Digital Microscopy, Image Analysis, and Virtual Slide Repository

An Artificial Intelligence-Based Digital Analysis of Immunolocalization of MMP2 and TIMP2 in the Jejunum of Rats Treated with Calcineurin Inhibitors

(1) Background: The main goal of this study was to analyze the morphology of the rat's jejunum after long-term treatment with calcineurin inhibitor-based immunosuppressive drugs and to investigate their impact on the location of MMP-2 and its inhibitor TIMP-2, as well as the balance between them. (2) Methods: Twenty-four rats were divided into four groups receiving different immunosuppressive regiments. After six months of treatment, the jejunums were collected and analyzed. (3) Results: immunosuppressive drug panels containing calcineurin inhibitors (CNIs) have a negative impact on the morphology and morphometry of the small intestinal wall. These drugs disrupt the MMP-2/TIMP-2 balance. Both CsA and TAC interfere with the synthesis of intercellular matrix components in the connective tissue of the small intestine. Furthermore, tacrolimus appears to disrupt the MMP-2/TIMP-2 balance in the small intestine the most, as the results show the highest difference between MMP-2 and TIMP-2 expression. The results were also confirmed by digital analysis of tissue segmentation. (4) Conclusions: The research conducted in this study is unique because there is limited information available on the direct effects of immunosuppressive drugs on the expression of MMP-2 and their inhibitors in the jejunum. Additionally, this study involves three drugs instead of one, which accurately reflects the panel of drugs used in organ recipients. Our results suggest that immunosuppressive drugs affect morphology and MMP2/TIMP2 immunoexpression; however, further studies are required. AI-based tools provide a reliable analysis of tissue samples, which represents an exciting approach for future histopathological studies. However, the results of the analyses generated by these tools need to be verified by specialists.

Invisible for a few but essential for many: the role of Histotechnologists in the establishment of digital pathology

Digital pathology (DP) is indisputably the future for histopathology laboratories. The process of digital implementation requires deep workflow reorganisation which involves an interdisciplinary team. This transformation may have the greatest impact on the Histotechnologist (HTL) profession. Our review of the literature has clearly revealed that the role of HTLs in the establishment of DP is being unnoticed and guidance is limited. This article aims to bring HTLs from behind-the-scenes into the spotlight. Our objective is to provide them guidance and practical recommendations to successfully contribute to the implementation of a new digital workflow. Furthermore, it also intends to contribute for improvement of study programs, ensuring the role of HTL in DP is addressed as part of graduate and post-graduate education. In our review, we report on the differences encountered between workflow schemes and the limitations observed in this process. The authors propose a digital workflow to achieve its limitless potential, focusing on the HTL's role. This article explores the novel responsibilities of HTLs during specimen gross dissection, embedding, microtomy, staining, digital scanning, and whole slide image quality control. Furthermore, we highlight the benefits and challenges that DP implementation might bring the HTLs career. HTLs have an important role in the digital workflow: the responsibility of achieving the perfect glass slide.

Optimized detection and segmentation of nuclei in gastric cancer images using stain normalization and blurred artifact removal

Histological analysis with microscopy is the gold standard to diagnose and stage cancer, where slides or whole slide images are analyzed for cell morphological and spatial features by pathologists. The nuclei of cancerous cells are characterized by nonuniform chromatin distribution, irregular shapes, and varying size. As nucleus area and shape alone carry prognostic value, detection and segmentation of nuclei are among the most important steps in disease grading. However, evaluation of nuclei is a laborious, time-consuming, and subjective process with large variation among pathologists. Recent advances in digital pathology have allowed significant applications in nuclei detection, segmentation, and classification, but automated image analysis is greatly affected by staining factors, scanner variability, and imaging artifacts, requiring robust image preprocessing, normalization, and segmentation methods for clinically satisfactory results. In this paper, we aimed to evaluate and compare the digital image analysis techniques used in clinical pathology and research in the setting of gastric cancer. A literature review was conducted to evaluate potential methods of improving nuclei detection. Digitized images of 35 patients from a retrospective cohort of gastric adenocarcinoma at Oulu University Hospital in 1987-2016 were annotated for nuclei (n = 9085) by expert pathologists and 14 images of different cancer types from public TCGA dataset with annotated nuclei (n = 7000) were used as a comparison to evaluate applicability in other cancer types. The detection and segmentation accuracy with the selected color normalization and stain separation techniques were compared between the methods. The extracted information can be supplemented by patient's medical data and fed to the existing statistical clinical tools or subjected to subsequent AI-assisted classification and prediction models. The performance of each method is evaluated by several metrics against the annotations done by expert pathologists. The F1-measure of 0.854 ± 0.068 is achieved with color normalization for the gastric cancer dataset, and 0.907 ± 0.044 with color deconvolution for the public dataset, showing comparable results to the earlier state-of-the-art works. The developed techniques serve as a basis for further research on application and interpretability of AI-assisted tools for gastric cancer diagnosis.

