TuBaFrost 6: Virtual microscopy in virtual tumour banking

Virtual Microscopy Goes Global: The Images Are Virtual and the Problems Are Real

For the last two centuries, the scholarly education of histology and pathology has been based on technology, initially on the availability of low-cost, high-quality light microscopes, and more recently on the introduction of computers and e-learning approaches to biomedical education. Consequently, virtual microscopy (VM) is replacing glass slides and the traditional light microscope as the main instruments of instruction in histology and pathology laboratories. However, as with most educational changes, there are advantages and disadvantages associated with a new technology. The use of VM for the teaching of histology and pathology requires an extensive infrastructure and the availability of computing devices to all learners, both posing a considerable financial strain on schools and students. Furthermore, there may be valid reasons for practicing healthcare professionals to maintain competency in using light microscopes. In addition, some educators may be reluctant to embrace new technologies. These are some of the reasons why the introduction of VM as an integral part of histology and pathology instruction has been globally uneven. This paper compares the teaching of histology and pathology using traditional or VM in five different countries and their adjacent regions, representing developed, as well as developing areas of the globe. We identify general and local roadblocks to the introduction of this still-emerging didactic technology and outline solutions for overcoming these barriers.

Accuracy of whole slide image based image analysis is adversely affected by preanalytical factors such as stained tissue slide and paraffin block age

Background

Personalized medicine and accurate quantification of tumor and biomarker expression have become the cornerstone of cancer diagnostics. This requires Quality Control (QC) of research tissue samples to confirm adequate targeted tumor tissue sampling. Digitalization of stained tissue slides offer a precious way to archive, preserve, and retrieve necessary information when needed. This study is aimed to assess the most significant pre-analytic and analytic factors that might contribute to the efficacy of obtaining accurate whole slide images (WSIs) interpretation. Various studies are needed to identifysuch factors to allow for appropriate AI application and adequate tumor area/percentage quantification.

Methods

Hematoxylene and Eosine (H&E) satined WSIs collected from tissue specimens provided by the Cooperative Human Tissue Network (CHTN) Midwestern Division (CHTNMWD) were analyzed. Tissue specimens were processed, fixed, stained, and scanned contemporaneously (within 1 month). Two cohorts of malignant, colorectal cancer, 20X WSI (ScanscopeXT, Leica Biosystems, Illinois), were assembled. The study identified a "recent cohort" that included 76 WSIs created on 2018 or later. "Aged cohort" included 73 WSIs from specimens procured in the period of (2012-2014). Twenty recent WSIs of adenocarcinoma cases were used to construct WSIs analysis algorithms (VIS, Visiopharm A/S, Denmark) using machine learning to produce morphometric maps and calculate tissue and tumor areas.

Results

Algorithmic analysis of 69 WSIs from rescanned aged slides vs. that of contemporaneous WSIs concluded 18 (28%) similar finding in tumor areas (within 10%), 56 (82%) had identicaltissue areas, and 54 (79%) had similar tumor percentages.

Conclusion

WSIs of aged H&E slides and stained paraffin block re-cuts produce different tumor quantification compared to those of original scanned sslides most likely due to pre-analytical factors. The difference in tumor area detected between original and rescanned WSIs trended upward in the period between 2012 and 2014. Less tumor area was detected as the slides age. Recut and H&E-stained tissues from stored paraffin blocks may detect more tumor due to excess eosinophilia. These results highlights the value of documenting archives of H&E WSIs collected at the procurement time. Such images provide a superior archive over glass slides and Formalin-Fixed Paraffin-Embedded (FFPE) blocks and contribute betterg to WSIs analysis application.

