Janusz Szymas

Five years of experience teaching pathology to dental students using the WebMicroscope

BackgroundWe describe development and evaluation of the user-friendly web based virtual microscopy - WebMicroscope for teaching and learning dental students basic and oral pathology. Traditional students microscopes were replaced by computer workstations.MethodsThe transition of the basic and oral pathology courses from light to virtual microscopy has been completed gradually over a five-year period. A pilot study was conducted in academic year 2005/2006 to estimate the feasibility of integrating virtual microscopy into a traditional light microscopy-based pathology course. The entire training set of glass slides was subsequently converted to virtual slides and placed on the WebMicroscope server. Giving access to fully digitized slides on the web with a browser and a viewer plug-in, the computer has become a perfect companion of the student.ResultsThe study material consists now of over 400 fully digitized slides which covering 15 entities in basic and systemic pathology and 15 entities in oral pathology. Digitized slides are linked with still macro- and microscopic images, organized with clinical information into virtual cases and supplemented with text files, syllabus, PowerPoint presentations and animations on the web, serving additionally as material for individual studies. After their examinations, the students rated the use of the software, quality of the images, the ease of handling the images, and the effective use of virtual slides during the laboratory practicals. Responses were evaluated on a standardized scale. Because of the positive opinions and support from the students, the satisfaction surveys had shown a progressive improvement over the past 5 years. The WebMicroscope as a didactic tool for laboratory practicals was rated over 8 on a 1-10 scale for basic and systemic pathology and 9/10 for oral pathology especially as various students’ suggestions were implemented. Overall, the quality of the images was rated as very good.ConclusionsAn overwhelming majority of our students regarded a possibility of using virtual slides at their convenience as highly desirable. Our students and faculty consider the use of the virtual microscope for the study of basic as well as oral pathology as a significant improvement over the light microscope.

Whole slide imaging for educational purposes.

Digitized slides produced by whole slide image scanners can be easily shared over a network or by transferring image files to optical or other data storage devices. Navigation of digitized slides is interactive and intended to simulate viewing glass slides with a microscope (virtual microscopy). Image viewing software permits users to edit, annotate, analyze, and easily share whole slide images (WSI). As a result, WSI have begun to replace the traditional light microscope, offering a myriad of opportunities for education. This article focuses on current applications of WSI in education and proficiency testing. WSI has been successfully explored for graduate education (medical, dental, and veterinary schools), training of pathology residents, as an educational tool in allied pathology schools (e.g., cytotechnology), for virtual tracking and tutoring, tele-education (tele-conferencing), e-learning, virtual workshops, at tumor boards, with interactive publications, and on examinations. WSI supports flexible and cost-effective distant learning and augments problem-oriented teaching, competency evaluation, and proficiency testing. WSI viewed on touchscreen displays and with tablet technology are especially beneficial for education. Further investigation is necessary to develop superior WSI applications that better support education and to design viewing stations with ergonomic tools that improve the WSI-human interface and navigation of virtual slides. Studies to determine the impact of training pathologists without exposure to actual glass slides are also needed.

Quality evaluation of virtual slides using methods based on comparing common image areas.

BackgroundThere are many scanners of glass slides on the market now. Quality of digital images produced by them may be different and pathologists who examine virtual slides on a monitor may subjectively evaluate it. However, objective comparison of quality of digital slides captured by various devices requires assessment algorithms, which will be automatically executed.MethodsIn this work such an algorithm is proposed and implemented. It is dedicated for comparing quality of virtual slides which show the same glass slide captured by two or more scanners. In the first step this method looks for the largest corresponding areas in the slides. This task is realized by defining boundaries of tissues and providing the relative scale factor. Then, a certain number of smaller areas, which show the same fragments of both slides, is selected. The chosen fragments are analyzed using Gray Level Co-occurrence Matrix (GLCM). For GLCM matrices some of the Haralick features are calculated, like contrast or entropy. Basing on results for some sample images, features appropriate for quality assessment are chosen. Aggregation of values from all selected fragments allows to compare the quality of images captured by tested devices.ResultsDescribed method was tested on two sets of ten virtual slides, acquired by scanning the same set of ten glass slides by two different devices. First set was scanned and digitized using the robotic microscope Axioscope2 (Zeiss) equipped with AxioCam Hrc CCD camera. Second set was scanned by DeskScan (Zeiss) with standard equipment. Before analyzing captured virtual slides, images were stitched and converted using software which utilizes advances in aerial and satellite imaging.The results of the experiment show that calculated quality factors are higher for virtual slides acquired using first mentioned device (Axioscope2 with AxioCam).ConclusionsResults of the tests are consistent with opinion of the pathologists who assessed quality of virtual slides captured by these devices. This shows that the method has potential in automatic evaluation of virtual slides’ quality.