Whole slide imaging (WSI) scanner differences influence optical and computed properties of digitized prostate cancer histology

Purpose

Digital pathology is becoming an increasingly popular area of advancement in both research and clinically. Pathologists are now able to manage and interpret slides digitally, as well as collaborate with external pathologists with digital copies of slides. Differences in slide scanners include variation in resolution, image contrast, and optical properties, which may influence downstream image processing. This study tested the hypothesis that varying slide scanners would result in differences in computed pathomic features on prostate cancer whole mount slides.

Design

This study collected 192 unique tissue slides from 30 patients following prostatectomy. Tissue samples were paraffin-embedded, stained for hematoxylin and eosin (H&E), and digitized using 3 different scanning microscopes at the highest available magnification rate, for a total of 3 digitized slides per tissue slide. These scanners included a (S1) Nikon microscope equipped with an automated sliding stage, an (S2) Olympus VS120 slide scanner, and a (S3) Huron TissueScope LE scanner. A color deconvolution algorithm was then used to optimize contrast by projecting the RGB image into color channels representing optical stain density. The resulting intensity standardized images were then computationally processed to segment tissue and calculate pathomic features including lumen, stroma, epithelium, and epithelial cell density, as well as second-order features including lumen area and roundness; epithelial area, roundness, and wall thickness; and cell fraction. For each tested feature, mean values of that feature per digitized slide were collected and compared across slide scanners using mixed effect models, fit to compare differences in the tested feature associated with all slide scanners for each slide, including a random effect of subject with a nested random effect of slide to account for repeated measures. Similar models were also computed for tissue densities to examine how differences in scanner impact downstream processing.

Results

Each mean color channel intensity (i.e., Red, Green, Blue) differed between slide scanners (all P<.001). Of the color deconvolved images, only the hematoxylin channel was similar in all 3 scanners (all P>.05). Lumen and stroma densities between S3 and S1 slides, and epithelial cell density between S3 and S2 (P>.05) were comparable but all other comparisons were significantly different (P<.05). The second-order features were found to be comparable for all scanner comparisons, except for lumen area and epithelium area.

Conclusion

This study demonstrates that both optical and computed properties of digitized histological samples are impacted by slide scanner differences. Future research is warranted to better understand which scanner properties influence the tissue segmentation process and to develop harmonization techniques for comparing data across multiple slide scanners.

Towards virtual histology with X-ray grating interferometry

Breast cancer is the most common type of cancer worldwide. Diagnosing breast cancer relies on clinical examination, imaging and biopsy. A core-needle biopsy enables a morphological and biochemical characterization of the cancer and is considered the gold standard for breast cancer diagnosis. A histopathological examination uses high-resolution microscopes with outstanding contrast in the 2D plane, but the spatial resolution in the third, Z-direction, is reduced. In the present paper, we propose two high-resolution table-top systems for phase-contrast X-ray tomography of soft-tissue samples. The first system implements a classical Talbot-Lau interferometer and allows to perform ex-vivo imaging of human breast samples with a voxel size of 5.57 μm. The second system with a comparable voxel size relies on a Sigray MAAST X-ray source with structured anode. For the first time, we demonstrate the applicability of the latter to perform X-ray imaging of human breast specimens with ductal carcinoma in-situ. We assessed image quality of both setups and compared it to histology. We showed that both setups made it possible to target internal features of breast specimens with better resolution and contrast than previously achieved, demonstrating that grating-based phase-contrast X-ray CT could be a complementary tool for clinical histopathology.

Machine learning for detection and classification of oral potentially malignant disorders: A conceptual review

Oral potentially malignant disorders represent precursor lesions that may undergo malignant transformation to oral cancer. There are many known risk factors associated with the development of oral potentially malignant disorders, and contribute to the risk of malignant transformation. Although many advances have been reported to understand the biological behavior of oral potentially malignant disorders, their clinical features that indicate the characteristics of malignant transformation are not well established. Early diagnosis of malignancy is the most important factor to improve patients' prognosis. The integration of machine learning into routine diagnosis has recently emerged as an adjunct to aid clinical examination. Increased performances of artificial intelligence AI-assisted medical devices are claimed to exceed the human capability in the clinical detection of early cancer. Therefore, the aim of this narrative review is to introduce artificial intelligence terminology, concepts, and models currently used in oncology to familiarize oral medicine scientists with the language skills, best research practices, and knowledge for developing machine learning models applied to the clinical detection of oral potentially malignant disorders.

