Final Report Virtual microscopy for enhancing learning and ... · Final Report Virtual microscopy for enhancing learning and teaching Project Leader Professor Rakesh Kumar Department

Virtual microscopy for enhancing learning and teaching 1

Final Report

Virtual microscopy for enhancing learning and teaching

Project LeaderProfessor Rakesh Kumar

Department of Pathology, School of Medical Sciences

Team MembersDr Gary Velan

Department of Pathology, School of Medical Sciences

Patrick de PermentierDepartment of Anatomy, School of Medical Sciences

Associate Professor Paul AdamDr Stephen Bonser

Associate Professor Michel BealSchool of Biological, Earth and Environmental Sciences

The University of New South Wales

http://virtualslides.unsw.edu.au

http://www.altcexchange.edu.au/invitation-view-virtual-microscopy-slide-collection

September 2009


Support for this project has been provided by the Australian Learning and Teaching Council, an initiative of the Australian Government Department of Education, Employment and Workplace Relations. The views expressed in this report do not necessarily reflect the views of the Australian Learning and Teaching Council Ltd.

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2009


Executive Summary

The primary goal of this project was to generate four sets of virtual slides selected for use in learning and teaching in human anatomy (histology), human pathology (histopathology), comparative anatomy/zoology and plant ecology/evolution. These were to be made available to educators across the sector without charge via a repository, with illustrative examples of the use of virtual slides in practical classes for Medicine and Science students, including sample practical class worksheets.

The project team has successfully achieved this goal and, with a variety of enhancements introduced in response to feedback, the repository became available on line in May, 2009. Viewing the collections requires a username and password, which can be obtained by lodging a request via a form on the website.

In addition, teaching using virtual slides was trialled for the first time in Botany/Ecology, with considerable success. Not only were student ratings exceptional but in addition there was measurable evidence of improved learning outcomes, as demonstrated by statistically significant improvement in assessment marks.

Dissemination activities are ongoing and further grant proposals to ALTC are in development.


Aims of this Project

This project was intended to provide resources for, and to promote the dissemination of, well-developed approaches to learning and teaching using virtual microscopy. We planned to generate sets of "virtual slides" for use in learning and teaching within Australian universities, particularly in Medicine, related Health Sciences, and Biological Science. These were to be made available to educators across the sector, without charge, via a repository. We also planned to help disseminate effective models of the pedagogies and processes involved in using virtual slides for teaching and learning.

Virtual microscopy is a key enabling technology for students, especially those students who have limited aptitude for traditional microscopy. Virtual slides can be used effectively with students at a variety of different levels of expertise. The project thus directly addressed two of the funding priorities of the Competitive Grants Program, namely Innovation in learning and teaching, particularly in relation to the role of new technologies and Strategic approaches to learning and teaching that address the increasing diversity of the student body. Furthermore, it aimed to help build the necessary capacity to enable systemic change, and – by supporting the development of collections for multiple disciplines – to facilitate cross-disciplinary approaches.

Approach and Methodology

Background Virtual slides are very high resolution scans of stained tissue sections on glass slides, which are acquired using a 40 microscope objective lens. They are stored in a special multi-layered file format so that with appropriate software, it is possible to display only the relevant portion (appropriate field and magnification) of a very large file (typically 0.25-1.5 GB) rapidly within a web browser window. As illustrated overleaf, the software permits the user to "click and drag" and to "zoom in" on the image, as well as to adjust apparent illumination, thus simulating the use of a real microscope but eliminating the skill barrier that disadvantages many students.

Virtual slides are gaining wide acceptance for use in Anatomy and Pathology, which are visual disciplines that require students to obtain an understanding of the normal microscopic structure of tissues (histology), as well as the microscopic appearances of diseased tissues (histopathology). We recognised that key topics in Botany and Zoology such as function, adaptation and diversity also required an understanding of structures at a microscopic level. However, at the time of commencing this project, no educational institution was using virtual slides for teaching in the latter disciplines.

