uses infrared radiation to image molecules of interest in thin tissue sections. A major advantage of this technology is the acquisition of local molecular expression profiles, while maintaining the topographic integrity of the tissue. Therefore, this technology has become an essential tool for the detection and characterization of the molecular components of many biological processes. Using this method, it is possible to investigate the spatial distribution of proteins and small molecules within biological systems by in situ analysis. In this study, we have evaluated the potential of mid-infrared microscopy imaging to study biochemical changes which distinguish between reactive lymphadenopathy and cancer in genetically modified mice with different phenotypes. We were able to demonstrate that MIR microscopy imaging and multivariate image analyses of different mouse genotypes correlated well with the morphological tissue features derived from HE staining. Using principal component analyses, we were also able to distinguish spectral clusters from different phenotype samples, particularly from reactive lymphadenopathy (follicular hyperplasia) and cancer (follicular lymphoma).

Post-mortem interval estimation of human skeletal remains by micro-computed tomography, mid-infrared microscopic imaging and energy dispersive X-ray mapping

In this study different state-of-the-art visualization methods such as micro-computed tomography (micro-CT), mid-infrared (MIR) microscopic imaging and energy dispersive X-ray (EDS) mapping were evaluated to study human skeletal remains for the determination of the post-mortem interval (PMI). PMI specific features were identified and visualized by overlaying molecular imaging data and morphological tissue structures generated by radiological techniques and microscopic images gained from confocal microscopy (Infinite Focus (IFM)). In this way, a more distinct picture concerning processes during the PMI as well as a more realistic approximation of the PMI were achieved. It could be demonstrated that the gained result in combination with multivariate data analysis can be used to predict the Ca/C ratio and bone volume (BV) over total volume (TV) for PMI estimation. Statistical limitation of this study is the small sample size, and future work will be based on more specimens to develop a screening tool for PMI based on the outcome of this multidimensional approach.

Simultaneous quantification of verbenalin and verbascoside in Verbena officinalis by ATR-IR and NIR spectroscopy

Attenuated-total-reflectance infrared spectroscopy (ATR-IR) and near-infrared diffuse reflectance spectroscopy (NIR) in hyphenation with multivariate analysis was utilized to quantify verbenalin and verbascoside in Verbena officinalis. A new high performance liquid chromatography (HPLC) method as a reference was established and validated. For both vibrational spectroscopic methods test-set and cross validation were performed. Different data-pre-treatments like SNV, 1st and 2nd derivative were applied to remove systematic errors and were evaluated. Quality parameters obtained for the test-set validation revealed that ATR-IR (verbenalin: R(2)=0.94, RPD=4.23; verbascoside: R(2)=0.93, RPD=3.63) has advantages over NIR (verbenalin: R(2)=0.91, RPD=3.75; verbascoside: R(2)=0.80, RPD=2.35) in the given application.

Fourier transform infrared imaging analysis in discrimination studies of squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) of the oral cavity and oropharynx represents more than 95% of all malignant neoplasms in the oral cavity. Histomorphological evaluation of this cancer type is invasive and remains a time consuming and subjective technique. Therefore, novel approaches for histological recognition are necessary to identify malignancy at an early stage. Fourier transform infrared (FTIR) imaging has become an essential tool for the detection and characterization of the molecular components of biological processes, such as those responsible for the dynamic properties of tumor progression. FTIR imaging is a modern analytical technique enabling molecular imaging of a complex biological sample and is based on the absorption of IR radiation by vibrational transitions in covalent bonds. One major advantage of this technique is the acquisition of local molecular expression profiles, while maintaining the topographic integrity of the tissue and avoiding time-consuming extraction, purification, and separation steps. With this imaging technique, it is possible to obtain unique images of the spatial distribution of proteins, lipids, carbohydrates, cholesterols, nucleic acids, phospholipids, and small molecules with high spatial resolution. Analysis and visualization of FTIR imaging datasets are challenging and the use of chemometric tools is crucial in order to take advantage of the full measurement. Therefore, methodologies for this task based on the novel developed algorithm for multivariate image analysis (MIA) are often necessary. In the present study, FTIR imaging and data analysis methods were combined to optimize the tissue measurement mode after deparaffinization and subsequent data evaluation (univariate analysis and MIAs). We demonstrate that it is possible to collect excellent IR spectra from formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMAs) of OSCC tissue sections employing an optimised analytical protocol. The correlation of FTIR imaging to the morphological tissue features obtained by histological staining of the sections demonstrated that many histomorphological tissue patterns can be visualized in the colour images. The different algorithms used for MIAs of FTIR imaging data dramatically increased the information content of the IR images from squamous cell tissue sections. These findings indicate that intra-operative and surgical specimens of squamous cell carcinoma tissue can be characterized by FTIR imaging.

Near infrared spectroscopy patents for the physicochemical characterization of nanomaterials: the road from production to routine high-throughput quality control

The measurement of the physical and chemical ("physicochemical") properties of nanomaterials used in industry and science including chemistry, pharmacy, medicine, toxicology, etc., is time-consuming, expensive and requires a lot of experience of a well trained lab staff. Near-infrared spectroscopy (NIR; 4.000-12.000 cm(-1)), working in the wavelength region with the highest IR energy, allows obtaining multifactorial information of the material under investigation due to the occurrence of a high number of combination and overtone vibrations. Coupling of an optimized and well-designed measurement technique with multivariate data analysis (MVA) leads to a non-destructive, fast, reliable and robust novel NIR technique for the fast and non-invasive physicochemical characterization, which is suitable for high-throughput quality control due to the short analyses times of only a few seconds. In the following chapters, the patented basic NIR techniques full-filling these aims are introduced, described, summarized and critically discussed.

Infrared-spectroscopy: a non-invasive tool for medical diagnostics and drug analysis

Constant development enabled Infrared (IR) spectroscopy to become a widely used, non-invasive tool for fast sample analyses with less to no pre-preparation. Furthermore, computational data handling is no more a limiting factor and hence, IR measurements are predestined for clinical diagnostics and drug analysis. Within this review the focus was put on clinical topics of high interest. One example is Alzheimer's disease, where the exact metabolism is still not clarified, or blood glucose monitoring for high throughput screening of patients without taking any drop of blood. The second section of this manuscript was focused on the analysis of drugs. The detection of physico-chemical parameters in pharmaceutics and the improvement of industrial proceedings allowed a dramatic increase of quality of produced medicine. In pharmaceutical industries problems with the equable allocation of agents occurs especially in scaling up processes. IR-analyzing-techniques serve as fast and precise indicators for the detection of active components and their distribution in tablets. In combination with statistical factors and medical investigations pharmaceuticals can be improved from their development until their application, and every step can be easily controlled by IR spectroscopy.