Quantitative Analysis of Inflammatory Uterine Lesions of Pregnant Gilts with Digital Image Analysis Following Experimental PRRSV-1 Infection

Reproductive disorders caused by porcine reproductive and respiratory syndrome virus-1 are not yet fully characterized. We report QuPath-based digital image analysis to count inflammatory cells in 141 routinely, and 35 CD163 immunohistochemically stained endometrial slides of vaccinated or unvaccinated pregnant gilts inoculated with a high or low virulent PRRSV-1 strain. To illustrate the superior statistical feasibility of the numerical data determined by digital cell counting, we defined the association between the number of these cells and endometrial, placental, and fetal features. There was strong concordance between the two manual scorers. Distributions of total cell counts and endometrial and placental qPCR results differed significantly between examiner1's endometritis grades. Total counts' distribution differed significantly between groups, except for the two unvaccinated. Higher vasculitis scores were associated with higher endometritis scores, and higher total cell counts were expected with high vasculitis/endometritis scores. Cell number thresholds of endometritis grades were determined. A significant correlation between fetal weights and total counts was shown in unvaccinated groups, and a significant positive correlation was found between these counts and endometrial qPCR results. We revealed significant negative correlations between CD163+ counts and qPCR results of the unvaccinated group infected with the highly virulent strain. Digital image analysis was efficiently applied to assess endometrial inflammation objectively.

Digital microscopy: A routine mandate in future? A leaf out of Covid-19 pandemic laboratory experience

The COVID-19 pandemic has brought out lot of changes among the way people and organisations function. It has also reduced social gatherings and hence social relations considerably, forcing people to adjust to new ways of work and life. An outstanding difference between the current COVID-19 pandemic and previous epidemics or pandemics is the increased availability and use of technology currently, which has been validated by various reports from across the globe. Thus, even with the ensuing pandemic, lockdown and decreased social gatherings, with the technology support we have devised ways to keep in contact with friends, family and work place, so as to continue our lives. Social distancing guidelines and regulations have put pressure on a great many organisations to find new ways of keeping employees and students connected while working remotely. For more deskbound occupations and roles, this can be relatively straightforward, but it is challenging if not impossible for lab-based quality control, research and study. The answer to this is digital remote microscopy which enables sharing of data online, carrying out collaborative work through multi-viewing in real time and facilitates remote training functions.

Development of an automated combined positive score prediction pipeline using artificial intelligence on multiplexed immunofluorescence images

Immunotherapy targeting immune checkpoint proteins, such as programmed cell death ligand 1 (PD-L1), has shown impressive outcomes in many clinical trials but only 20%-40% of patients benefit from it. Utilizing Combined Positive Score (CPS) to evaluate PD-L1 expression in tumour biopsies to identify patients with the highest likelihood of responsiveness to anti-PD-1/PD-L1 therapy has been approved by the Food and Drug Administration for several solid tumour types. Current CPS workflow requires a pathologist to manually score the two-colour PD-L1 chromogenic immunohistochemistry image. Multiplex immunofluorescence (mIF) imaging reveals the expression of an increased number of immune markers in tumour biopsies and has been used extensively in immunotherapy research. Recent rapid progress of Artificial Intelligence (AI)-based imaging analysis, particularly Deep Learning, provides cost effective and high-quality solutions to healthcare. In this article, we propose an imaging pipeline that utilizes three-colour mIF images (DAPI, PD-L1, and Pan-cytokeratin) as input and predicts the CPS using AI techniques. Our novel pipeline is composed of three modules employing algorithms of image processing, machine learning, and deep learning techniques. The first module of quality check (QC) detects and removes the image regions contaminated with sectioning and staining artefacts. The QC module ensures that only image regions free of the three common artefacts are used for downstream analysis. The second module of nuclear segmentation uses deep learning to segment and count nuclei in the DAPI images wherein our specialized method can accurately separate touching nuclei. The third module of cell phenotyping calculates CPS by identifying and counting PD-L1 positive cells and tumour cells. These modules are data-efficient and require only few manual annotations for training purposes. Using tumour biopsies from a clinical trial, we found that the CPS from the AI-based models shows a high Spearman correlation (78%, p = 0.003) to the pathologist-scored CPS.

Virtual Microscopy Tagging and Its Benefits for Students, Faculty, and Interprofessional Programs Alike

Background

Over the years, due to technological innovations in medical education, virtual microscopy has become a popular tool used to teach histology. The Virtual Microscopy Project is a faculty and student collaborative project at the University of South Florida (USF) Health to transfer and update online histology slides from an outdated viewer to a completely new viewer.

Methodology

The project goal is to better facilitate the educational experience for students and faculty through the implementation of updated technology and features.

Results

At USF Health, multiple programs use the online histology slide viewer to teach normal histology. The previous website’s organization and lack of additional features severely hindered opportunities for personalized education; users could not write any notes, circle or point to important features, or easily search for specific organs or tissue. An updated website user interface and additional instructional features will improve the students’ accessibility and overall quality of their learning. The updated viewer will be more integrated into the USF Health Morsani College of Medicine (MCOM) curriculum, providing faculty with organized and readily available material. USF MCOM has faculty integration directors to create a balanced curriculum that can be reviewed by faculty for consistency and accuracy. Adding this same organizational structure to the online microscopy viewer will assist directors in forming and modifying the curriculum and may also provide them with additional resources for their education delivery.

Conclusion

The Virtual Microscopy Project hopes to produce an accessible, user-friendly online microscopy viewer that is beneficial to students for learning, to faculty for teaching/curriculum planning, and to medical education as a whole.