Histopathologic Patterns of Nervous System Tumors Based on Computer Vision Methods and Whole Slide Imaging (WSI)

Background: Making an automatic diagnosis based on virtual slides and whole slide imaging or even determining whether a case belongs to a single class, representing a specific disease, is a big challenge. In this work we focus on WHO Classification of Tumours of the Central Nervous System. We try to design a method which allows to automatically distinguish virtual slides which contain histopathologic patterns characteristic of glioblastoma – pseudopalisading necrosis and discriminate cases with neurinoma (schwannoma), which contain similar structures – palisading (Verocay bodies). Methods: Our method is based on computer vision approaches like structural analysis and shape descriptors. We start with image segmentation in a virtual slide, find specific patterns and use a set of features which can describe pseudopalisading necrosis and distinguish it from palisades. Type of structures found in a slide decides about its classification. Results: Described method is tested on a set of 49 virtual slides, captured using robotic microscope. Results show that 82% of glioblastoma cases and 90% of neurinoma cases were correctly identified by the proposed algorithm. Conclusion: Our method is a promising approach to automatic detection of nervous system tumors using virtual slides.

Teachers’ impact on dental students’ exam scores in teaching pathology of the oral cavity using WSI

We have developed and evaluated a user-friendly on-line interactive teaching and examination system for Pathology of the Oral Cavity. Abandoning the use of conventional training microscopes and glass slides since 2005, we decided to rely on virtual microscopy to facilitate learning of oral cavity pathology to dental students. Because of a high number of new students enrolling every academic year, students work in groups supervised by different teaching assistants with heterogeneous teaching experience. The aim of this study was determining whether in this context the teacher has still an impact on students’ exam scores.

Exploring viewing behavior data from whole slide images to predict correctness of students' answers during practical exams in oral pathology

The way of viewing whole slide images (WSI) can be tracked and analyzed. In particular, it can be useful to learn how medical students view WSIs during exams and how their viewing behavior is correlated with correctness of the answers they give. We used software-based view path tracking method that enabled gathering data about viewing behavior of multiple simultaneous WSI users. This approach was implemented and applied during two practical exams in oral pathology in 2012 (88 students) and 2013 (91 students), which were based on questions with attached WSIs. Gathered data were visualized and analyzed in multiple ways. As a part of extended analysis, we tried to use machine learning approaches to predict correctness of students′ answers based on how they viewed WSIs. We compared the results of analyses for years 2012 and 2013 - done for a single question, for student groups, and for a set of questions. The overall patterns were generally consistent across these 3 years. Moreover, viewing behavior data appeared to have certain potential for predicting answers′ correctness and some outcomes of machine learning approaches were in the right direction. However, general prediction results were not satisfactory in terms of precision and recall. Our work confirmed that the view path tracking method is useful for discovering viewing behavior of students analyzing WSIs. It provided multiple useful insights in this area, and general results of our analyses were consistent across two exams. On the other hand, predicting answers′ correctness appeared to be a difficult task - students′ answers seem to be often unpredictable.

Exploring Viewing Behavior Data from Whole Slide Images to Predict Correctness of Students’ Answers during Practical Exams in Oral Pathology

The use of whole slide images (WSIs) allows tracking and recording how a histological slide is viewed. Gathered data about viewing behavior while interpreting WSIs may result in a variety of analyses. When the tracking is done during an exam, we can discover how students view WSIs. Moreover, we may try to correlate their way of viewing slides with correctness of the answers they give. Particularly, we can potentially find out to what extent a specific viewing behavior is likely to result in a correct or incorrect answer from a student.

Four years experiences teaching pathology with the WebMicroscope to dental students

Background We have developed and evaluated a user-friendly on-line interactive teaching and examination system for pathology. Since 2005 all laboratory lessons have moved to computer class-room. Traditional microscopes for students were replaced by computers and interactive sessions using Internet based WebMicroscope. By accessing full digitized slides on web with a browser and viewer plugin, computer got perfectly companion of the student. All laboratory sessions are still supervised by pathologists.