The Utilization of Biospecimens: Impact of the Choice of Biobanking Model

The term research "biobank" is one of multiple names (e.g., bioresource, biorepository,) used to designate an entity that receives, collects, processes, stores, and/or distributes biospecimens or other biospecimen-related products (e.g., data) to support research. There are multiple organizational models of biobanking used by bioresources, but the primary goal of all bioresources should not be simply to collect biospecimens, but ultimately to distribute almost all collected biospecimens and/or data to support scientific research; bioresources should serve as "biodistributors" rather than "biovaults." The appropriate choice of model is the first step in ensuring optimal biospecimen utilization by a bioresource. This article discusses some of the different models that may be used alone or in combination by a bioresource providing biospecimens for research; it describes the factors affecting the choice of the most appropriate model or models, the advantages and disadvantages of the various models, and a discussion of the impact of the choice of the model on biospecimen utilization. Frequently, problems with biospecimen utilization are not caused by any single model, but rather a mismatch between the choice of model and goals of the bioresource, and/or problems with the subsequent design, goals, operations, and management of the bioresource after a model is selected.

Combining Diagnostic Imaging and Pathology for Improving Diagnosis and Prognosis of Cancer

In the era of personalized medicine, the management of oncological patients requires a translational and multidisciplinary approach. During early phases of cancer development, biochemical alterations of cell metabolism occur much before the formation of detectable tumour masses. Current molecular imaging techniques, targeted to the study of molecular kinetics, employ molecular tracers capable of detecting cancer lesions with both high sensitivity and specificity while also providing essential information for both prognosis and therapy. On the contrary, complementary and crucial information is provided by histopathological examination and ancillary techniques such as immunohistochemistry. Thus, the successful collaboration between diagnostic imaging and anatomic pathology can represent a fundamental step in the "tortuous" but decisive path towards personalized medicine.

The virtual microscopy database-sharing digital microscope images for research and education

Over the last 20 years, virtual microscopy has become the predominant modus of teaching the structural organization of cells, tissues, and organs, replacing the use of optical microscopes and glass slides in a traditional histology or pathology laboratory setting. Although virtual microscopy image files can easily be duplicated, creating them requires not only quality histological glass slides but also an expensive whole slide microscopic scanner and massive data storage devices. These resources are not available to all educators and researchers, especially at new institutions in developing countries. This leaves many schools without access to virtual microscopy resources. The Virtual Microscopy Database (VMD) is a new resource established to address this problem. It is a virtual image file-sharing website that allows researchers and educators easy access to a large repository of virtual histology and pathology image files. With the support from the American Association of Anatomists (Bethesda, MD) and MBF Bioscience Inc. (Williston, VT), registration and use of the VMD are currently free of charge. However, the VMD site is restricted to faculty and staff of research and educational institutions. Virtual Microscopy Database users can upload their own collection of virtual slide files, as well as view and download image files for their own non-profit educational and research purposes that have been deposited by other VMD clients. Anat Sci Educ 11: 510-515. © 2018 American Association of Anatomists.

The Empirical Foundations of Telepathology: Evidence of Feasibility and Intermediate Effects

INTRODUCTION

Telepathology evolved from video microscopy (i.e., "television microscopy") research in the early 1950s to video microscopy used in basic research in the biological sciences to a basic diagnostic tool in telemedicine clinical applications. Its genesis can be traced to pioneering feasibility studies regarding the importance of color and other image-based parameters for rendering diagnoses and a series of studies assessing concordance of virtual slide and light microscopy diagnoses. This article documents the empirical foundations of telepathology.

METHODS

A selective review of the research literature during the past decade (2005-2016) was conducted using robust research design and adequate sample size as criteria for inclusion.

CONCLUSIONS

The evidence regarding feasibility/acceptance of telepathology and related information technology applications has been well documented for several decades. The majority of evidentiary studies focused on intermediate outcomes, as indicated by comparability between telepathology and conventional light microscopy. A consistent trend of concordance between the two modalities was observed in terms of diagnostic accuracy and reliability. Additional benefits include use of telepathology and whole slide imaging for teaching, research, and outreach to resource-limited countries. Challenges still exist, however, in terms of use of telepathology as an effective diagnostic modality in clinical practice.

"Slide less pathology": Fairy tale or reality?