Artificial Intelligence-Assisted Image Analysis of Acetaminophen-Induced Acute Hepatic Injury in Sprague-Dawley Rats

Although drug-induced liver injury (DILI) is a major target of the pharmaceutical industry, we currently lack an efficient model for evaluating liver toxicity in the early stage of its development. Recent progress in artificial intelligence-based deep learning technology promises to improve the accuracy and robustness of current toxicity prediction models. Mask region-based CNN (Mask R-CNN) is a detection-based segmentation model that has been used for developing algorithms. In the present study, we applied a Mask R-CNN algorithm to detect and predict acute hepatic injury lesions induced by acetaminophen (APAP) in Sprague-Dawley rats. To accomplish this, we trained, validated, and tested the model for various hepatic lesions, including necrosis, inflammation, infiltration, and portal triad. We confirmed the model performance at the whole-slide image (WSI) level. The training, validating, and testing processes, which were performed using tile images, yielded an overall model accuracy of 96.44%. For confirmation, we compared the model’s predictions for 25 WSIs at 20× magnification with annotated lesion areas determined by an accredited toxicologic pathologist. In individual WSIs, the expert-annotated lesion areas of necrosis, inflammation, and infiltration tended to be comparable with the values predicted by the algorithm. The overall predictions showed a high correlation with the annotated area. The R square values were 0.9953, 0.9610, and 0.9445 for necrosis, inflammation plus infiltration, and portal triad, respectively. The present study shows that the Mask R-CNN algorithm is a useful tool for detecting and predicting hepatic lesions in non-clinical studies. This new algorithm might be widely useful for predicting liver lesions in non-clinical and clinical settings.

Scientific and Regulatory Policy Committee Points to Consider: Primary Digital Histopathology Evaluation and Peer Review for Good Laboratory Practice (GLP) Nonclinical Toxicology Studies

The Society of Toxicologic Pathology's Scientific and Regulatory Policy Committee formed a working group to consider the present and future use of digital pathology in toxicologic pathology in general and specifically its use in primary evaluation and peer review in Good Laboratory Practice (GLP) environments. Digital histopathology systems can save costs by reducing travel, enhancing organizational flexibility, decreasing slide handling, improving collaboration, increasing access to historical images, and improving quality and efficiency through integration with laboratory information management systems. However, the resources to implement and operate a digital pathology system can be significant. Given the magnitude and risks involved in the decision to adopt digital histopathology, this working group used pertinent previously published survey results and its members' expertise to create a Points-to-Consider article to assist organizations with building and implementing digital pathology workflows. With the aim of providing a comprehensive perspective, the current publication summarizes aspects of digital whole-slide imaging relevant to nonclinical histopathology evaluations, and then presents points to consider applicable to both primary digital histopathology evaluation and digital peer review in GLP toxicology studies. The Supplemental Appendices provide additional tabulated resources.

The Effect of Chronic Immunosuppressive Regimens Treatment on Aortal Media Morphology and the Balance between Matrix Metalloproteinases (mmp-2 and mmp-9) and Their Inhibitors in the Abdominal Aorta of Rats

Immunosuppressive drugs are widely and chronically used to avoid graft rejection in transplant recipients. However, they are also known to have organotoxic effects and can exert numerous side effects. The aim of this study was to assess whether the chronic treatment of rats with the most commonly used clinical immunosuppressive regimens in organ recipients had an effect on the morphology and function of the aorta. The rats were divided into five groups and each group was chronically treated with different sets of three immunosuppressive drugs (TRG, CRG, MRG, CMG, TMG) for 6 months. The changes were most profound in calcineurin inhibitor-based protocols. TMG protocol treatment was characterized by the most numerous alterations such as morphological changes, changes in the thickness of the tunic media, wider distances between elastic lamellae, an increase in the number of vSMCs and changes in collagen deposition. We concluded that the morphological changes were connected with MMP-2 and MMP-9/TIMP-2 and TIMP-1 imbalances, which was also determined and noticed.

A low-cost pathological image digitalization method based on 5 times magnification scanning

BACKGROUND

Digital pathology has aroused widespread interest in modern pathology. The key to digitalization is to scan the whole slide image (WSI) at high magnification. The file size of each WSI at 40 times magnification (40×) may range from 1 gigabyte (GB) to 5 GB depending on the size of the specimen, which leads to huge storage capacity, very slow scanning and network exchange, seriously increasing time and storage costs for digital pathology.

METHODS

We design a strategy to scan slides with low resolution (LR) (5×), and a superresolution (SR) method is proposed to restore the image details during diagnosis. The method is based on a multiscale generative adversarial network, which can sequentially generate three high-resolution (HR) images: 10×, 20×, and 40×. A dataset consisting of 100,000 pathological images from 10 types of human body systems is used for training and testing. The differences between the generated images and the real images have been extensively evaluated using quantitative evaluation, visual inspection, medical scoring, and diagnosis.