One of the major barriers to learning in all such disciplines has been that students experience technical and practical difficulties in mastering the use of microscopes. To create an environment that supports student learning, some members of the project team have since 2002 been involved in a project to replace microscopic examination of glass slides, in histology/histopathology practical classes for Medicine and Science students, with computer-based virtual microscopy. This made UNSW the first institution outside North America to employ this method of teaching. UNSW was also the first institution to successfully employ virtual slides in formal assessments, in which images are presented in a secure browser environment. The approach has ensured effective alignment between learning and assessment, as well as consistency between students with respect to the specimens being examined. Our success in using virtual microscopy in various settings, as described below, was the primary reason for initiating this project.


Evidence of impact on student learning and the student experience

Virtual microscopy teaching was initially implemented at UNSW in 2003, for teaching in Pathology. The technology was introduced in a hybrid format i.e. traditional glass slides of microscopic slides in parallel with corresponding virtual slides. As in traditional classes, histopathology slides provided the focus for discussion of a clinical problem and structured worksheets, which include learning objectives for each class, were supplied. Although students had previously worked at individual microscopes, deliberate arrangements were made for two students to share one computer workstation, to promote collaboration. There was no reduction in the number of demonstrators in the class, but rather the intention was to enhance the quality of the interaction between students and demonstrators.

The approach was accepted with alacrity by this highly computer-literate generation of students. We found that when a glass slide was scheduled for a particular class, students regularly examined and discussed the corresponding virtual slide out of interest before the class began. They also requested that the virtual slides be made accessible for revision from home, and made extensive use of this facility. In feedback questionnaires, there was overwhelming support for the introduction of virtual microscopy. Importantly, in response to “How does using virtual slides compare with microscopic examination of glass slides?” over 75% respondents indicated that the virtual slide system solved problems they had experienced when using a binocular microscope. Comments included: “Doesn’t hurt my eyes. Clear image always in focus”; “Much better. Faster to use, therefore more efficient.”; “Less dizzy, less fuss, quicker learning”; and “More convenient to use and about same quality image if not better”.

Following this initial success, and coinciding with the introduction of the new Medicine program at UNSW, we undertook major reform of teaching in microscopy practical classes in Phase 1 of the new program. Agreement was reached to abandon the use of conventional student microscopes and glass slides, and to redesign practical classes quite radically, for simultaneous teaching of normal histology and histopathology. This involved team teaching by staff from Anatomy and Pathology, with an emphasis on the value of understanding the normal in order to be able to explain abnormalities, and appropriate structured worksheets were developed for these new classes. Questionnaire feedback was again overwhelmingly


positive. Typical of the comments were: "Great! It's good to learn when you can see the clinical application. It's what keeps us interested." and "Integrating normal and abnormal really allows a direct comparison and aids my understanding. I really like working through case studies as it integrates clinically as well."

Specific aims of the project This project involved completing the development of the UNSW Anatomy and Pathology slide collections, as well as extending the use of virtual slides to the disciplines of Botany and Zoology. Thus we aimed to provide four sets of virtual slides (150-200 per discipline) selected for use in learning and teaching within Australian universities, particularly in Biological Science and Medicine:

Human anatomy (histology)

Human pathology (histopathology)

Comparative anatomy/zoology

Plant ecology/evolution.

A particular goal was that the latter two collections would focus on Australian specimens and would therefore be unique collections that documented functional/morphological variability in native flora and fauna.

All of the slide sets, as well as worksheets for model practical classes, were to be made freely available to educators across the sector, for installation on either a local web server (this will require purchase of appropriate server software) or on a file server or individual teaching laboratory computers (using free viewer software).

Methodology

Collection development involved:

1. Assembling suitable collections of representative glass slides that would be considered optimal as teaching specimens in each of the discipline areas. Where necessary, this included acquiring new specimens, or re-staining archival specimens.

2. Having the slides scanned by the Royal College of Pathologists of Australasia.

3. Undertaking appropriate post-processing of the slides. Generating thumbnail images to use as links on web pages.

4. Arranging for peer review of the slides to confirm that they were of sufficient quality for inclusion in the repository

5. In addition, illustrative examples of the use of virtual slides in practical classes for Medicine and Science students, including sample practical class worksheets, were selected or developed de novo.

