Improved tissue preparation for multimodal vibrational imaging of biological tissues

Gassner, Callum; Adegoke, John A.; Patel, Sheila K.; Sharma, Varun; Kochan, Kamila; Burrell, Louise M.; Raman, Jaishankar; Wood, Bayden Robert

doi:10.1016/j.clispe.2022.100021

Cited by 4 publications

(4 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, various methods of multivariate analysis are used to help with data interpretation[ 78 ]. Hyperspectral mapping with K-means clustering and principal component analysis (PCA) is commonly performed to explore spectral variation[ 79 - 81 ]. Pre-processing of the spectroscopic data involves cosmic rays removal, baseline correction, and smoothing (adaptive multi-round smoothing based on the Savitzky-Golay filter).…”

Section: Multivariate Data Analysismentioning

confidence: 99%

Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis?

Szymoński¹,

Chmura²,

Lipiec³

et al. 2023

World J Gastroenterol

View full text Add to dashboard Cite

Pancreatic cancer (PC) is an aggressive and lethal neoplasm, ranking seventh in the world for cancer deaths, with an overall 5-year survival rate of below 10%. The knowledge about PC pathogenesis is rapidly expanding. New aspects of tumor biology, including its molecular and morphological heterogeneity, have been reported to explain the complicated “cross-talk” that occurs between the cancer cells and the tumor stroma or the nature of pancreatic ductal adenocarcinoma-associated neural remodeling. Nevertheless, currently, there are no specific and sensitive diagnosis options for PC. Vibrational spectroscopy (VS) shows a promising role in the development of early diagnosis technology. In this review, we summarize recent reports about improvements in spectroscopic methodologies, briefly explain and highlight the drawbacks of each of them, and discuss available solutions. The important aspects of spectroscopic data evaluation with multivariate analysis and a convolutional neural network methodology are depicted. We conclude by presenting a study design for systemic verification of the VS-based methods in the diagnosis of PC.

show abstract

Section: Multivariate Data Analysismentioning

confidence: 99%

Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis?

Szymoński¹,

Chmura²,

Lipiec³

et al. 2023

World J Gastroenterol

View full text Add to dashboard Cite

show abstract

“…The embedding media typically used are strong IR absorbers and as such the removal of these substances by further processing prior to analysis is often desirable to avoid spectral contributions from the embedding medium. 83,84 Although these protocols are unavoidable for many IR spectroscopic measurements, the use of fixatives and the processes used to embed samples have been shown to induce chemical alterations that manifest as spectral variances. 84,85 Furthermore, the process of removing some embedding materials is itself problematic, with the efficient removal of these substances proving to be elusive.…”

Section: Sample Preparation and Propertiesmentioning

confidence: 99%

“…8 (mirrored) finished, grade 304 stainless-steel slide. 83 Subsequent analysis was performed in transflection mode with the offline Bruker Hyperion 3000 IR microscope equipped with a 15× objective and a 64 × 64-pixel FPA which was coupled to a Bruker Vertex 70 Spectrometer (Australian Synchrotron). To perform polarized measurements, a wire-grid polarizer was inserted in the beam path prior to (polarizer) and after (analyzer) the sample, and the sample was analyzed with four polarization angles (0°, 45°, 90°, and 135°).…”

Section: Instrumentationmentioning

confidence: 99%

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

Gassner

Vongsvivut

et al. 2023

Appl Spectrosc

Self Cite

View full text Add to dashboard Cite

The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward “real-world” applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.

show abstract

“…To reduce data dimensionality and extract the most important information-marker bands of molecular pathologies, from the acquired data, various methods of multivariate data analysis are used [252]. K-means clustering (KMC), and principal component analysis (PCA) are commonly performed to explore spectral variation in maps acquired from tissue sections [253][254][255].…”

Section: Molecular Characteristics Of Malignant Pancreatic Tissuesmentioning

confidence: 99%

Current Pathology Model of Pancreatic Cancer

Szymoński

Milian-Ciesielska²,

Lipiec

et al. 2022

Cancers

View full text Add to dashboard Cite

Pancreatic cancer (PC) is one of the most aggressive and lethal malignant neoplasms, ranking in seventh place in the world in terms of the incidence of death, with overall 5-year survival rates still below 10%. The knowledge about PC pathomechanisms is rapidly expanding. Daily reports reveal new aspects of tumor biology, including its molecular and morphological heterogeneity, explain complicated “cross-talk” that happens between the cancer cells and tumor stroma, or the nature of the PC-associated neural remodeling (PANR). Staying up-to-date is hard and crucial at the same time. In this review, we are focusing on a comprehensive summary of PC aspects that are important in pathologic reporting, impact patients’ outcomes, and bring meaningful information for clinicians. Finally, we show promising new trends in diagnostic technologies that might bring a difference in PC early diagnosis.

show abstract

Improved tissue preparation for multimodal vibrational imaging of biological tissues

Cited by 4 publications

References 27 publications

Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis?

Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis?

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

Current Pathology Model of Pancreatic Cancer

Contact Info

Product

Resources

About