RESULTS

The file size of each 5× WSI is approximately 15 Megabytes. The peak-signal-to-noise ratios (PSNRs) of 10× to 40× generated images are 24.167±3.734 dB, 22.272±4.272 dB, and 20.436±3.845 dB, and the structural similarity (SSIM) index values are 0.845±0.089, 0.680±0.150, and 0.559±0.179, which are better than those of other SR networks and conventional digital zoom methods. Visual inspections show that the generated images have details similar to the real images. Visual scoring average with 0.95 confidence interval from three pathologists are 3.630±1.024, 3.700±1.126, and 3.740±1.095, respectively, and the P value of analysis of variance is 0.367, indicating the pathologists confirm that generated images include sufficient information for diagnosis. The average value of the Kappa test of the diagnoses of paired generated and real images is 0.990, meaning the diagnosis of generated images is highly consistent with that of the real images.

CONCLUSIONS

The proposed method can generate high-quality 10×, 20×, 40× images from 5× images, which can effectively reduce the time and storage costs of digitalization up to 1/64 of the previous costs, which shows the potential for clinical applications and is expected to be an alternative digitalization method after large-scale evaluation.

Chip-based multimodal super-resolution microscopy for histological investigations of cryopreserved tissue sections

Histology involves the observation of structural features in tissues using a microscope. While diffraction-limited optical microscopes are commonly used in histological investigations, their resolving capabilities are insufficient to visualize details at subcellular level. Although a novel set of super-resolution optical microscopy techniques can fulfill the resolution demands in such cases, the system complexity, high operating cost, lack of multi-modality, and low-throughput imaging of these methods limit their wide adoption for histological analysis. In this study, we introduce the photonic chip as a feasible high-throughput microscopy platform for super-resolution imaging of histological samples. Using cryopreserved ultrathin tissue sections of human placenta, mouse kidney, pig heart, and zebrafish eye retina prepared by the Tokuyasu method, we demonstrate diverse imaging capabilities of the photonic chip including total internal reflection fluorescence microscopy, intensity fluctuation-based optical nanoscopy, single-molecule localization microscopy, and correlative light-electron microscopy. Our results validate the photonic chip as a feasible imaging platform for tissue sections and pave the way for the adoption of super-resolution high-throughput multimodal analysis of cryopreserved tissue samples both in research and clinical settings.

L’intelligence artificielle pourrait-elle intervenir dans l’aide au diagnostic des cancers du sein ? – L’exemple de HER2

HER2 is an important prognostic and predictive biomarker in breast cancer. Its detection makes it possible to define which patients will benefit from a targeted treatment. While assessment of HER2 status by immunohistochemistry in positive vs negative categories is well implemented and reproducible, the introduction of a new "HER2-low" category could raise some concerns about its scoring and reproducibility. We herein described the current HER2 testing methods and the application of innovative machine learning techniques to improve these determinations, as well as the main challenges and opportunities related to the implementation of digital pathology in the up-and-coming AI era.

Digital workflows for pathological assessment of rat estrous cycle stage using images of uterine horn and vaginal tissue

Assessment of the estrous cycle of mature female mammals is an important component of verifying the efficacy and safety of drug candidates. The common pathological approach of relying on expert observation has several drawbacks, including laborious work and inter-viewer variability. The recent advent of image recognition technologies using deep learning is expected to bring substantial benefits to such pathological assessments. We herein propose 2 distinct deep learning-based workflows to classify the estrous cycle stage from tissue images of the uterine horn and vagina, respectively. These constructed models were able to classify the estrous cycle stages with accuracy comparable with that of expert pathologists. Our digital workflows allow efficient pathological assessments of the estrous cycle stage in rats and are thus expected to accelerate drug research and development.

Deep Learning Approaches and Applications in Toxicologic Histopathology: Current Status and Future Perspectives

Whole slide imaging enables the use of a wide array of digital image analysis tools that are revolutionizing pathology. Recent advances in digital pathology and deep convolutional neural networks have created an enormous opportunity to improve workflow efficiency, provide more quantitative, objective, and consistent assessments of pathology datasets, and develop decision support systems. Such innovations are already making their way into clinical practice. However, the progress of machine learning - in particular, deep learning (DL) - has been rather slower in nonclinical toxicology studies. Histopathology data from toxicology studies are critical during the drug development process that is required by regulatory bodies to assess drug-related toxicity in laboratory animals and its impact on human safety in clinical trials. Due to the high volume of slides routinely evaluated, low-throughput, or narrowly performing DL methods that may work well in small-scale diagnostic studies or for the identification of a single abnormality are tedious and impractical for toxicologic pathology. Furthermore, regulatory requirements around good laboratory practice are a major hurdle for the adoption of DL in toxicologic pathology. This paper reviews the major DL concepts, emerging applications, and examples of DL in toxicologic pathology image analysis. We end with a discussion of specific challenges and directions for future research.

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.