Pathology practice is significantly advanced in various frontiers. Therefore, "slide less digital" pathology will not be a mere imagination in near future. Digitalization of histopathological slides (whole slide imaging [WSI]) is possible with the help of whole slide scanner. The WSI has a positive impact not only in routine practice but also in research field, medical education and bioindustry. Even if digital pathology has definitive advantages, its widespread use is not yet possible. As it is an upcoming technology in our field, this article is aimed to discussessential aspects of WSI.

Establishment and maintenance of a standardized glioma tissue bank: Huashan experience

Cerebral glioma is the most common brain tumor as well as one of the top ten malignant tumors in human beings. In spite of the great progress on chemotherapy and radiotherapy as well as the surgery strategies during the past decades, the mortality and morbidity are still high. One of the major challenges is to explore the pathogenesis and invasion of glioma at various "omics" levels (such as proteomics or genomics) and the clinical implications of biomarkers for diagnosis, prognosis or treatment of glioma patients. Establishment of a standardized tissue bank with high quality biospecimens annotated with clinical information is pivotal to the solution of these questions as well as the drug development process and translational research on glioma. Therefore, based on previous experience of tissue banks, standardized protocols for sample collection and storage were developed. We also developed two systems for glioma patient and sample management, a local database for medical records and a local image database for medical images. For future set-up of a regional biobank network in Shanghai, we also founded a centralized database for medical records. Hence we established a standardized glioma tissue bank with sufficient clinical data and medical images in Huashan Hospital. By September, 2013, tissues samples from 1,326 cases were collected. Histological diagnosis revealed that 73 % were astrocytic tumors, 17 % were oligodendroglial tumors, 2 % were oligoastrocytic tumors, 4 % were ependymal tumors and 4 % were other central nervous system neoplasms.

Digital pathology and image analysis augment biospecimen annotation and biobank quality assurance harmonization

Standardization of biorepository best practices will enhance the quality of translational biomedical research utilizing patient-derived biobank specimens. Harmonization of pathology quality assurance procedures for biobank accessions has lagged behind other avenues of biospecimen research and biobank development. Comprehension of the cellular content of biorepository specimens is important for discovery of tissue-specific clinically relevant biomarkers for diagnosis and treatment. While rapidly emerging technologies in molecular analyses and data mining create focus on appropriate measures for minimizing pre-analytic artifact-inducing variables, less attention gets paid to annotating the constituent makeup of biospecimens for more effective specimen selection by biobank clients. Both pre-analytic tissue processing and specimen composition influence acquisition of relevant macromolecules for downstream assays. Pathologist review of biorepository submissions, particularly tissues as part of quality assurance procedures, helps to ensure that the intended target cells are present and in sufficient quantity in accessioned specimens. This manual procedure can be tedious and subjective. Incorporating digital pathology into biobank quality assurance procedures, using automated pattern recognition morphometric image analysis to quantify tissue feature areas in digital whole slide images of tissue sections, can minimize variability and subjectivity associated with routine pathologic evaluations in biorepositories. Whole-slide images and pathologist-reviewed morphometric analyses can be provided to researchers to guide specimen selection. Harmonization of pathology quality assurance methods that minimize subjectivity and improve reproducibility among collections would facilitate research-relevant specimen selection by investigators and could facilitate information sharing in an integrated network approach to biobanking.

Digital slide images for primary diagnostics in breast pathology: a feasibility study

Digital slide images have been used in many areas of pathology such as teaching, research, digital archiving, teleconsultation, and quality assurance testing. However, they have not much been used as yet for upfront diagnostics. The aim of this study was therefore to test the feasibility of digital slide image-based diagnosis of breast specimens. Sections of 100 breast specimens previously diagnosed conventionally were scanned and rediagnosed on digital slide images by the same pathologists who performed the initial light microscopy-based diagnosis. The digital slide image diagnoses were compared with the light microscopy diagnoses and classified as concordant, slightly discrepant (without clinical or prognostic consequences), or discrepant. The original light microscopy- and digital slide image-based diagnoses were concordant in 93% and slightly discrepant in 6% of cases. There was only 1 discrepant case with clinical or prognostic implication to the patient. However, for this case, no final agreement could be achieved. For 4 of the 6 slightly discrepant cases, digital slide image diagnosis was considered the better one, whereas the original diagnosis was preferred in only 1 case. In addition, for 1 case categorized as slightly discrepant, both the digital slide image and conventional diagnosis were imperfect according to 2 reviewing breast pathologists. This study demonstrates that upfront histopathologic diagnosis of breast biopsies and resections can reliably be done on digital slide image.