Development of the repository, a password-protected web server maintained by the Faculty of Medicine, UNSW, involved:

1. Design and layout in consultation with a web developer.

2. Appropriate interfacing with the Neuroinformatica web server application.

3. Preliminary testing, followed by evaluation by peer reviewers.

4. Implementation of enhancements based on feedback.


The Virtual Slide Repository

A preliminary version of the repository was made accessible via the internet at http://virtualslides.unsw.edu.au/joomla in October 2008. In response to feedback, we subsequently rebuilt the website completely using a content management system and implementing a variety of other improvements.

The "finalised" version of the website went live in May 2009 at http://virtualslides.unsw.edu.au/

Further enhancements will continue and the repository will have additional slides included during its life, which will be a minimum of 3 years.

Viewing the collections requires a username and password, which can be obtained by lodging a request via a form on the website.

Copyright and intellectual property All of the collections and worksheets are available to Australian educational institutions without charge (other than a nominal fee for processing and shipment of data on a portable hard drive).

All of the virtual slides in this repository are scans of glass slides from UNSW teaching slide sets. Therefore UNSW owns the intellectual property for these resources. However, provided the source of the images is appropriately acknowledged (including by using the UNSW-branded thumbnail images as links to the virtual slide files) members of the project team are keen to make the virtual slides available to educators across the Australian tertiary sector. Accordingly, all image files and derivatives may be used by individuals within their own institution, but may not be used or distributed, via removable media or on the internet, without written consent. Implementation of teaching using virtual microscopy (either local availability or web-enabled access) is the responsibility of the recipient institution.

Virtual Slides in Botany – a Success Story

In Botany/Ecology, the ready availability – for the first time – of tissues from specimens collected from a range of species and environments facilitated teaching about adaptation and diversification. Students were asked to rate the use of virtual slides as a measure of satisfaction with this approach to teaching. In addition, students' performance in selected assessment tasks, with or without teaching using virtual slides, was compared.

The approach was extremely well received by students, with mean ratings above 4 (on a scale from 1 to 5) for effectiveness, quality of images, ease of use and capacity for promoting discussion. Remarkably, over 80% of students described virtual slides as "fun" and almost 90% rated using them as better than traditional microscopy.

The benefits extended to measurable learning outcomes, with a statistically significant improvement in student marks in a virtual slides practical as compared to a traditional practical (P <0.0001). These results are being submitted to an appropriate journal for publication.


Other positive outcomes

An unexpected positive impact on the sector has been a request for virtual slides to be hosted by The Curriculum Corporation in Melbourne. The Curriculum Corporation is a partnership of all Australian Education Ministers and undertakes activities that support and augment the work of the States and Territories in providing educational experiences for school students. Through its associated entity The Le@rning Federation (http://www.tlf.edu.au/), the Corporation makes and licenses digital curriculum content to support teaching and learning, and these materials are available free of charge to all Australian and New Zealand schools. TLF experts have selected around 120 slides they believe will be highly relevant to Science students in the middle years, as well as to years 11 & 12 Biology students. They noted that the slides would quite possibly also be of interest for students doing some VET/TAFE electives. Thus our Repository is already having an impact beyond the tertiary education sector.

Another unanticipated but very pleasing outcome has been that because the Biology teaching set is now available as virtual slides, it has been possible for a vision-impaired student, who otherwise would not have been able to enrol, to undertake the first-year course BIOS1101 (Evolutionary and Functional Biology) at UNSW this year. This course has a significant practical component; in the past, conventional microscope slides have been used in almost all practical classes and these could not be used by vision-impaired students. In addition, having the slides available electronically allows other students access to the material for revision.