In vivo and in vitro short-term bisphenol A exposures disrupt testicular energy metabolism and negatively impact spermatogenesis in zebrafish

This study investigated the in vitro and short-term in vivo effects of Bisphenol A (BPA) on testicular energy metabolism and morphology in the zebrafish (Danio rerio). Testes were incubated in vitro for 1 h or fish were exposed in vivo to BPA in the tank water for 12 h. Testicular lactate, glycogen and cholesterol were measured and ¹⁴C-deoxy-d-glucose uptake and activity of lactate dehydrogenase (LDH), alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined. In addition, testis samples from the in vivo exposures were subject to digital analysis of testicular cells using Ilastik software and the Pixel Classification module and estimation of apoptosis by Terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) immunohistochemical analysis. Our results from in vitro studies showed that BPA at 10 pM and 10 μM decreased testicular lactate content, glycogen content and LDH activity, but increased testicular AST activity. In addition, only BPA at 10 pM significantly decreased testicular ALT activity and cholesterol content. However, ¹⁴C-deoxy-d-glucose uptake was not changed. Furthermore, our results from in vivo studies showed that 10 pM BPA but not 10 μM BPA reduced testicular content of lactate and glycogen. In addition, both BPA concentrations decreased AST activity, whereas only BPA at 10 μM reduced ALT activity. However, LDH activity was not changed. Additionally, both concentrations of BPA induced spermatocyte apoptosis and a decrease in the proportion of the surface area of spermatids and spermatozoa. Collectively these data suggest that short-term BPA exposure affects energy metabolism and spermatogenesis in male zebrafish.

Whole-slide imaging, tissue image analysis, and artificial intelligence in veterinary pathology: An updated introduction and review

Since whole-slide imaging has been commercially available for over 2 decades, digital pathology has become a constantly expanding aspect of the pathology profession that will continue to significantly impact how pathologists conduct their craft. While some aspects, such as whole-slide imaging for archiving, consulting, and teaching, have gained broader acceptance, other facets such as quantitative tissue image analysis and artificial intelligence-based assessments are still met with some reservations. While most vendors in this space have focused on diagnostic applications, that is, viewing one or few slides at a time, some are developing solutions tailored more specifically to the various aspects of veterinary pathology including updated diagnostic, discovery, and research applications. This has especially advanced the use of digital pathology in toxicologic pathology and drug development, for primary reads as well as peer reviews. It is crucial that pathologists gain a deeper understanding of digital pathology and tissue image analysis technology and their applications in order to fully use these tools in a way that enhances and improves the pathologist's assessment as well as work environment. This review focuses on an updated introduction to the basics of digital pathology and image analysis and introduces emerging topics around artificial intelligence and machine learning.

PD-1/PD-L1 in Cancer: Pathophysiological, Diagnostic and Therapeutic Aspects

Immune evasion is a key strategy adopted by tumor cells to escape the immune system while promoting their survival and metastatic spreading. Indeed, several mechanisms have been developed by tumors to inhibit immune responses. PD-1 is a cell surface inhibitory receptor, which plays a major physiological role in the maintenance of peripheral tolerance. In pathological conditions, activation of the PD-1/PD-Ls signaling pathway may block immune cell activation, a mechanism exploited by tumor cells to evade the antitumor immune control. Targeting the PD-1/PD-L1 axis has represented a major breakthrough in cancer treatment. Indeed, the success of PD-1 blockade immunotherapies represents an unprecedented success in the treatment of different cancer types. To improve the therapeutic efficacy, a deeper understanding of the mechanisms regulating PD-1 expression and signaling in the tumor context is required. We provide an overview of the current knowledge of PD-1 expression on both tumor-infiltrating T and NK cells, summarizing the recent evidence on the stimuli regulating its expression. We also highlight perspectives and limitations of the role of PD-L1 expression as a predictive marker, discuss well-established and novel potential approaches to improve patient selection and clinical outcome and summarize current indications for anti-PD1/PD-L1 immunotherapy.

Dissecting the Business Case for Adoption and Implementation of Digital Pathology: A White Paper from the Digital Pathology Association

We believe the switch to a digital pathology (DP) workflow is imminent and it is essential to understand the economic implications of conversion. Many aspects of the adoption of DP will be disruptive and have a direct financial impact, both in short term costs, such as investment in equipment and personnel, and long term revenue potential, such as improved productivity and novel tests. The focus of this whitepaper is to educate pathologists, laboratorians and other stakeholders about the business and monetary considerations of converting to a digital pathology workflow. The components of a DP business plan will be thoroughly summarized, and guidance will be provided on how to build a case for adoption and implementation as well as a roadmap for transitioning from an analog to a digital pathology workflow in various laboratory settings. It is important to clarify that this publication is not intended to list prices although some financials will be mentioned as examples. The authors encourage readers who are evaluating conversion to a DP workflow to use this paper as a foundational guide for conducting a thorough and complete assessment while incorporating in current market pricing. Contributors to this paper analyzed peer-reviewed literature and data collected from various institutions, some of which are mentioned. Digital pathology will change the way we practice through facilitating patient access to expert pathology services and enabling image analysis tools and assays to aid in diagnosis, prognosis, risk stratification and therapeutic selection. Together, they will result in the delivery of valuable information from which to make better decisions and improve the health of patients.