Digital pathology: current status and future perspectives

During the last decade pathology has benefited from the rapid progress of image digitizing technology. The improvement in this technology had led to the creation of slide scanners which are able to produce whole slide images (WSI) which can be explored by image viewers in a way comparable to the conventional microscope. The file size of the WSI ranges from a few megabytes to several gigabytes, leading to challenges in the area of image storage and management when they will be used routinely in daily clinical practice. Digital slides are used in pathology for education, diagnostic purposes (clinicopathological meetings, consultations, revisions, slide panels and, increasingly, for upfront clinical diagnostics) and archiving. As an alternative to conventional slides, WSI are generally well accepted, especially in education, where they are available to a large number of students with the full possibilities of annotations without the problem of variation between serial sections. Image processing techniques can also be applied to WSI, providing pathologists with tools assisting in the diagnosis-making process. This paper will highlight the current status of digital pathology applications and its impact on the field of pathology.

The interface of population-based cancer registries and biobanks in etiological and clinical research--current and future perspectives

BACKGROUND

The availability of quality assured, population-based cancer registries and biobanks with high quality samples makes it possible to conduct research on large samples sets with long follow-up within a reasonable time frame. Defined quality for both cancer registries and biobanks is essential for enabling high quality biobank-based research. Recent networking projects have brought these infrastructures together to promote the combined use of cancer registries and biobanks in cancer research.

MATERIALS AND METHODS

In this report we review the current status and future perspectives of cancer registries and biobanks and how the interface between them should be developed to optimally further cancer research.

RESULTS AND DISCUSSION

Major conclusions for future improvements are that the research exploiting cancer registries and biobanks, and the research that is building and optimising the infrastructure, should evolve together for maximally relevant progress. Population-based and sustainable biobanks that continuously and consecutively store all samples ("Biological registries") under strict quality control are needed. There is also a need for increased education, information and visibility of the interdisciplinary sciences required for optimal exploitation of these resources.

Epidemiology of multiple primary cancers

Cancer patients have a 20% higher risk of new primary cancer compared with the general population. Approximately one third of cancer survivors aged >60 years were diagnosed more than once with another cancer. As the number of cancer survivors and of older people increases, occurrence of multiple primary cancers is also likely to increase. An increasing interest from epidemiologic and clinical perspectives seems logical. This chapter begins with the risk pattern of multiple cancers in the population of a developed country with high survival rates. Multiple cancers comprise two or more primary cancers occurring in an individual that originate in a primary site or tissue and that are neither an extension, nor a recurrence or metastasis. Studies of multiple cancers have been mainly conducted in population-based settings, and more recently in clinical trials and case control studies leading to further understanding of risk factors for the development of multiple primary cancers. These factors include an inherited predisposition to cancer; the usual carcinogenic or cancer-promoting aspects of lifestyle, hormonal, and environmental factors; treatment of the previous primary cancer; and increased surveillance of cancer survivors. Finally, implication on research strategies and clinical practice are discussed, covering the whole range of epidemiologic approach.

[On line digital microscopy in 2007: One technology, many uses]

Digital microscopy enables several observers to look at any field of one microscopical section, at any magnification, through an Internet connexion. An overview of the systems used to digitize microscopy slides and to put them on line is presented. This technique is already used in many fields of pathology, for teaching, research and, to a lesser extent, diagnostic purposes. Several examples are given in this review, some of them with a true evaluation process, and strong points and weaker points are addressed. While conventional microscopy remains the keystone method in 2007 and for the coming years, it is also obvious that digital microscopy will be playing an increasing role. It is our task to make it evolve according to our needs.