Factors that Affected Progress/Lessons Learnt

In building a website for educational use, unsurprisingly there turned out to be a number of technical issues that required resolution. A major issue arose with respect to external users being able to view multiple slides. When Java updated to version 6 last year, difficulties arose at the user end, making the website appear slow and eventually causing "freezes". This was despite further updates to both the server and client side software. As a result, we were forced to retain Java 5 on our teaching laboratory computers and the University of Iowa (the world's largest virtual microscopy site, which also uses Neuroinformatica) was forced to advise users how to revert to Java 5 if their computers had been updated. It was altogether too much to expect those using our repository to undertake major changes to their computers just to be able to view our slides comfortably. As a result of collaboration with the Adaptive eLearning Group at UNSW, we solved the problem by replacing the Java viewer applet that normally provides web page display of image tiles from a virtual slide with a completely new viewer. This viewer is based on Flash Player version 10 and was developed by the Adaptive eLearning Group as part of a separate project focused on interactive tutorials using virtual slides. Because it is not based on Java, it is not subject to the effects of unexpected interactions between Neuroinformatica, our server software, and new versions of Java. Therefore, we changed the web pages to run the Flash Player viewer, which although slightly slower than the Java viewer is stable on all platforms. An image of a Repository slide displayed using the new viewer is shown overleaf.

Another problem that seriously affected the initial implementation of the website was the inadequate search function. We subsequently rebuilt the website completely using a content management system, as used across UNSW for web development. We took advantage of expertise in the Medicine Computing Support Unit and were able to achieve this within a period of 8 weeks. The finalised version of the website provides a better ordering of the collection as well as a much-improved search function. Importantly, maintenance of this site no longer requires any hand-coding of HTML pages, thus improving consistency and reliability. The resultant home page of the Repository is shown below. Crucial to the success of this approach was the short-term employment of a full-time web developer.


As in all developmental activities, critical ingredients for success are an understanding of the goals of the project and a commitment by the individuals involved to solve problems and ensure that target dates are met. For the repository, the project team was a coalition of busy academics working across multiple disciplines, and an important contributor to the coherence of activities and the successful outcome was the presence of our part-time research assistant Ms. Jacinta Green, who provided understanding and commitment across the various components of the work. Our ongoing co-operative interaction with the Medicine Computing Support Unit was also vital to the success of the project.

Although it had been part of the original proposal, no attempt was made to develop a veterinary pathology collection, because ALTC funded the virtual microscopy application from the University of Queensland and the UNSW project team ceded that area of development to them.


Dissemination

Because the repository is now readily retrieved via Google (at the time of writing, it appears on the first page of a search for "virtual slides" next to major collections such as the University of Iowa and Leeds) it has good internet visibility.

We have, as originally planned, sought to disseminate information via seminars and conference presentations. At the time of writing, a presentation about the Anatomy and Pathology collections has been made to the ANZ Association for Clinical Anatomy (at the annual conference in Auckland, New Zealand) and seminar presentations have been made or are planned at the University of Melbourne, the University of Newcastle and Monash University. A presentation about the Botany/Ecology collection has been made to the ARC-NZ Network for Vegetation Function meeting for Phenotypic Plasticity in Plants, held at the Australian National University in April.

To date, the Anatomy/Pathology collections have been shipped/are being shipped to colleagues at Monash University, Charles Sturt University and James Cook University. In response to a request, the complete collections are being shipped to the Faculty of Health Sciences, University of Stellenbosch, South Africa. As noted above, a subset of all of the collections has also been shipped to The Curriculum Corporation.

In addition, there has been particular interest in the Botany virtual slides from colleagues all around Australia. At the time of writing, this collection is being shipped to colleagues at Bond University and the Australian National University. Interest has also been expressed by colleagues at the University of Bern (Switzerland) and New York University.

Additional strategies for dissemination have included listing on the ALTC Exchange at http://www.altcexchange.edu.au/invitation-view-virtual-microscopy-slide-collection; creation of a Virtual Slide Repository bookmark for distribution at scientific and education meetings and filming of a promotional video by UNSW TV, available on line at http://www.tv.unsw.edu.au/. The bookmark was particularly successful, generating the requests from James Cook University and University of Stellenbosch listed above.

Future Directions

The availability of virtual slides for learning and teaching has led to development of another proposal for an ALTC competitive grant, based on a new collaboration with the Adaptive eLearning Group at UNSW. This is focused on interactive tutorials in Pathology using virtual slides and the virtual apparatus framework developed by the Group. In its pilot implementation, the approach has been extremely well received by students.

The success of the trial of virtual slides in Botany/Ecology may also provide the basis for a further proposal to ALTC.

Final Report Virtual microscopy for enhancing learning and ... · Final Report Virtual microscopy for enhancing learning and teaching Project Leader Professor Rakesh Kumar Department

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