Histopathological Classification of Canine Cutaneous Round Cell Tumors Using Deep Learning: A Multi-Center Study

Canine cutaneous round cell tumors (RCT) represent one of the routine diagnostic challenges for veterinary pathologists. Computer-aided approaches are developed to overcome these restrictions and to increase accuracy and consistency of diagnosis. These systems are also of high benefit reducing errors when a large number of cases are screened daily. In this study we describe ARCTA (Automated Round Cell Tumors Assessment), a fully automated algorithm for cutaneous RCT classification and mast cell tumors grading in canine histopathological images. ARCTA employs a deep learning strategy and was developed on 416 RCT images and 213 mast cell tumors images. In the test set, our algorithm exhibited an excellent classification performance in both RCT classification (accuracy: 91.66%) and mast cell tumors grading (accuracy: 100%). Misdiagnoses were encountered for histiocytomas in the train set and for melanomas in the test set. For mast cell tumors the reduction of a grade was observed in the train set, but not in the test set. To the best of our knowledge, the proposed model is the first fully automated algorithm in histological images specifically developed for veterinary medicine. Being very fast (average computational time 2.63 s), this algorithm paves the way for an automated and effective evaluation of canine tumors.

Microscope-Based Automated Quantification of Liver Fibrosis in Mice Using a Deep Learning Algorithm

In preclinical studies that involve animal models for hepatic fibrosis, accurate quantification of the fibrosis is of utmost importance. The use of digital image analysis based on deep learning artificial intelligence (AI) algorithms can facilitate accurate evaluation of liver fibrosis in these models. In the present study, we compared the quantitative evaluation of collagen proportionate area in the carbon tetrachloride model of liver fibrosis in the mouse by a newly developed AI algorithm to the semiquantitative assessment of liver fibrosis performed by a board-certified toxicologic pathologist. We found an excellent correlation between the 2 methods of assessment, most evident in the higher magnification (×40) as compared to the lower magnification (×10). These findings strengthen the confidence of using digital tools in the toxicologic pathology field as an adjunct to an expert toxicologic pathologist.

PD-L1 as a biomarker of response to immune-checkpoint inhibitors

Immune-checkpoint inhibitors targeting PD-1 or PD-L1 have already substantially improved the outcomes of patients with many types of cancer, although only 20-40% of patients derive benefit from these new therapies. PD-L1, quantified using immunohistochemistry assays, is currently the most widely validated, used and accepted biomarker to guide the selection of patients to receive anti-PD-1 or anti-PD-L1 antibodies. However, many challenges remain in the clinical use of these assays, including the necessity of using different companion diagnostic assays for specific agents, high levels of inter-assay variability in terms of both performance and cut-off points, and a lack of prospective comparisons of how PD-L1⁺ disease diagnosed using each assay relates to clinical outcomes. In this Review, we describe the current role of PD-L1 immunohistochemistry assays used to inform the selection of patients to receive anti-PD-1 or anti-PD-L1 antibodies, we discuss the various technical and clinical challenges associated with these assays, including regulatory issues, and we provide some perspective on how to optimize PD-L1 as a selection biomarker for the future treatment of patients with solid tumours.

Challenges and Opportunities for the Veterinary Pathologist in Biomedical Research

Animal models have critical roles in biomedical research in promoting understanding of human disease and facilitating development of new therapies and diagnostic techniques to improve human and animal health. In the study of myriad human conditions, each model requires in-depth characterization of its assets and limitations in order for it to be used to greatest advantage. Veterinary pathology expertise is critical in understanding the relevance and translational validity of animal models to conditions under study, assessing morbidity and mortality, and validating outcomes as relevant or not to the study interventions. Clear communication with investigators and education of research personnel on the use and interpretation of pathology endpoints in animal models are critical to the success of any research program. The veterinary pathologist is underutilized in biomedical research due to many factors including misconceptions about high fiscal costs, lack of perceived value, limited recognition of their expertise, and the generally low number of veterinary pathologists currently employed in biomedical research. As members of the multidisciplinary research team, veterinary pathologists have an important role to educate scientists, ensure accurate interpretation of pathology data, maximize rigor, and ensure reproducibility to provide the most reliable data for animal models in biomedical research.

The Application, Challenges, and Advancement Toward Regulatory Acceptance of Digital Toxicologic Pathology: Results of the 7th ESTP International Expert Workshop (September 20-21, 2019)

With advancements in whole slide imaging technology and improved understanding of the features of pathologist workstations required for digital slide evaluation, many institutions are investigating broad digital pathology adoption. The benefits of digital pathology evaluation include remote access to study or diagnostic case materials and integration of analysis and reporting tools. Diagnosis based on whole slide images is established in human medical pathology, and the use of digital pathology in toxicologic pathology is increasing. However, there has not been broad adoption in toxicologic pathology, particularly in the context of regulatory studies, due to lack of precedence. To address this topic, as well as practical aspects, the European Society of Toxicologic Pathology coordinated an expert international workshop to assess current applications and challenges and outline a set of minimal requirements needed to gain future regulatory acceptance for the use of digital toxicologic pathology workflows in research and development, so that toxicologic pathologists can benefit from digital slide technology.