Biobanking for interdisciplinary clinical research

Biobanking nowadays is mostly strongly determined by the specific aims of a research group in charge of the biobank, determining their own standards for the collection and annotation of samples. Often a long period is needed to build up the sample and data collections, especially when long-term follow-up data is required. Such collections need a long-term dedication and proper funding. Neglecting either sample number or annotation can result in insignificant or poor results. However, outcome of translational research does not only depend on the sample quality. In many cases it can also be improved to start the experimental design within a multidisciplinary team composed of clinicians including pathologists, molecular biologists, statisticians, bioinformaticians and tissue resource managers. Such a team, capable of careful evaluation of the numbers needed and which or what part of the samples are to be included, could help in obtaining far better results. Many lines of clinical research could benefit more efficiently from the wealth of information stored in well-preserved disease-oriented tissue sample collections with the proper annotations, when the infrastructure around biobanks and new collection build-up is well organized, standardized and streamlined. Future medical research will refine its scientific questions, demanding even further refinement of corresponding clinical information. In addition, larger sample collections are needed to study for instance multifactorial diseases. Today, the samples are collected for tomorrow, therefore, improvement is needed now in standardization, automated enrichment of annotations from hospital information systems and disease registries, insight in overlapping collections of different forms of tissue banking and cooperation in national and international networks.

An application of virtual microscopy in the teaching of an oral and maxillofacial pathology laboratory course

OBJECTIVE

The aim of this study is to share the experience of establishing a virtual microscope and telepathology system for the oral and maxillofacial pathology laboratory course in a dental school.

STUDY DESIGN

A dot-slide system has been used to generate digitized microscopic slides, which are placed on an image server that is available online.

RESULTS

Using software that is available as a free download (OlyVIA), students are able to select a teaching slide record, view at magnifications comparable with those of a conventional microscope, and navigate to any area on the matching virtual slide image that is stored on the image server database. Before class, the students can review the findings of the virtual teaching slides at any time or any place via broadband internet by using the instructions available on DVD. During class, students report and discuss the histological findings of the virtual teaching slides with tutors who evaluate, test, and make constructive comments on the presentations in a Web-based computer classroom. After class, students can revise the histological findings of the microscopic virtual slides available on the server.

CONCLUSIONS

Virtual microscopy has many advantages over real microscopy in oral and maxillofacial pathology education. Furthermore, telepathology could also be applied in other pathological services, such as intraoperative frozen sections, routine surgical pathology, and subspecialty consultation.

TuBaFrost 5: multifunctional central database application for a European tumor bank

Developing a tissue bank database has become more than just logically arranging data in tables combined with a search engine. Current demand for high quality samples and data, and the ever-changing legal and ethical regulations mean that the application must reflect TuBaFrost rules and protocols for the collection, exchange and use of tissue. To ensure continuation and extension of the TuBaFrost European tissue bank, the custodianship of the samples, and hence the decision over whether to issue samples to requestors, remains with the local collecting centre. The database application described in this article has been developed to facilitate this open structure virtual tissue bank model serving a large group. It encompasses many key tasks, without the requirement for personnel, hence minimising operational costs. The Internet-accessible database application enables search, selection and request submission for requestors, whereas collectors can upload and edit their collection. Communication between requestor and involved collectors is started with automatically generated e-mails.

TuBaFrost 1: Uniting local frozen tumour banks into a European network: an overview

TuBaFrost is the consortium responsible for the creation of a virtual European human frozen tumour tissue bank: a collection of high quality frozen residual, accurately classified tumour tissue samples, which are stored in European cancer centres and universities. This virtual tissue bank, searchable on the internet, has rules for access and use, and a code of conduct to comply with the various legal and ethical regulations in European countries. The easy accessibility and the European scale of the bank will result in the availability of a large number of samples even of rarer tumour types. Standardisation of collection, storage and quality control throughout the network is achieved minimising inter-institutional variability. A website providing access to upload, search and request samples is a key tool of the tissue bank. The search engine makes use of virtual microscopy. An overview of the development of the European virtual frozen tissue bank infrastructure is described in this paper. The various key aspects are described in more detail in a series of articles to appear in this Journal.