Microscopy and Image Analysis

Digital pathology systems enabling quality patient care

Pathology laboratories are undergoing digital transformations, adopting innovative technologies to enhance patient care. Digital pathology systems impact clinical, education, and research use cases where pathologists use digital technologies to perform tasks in lieu of using glass slides and a microscope. Pathology professional societies have established clinical validation guidelines, and the US Food and Drug Administration have also authorized digital pathology systems for primary diagnosis, including image analysis and machine learning systems. Whole slide images, or digital slides, can be viewed and navigated similar to glass slides on a microscope. These modern tools not only enable pathologists to practice their routine clinical activities, but can potentially enable digital computational discovery. Assimilation of whole slide images in pathology clinical workflow can further empower machine learning systems to support computer assisted diagnostics. The potential enrichment these systems can provide is unprecedented in the field of pathology. With appropriate integration, these clinical decision support systems will allow pathologists to increase the delivery of quality patient care. This review describes the digital pathology transformation process, applicable clinical use cases, incorporation of image analysis and machine learning systems in the clinical workflow, as well as future technologies that may further disrupt pathology modalities to deliver quality patient care.

In vitro model systems for exploring oral biofilms: From single-species populations to complex multi-species communities

Numerous in vitro biofilm model systems are available to study oral biofilms. Over the past several decades, increased understanding of oral biology and advances in technology have facilitated more accurate simulation of intraoral conditions and have allowed for the increased generalizability of in vitro oral biofilm studies. The integration of contemporary systems with confocal microscopy and 16S rRNA community profiling has enhanced the capabilities of in vitro biofilm model systems to quantify biofilm architecture and analyse microbial community composition. In this review, we describe several model systems relevant to modern in vitro oral biofilm studies: the constant depth film fermenter, Sorbarod perfusion system, drip-flow reactor, modified Robbins device, flowcells and microfluidic systems. We highlight how combining these systems with confocal microscopy and community composition analysis tools aids exploration of oral biofilm development under different conditions and in response to antimicrobial/anti-biofilm agents. The review closes with a discussion of future directions for the field of in vitro oral biofilm imaging and analysis.

Contemporary Whole Slide Imaging Devices and Their Applications within the Modern Pathology Department: A Selected Hardware Review

Digital pathology (DP) has disrupted the practice of traditional pathology, including applications in education, research, and clinical practice. Contemporary whole slide imaging (WSI) devices include technological advances that help address some of the challenges facing modern pathology, such as increasing workloads with fewer subspecialized pathologists, expanding integrated delivery networks with global reach, and greater customization when working up cases for precision medicine. This review focuses on integral hardware components of 43 market available and soon-to-be released digital WSI devices utilized throughout the world. Components such as objective lens type and magnification, scanning camera, illumination, and slide capacity were evaluated with respect to scan time, throughput, accuracy of scanning, and image quality. This analysis of assorted modern WSI devices offers essential, valuable information for successfully selecting and implementing a digital WSI solution for any given pathology practice.

A digital image analysis study on the disintegration kinetics of reticular fibers in the ethylene glycol-induced rat liver tissue

Ethylene glycol (EG), the raw material of polyethylenterephthalate, which is the most consumed plastic in the world, has low toxicity, but its metabolites are toxic. EG metabolites can cause acidosis, fibrosis, and eventually cirrhosis in the liver. This study aimed to investigate the effect of EG on rat liver and to determine the quantitative values of the disintegration of reticular fibers (RF) in the liver with the dose duration and to investigate the changes by digital image analysis (DIA). For this purpose, Wistar albino rats were divided into control, and five different daily experimental groups. The control group received saline, and the experimental groups received EG. At the end of experiments, liver tissues of all euthanized rats were removed, and sections were taken, and RF was shown by silver staining. It was observed that the RF fragments in the experimental groups were less than the control group. DIA of RF fragments was then performed with Olympus cellSensDimension 1.15 software and number, area, and ROI% values of the fragments were determined. Statistical analysis revealed that there was a significant difference between control and all experimental groups. RF fragments showed first-order disintegration kinetics, mean disintegration rate constant, and half-time values were 0.1 day^-1 and 7 days, respectively. Consequently, the digital image analysis approach can be a useful tool for the biologist, pathologist, fibrosis-cirrhosis specialist, and computer scientist to understand the effects of toxic chemicals in the liver and analyze reticular fiber disintegration.

New Technologies to Image Tumors

The premise of this book is the importance of the tumor microenvironment (TME). Until recently, most research on and clinical attention to cancer biology, diagnosis, and prognosis were focused on the malignant (or premalignant) cellular compartment that could be readily appreciated using standard morphology-based imaging.

Design of an automated capillary electrophoresis platform for single-cell analysis

Single-cell analysis of cellular contents by highly sensitive analytical instruments is known as chemical cytometry. A chemical cytometer typically samples one cell at a time, quantifies the cellular contents of interest, and then processes and reports that data. Automation adds the potential to perform this entire sequence of events with minimal intervention, increasing throughput and repeatability. In this chapter, we discuss the design considerations for an automated capillary electrophoresis-based instrument for assay of enzymatic activity within single cells. We describe the key requirements of the microscope base and capillary electrophoresis platforms. We also provide detailed protocols and schematic designs of our cell isolation, lysis, sampling, and detection strategies. Additionally, we describe our signal processing and instrument automation workflows. The described automated system has demonstrated single-cell throughput at rates above 100cells/h and analyte limits of detection as low as 10^-20mol.

Quantifying Cellular Internalization with a Fluorescent Click Sensor

The ability to determine the amount of material endocytosed by a cell is important for our understanding of cell biology and in the design of effective carriers for drug delivery. To quantify internalization by fluorescence, the signal from material remaining on the cell surface must be differentiated from endocytosed material. Sensors for internalization offer advantages over traditional methods for achieving this as they exhibit improved sensitivity, allow for multiple fluorescent markers to be used simultaneously, and are amenable to high-throughput analysis. We have developed a small fluorescent internalization sensor, similar in size to a standard fluorescent dye, that can be conjugated to proteins and uses the rapid and highly specific bio-orthogonal reaction between a tetrazine and a trans-cyclooctene group to switch off the surface signal. The sensor can be attached to a variety of materials using simple chemistry and is compatible with flow cytometry and fluorescence microscopy, making it a useful tool to study the uptake of material into cells.