A Workflow for the Performance of the Differential Ovarian Follicle Count Using Deep Neuronal Networks

In order to automate the counting of ovarian follicles required in multigeneration reproductive studies performed in the rat according to Organization for Economic Co-operation and Development guidelines 443 and 416, the application of deep neural networks was tested. The manual evaluation of the differential ovarian follicle count is a tedious and time-consuming task that requires highly trained personnel. In this regard, deep learning outputs provide overlay pictures for a more detailed documentation, together with an increased reproducibility of the counts. To facilitate the planned good laboratory practice (GLP) validation a workflow was set up using MLFlow to make all steps from generating of scans, training of the neural network, uploading of study images to the neural network, generation and storage of the results in a compliant manner controllable and reproducible. PyTorch was used as main framework to build the Faster region-based convolutional neural network for the training. We compared the performances of different depths of ResNet models with specific regard to the sensitivity, specificity, accuracy of the models. In this paper, we describe all steps from data labeling, training of networks, and the performance metrics chosen to evaluate different network architectures. We also make recommendation on steps, which should be taken into consideration when GLP validation is aimed for.

Challenges Developing Deep Learning Algorithms in Cytology

BACKGROUND

The incorporation of digital pathology into routine pathology practice is becoming more widespread. Definite advantages exist with respect to the implementation of artificial intelligence (AI) and deep learning in pathology, including cytopathology. However, there are also unique challenges in this regard.

SUMMARY

This review discusses cytology-specific challenges, including the need to implement digital cytology prior to AI; the large file sizes and increased acquisition times for whole slide images in cytology; the routine use of multiple stains, such as Papanicolaou and Romanowsky stains; the lack of high-quality annotated datasets on which to train algorithms; and the considerable computer resources required, in terms of both computer infrastructure and skilled personnel, for computing and storage of data. Global concerns regarding AI that are certainly applicable to cytology include the need for model validation and continued quality assurance, ethical issues such as the use of patient data in developing algorithms, the need to develop regulatory frameworks regarding what type of data can be utilized and ensuring cybersecurity during data collection and storage, and algorithm development. Key Messages: While AI will likely play a role in cytology practice in the future, applying this technology to cytology poses a unique set of challenges. A broad understanding of digital pathology and algorithm development is desirable to guide the development of algorithms, as well as the need to be cognizant of potential pitfalls to avoid when incorporating the technology in practice.

Histopathologic Evaluation and Scoring of Viral Lung Infection

Emergent coronaviruses such as MERS-CoV and SARS-CoV can cause significant morbidity and mortality in infected individuals. Lung infection is a common clinical feature and contributes to disease severity as well as viral transmission. Animal models are often required to study viral infections and therapies, especially during an initial outbreak. Histopathology studies allow for identification of lesions and affected cell types to better understand viral pathogenesis and clarify effective therapies. Use of immunostaining allows detection of presumed viral receptors and viral tropism for cells can be evaluated to correlate with lesions. In the lung, lesions and immunostaining can be qualitatively described to define the cell types, microanatomic location, and type of changes seen. These features are important and necessary, but this approach can have limitations when comparing treatment groups. Semiquantitative and quantitative tissue scores are more rigorous as these provide the ability to statistically compare groups and increase the reproducibility and rigor of the study. This review describes principles, approaches, and resources that can be useful to evaluate coronavirus lung infection, focusing on MER-CoV infection as the principal example.

Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology

Toxicologic pathology is transitioning from analog to digital methods. This transition seems inevitable due to a host of ongoing social and medical technological forces. Of these, artificial intelligence (AI) and in particular machine learning (ML) are globally disruptive, rapidly growing sectors of technology whose impact on the long-established field of histopathology is quickly being realized. The development of increasing numbers of algorithms, peering ever deeper into the histopathological space, has demonstrated to the scientific community that AI pathology platforms are now poised to truly impact the future of precision and personalized medicine. However, as with all great technological advances, there are implementation and adoption challenges. This review aims to define common and relevant AI and ML terminology, describe data generation and interpretation, outline current and potential future business cases, discuss validation and regulatory hurdles, and most importantly, propose how overcoming the challenges of this burgeoning technology may shape toxicologic pathology for years to come, enabling pathologists to contribute even more effectively to answering scientific questions and solving global health issues. [Box: see text]

Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association

The advent of whole-slide imaging in digital pathology has brought about the advancement of computer-aided examination of tissue via digital image analysis. Digitized slides can now be easily annotated and analyzed via a variety of algorithms. This study reviews the fundamentals of tissue image analysis and aims to provide pathologists with basic information regarding the features, applications, and general workflow of these new tools. The review gives an overview of the basic categories of software solutions available, potential analysis strategies, technical considerations, and general algorithm readouts. Advantages and limitations of tissue image analysis are discussed, and emerging concepts, such as artificial intelligence and machine learning, are introduced. Finally, examples of how digital image analysis tools are currently being used in diagnostic laboratories, translational research, and drug development are discussed.