UniServe Science News Volume 12 March 1999


The Virtual Cell Biology Laboratory

Grahame J. Kidd and Joseph A. Rothnagel
Department of Biochemistry, The University of Queensland


A number of major difficulties limit effective instruction in cell biology. Chief among these is that cell biology relies heavily on advanced microscopes for the acquisition of data. These microscopes are expensive ($200,000 for an electron microscope, $300,000 for a confocal scanning laser microscope) and require skilled personnel for their instruction as well as a substantial investment in infrastructure. Not surprisingly, these facilities are rarely available for undergraduate teaching and where they are available, instruction is limited to brief superficial demonstrations. Moreover, this equipment is housed in small dark rooms that are highly soporific and not conducive to a good teaching environment. The number of students that can be accommodated around a microscope is usually fewer than five. Student access to microscopy images is typically restricted to a small variety of pictures in textbooks. As a result, students do not acquire skills needed to interpret real images and gain little understanding of the complimentary information that different techniques provide. In an attempt to address these difficulties, we have developed a CD-ROM based microscope simulator that is embedded within an interactive laboratory environment.

Description of the project

The aim of the Virtual Cell Biology Laboratory (VCBL) project was to develop a set of computer based interactive programs that allow students to research problems using state-of-the-art laboratory techniques. At the heart of the project is a gallery of stored images taken from light, confocal and electron microscopy experiments. These images are linked to the various experimental procedures and are accessed by students through choice-directed pathways. The selected images can be manipulated to simulate changes in magnification, contrast, filters and focus.

The simulated research project revolves around a laboratory environment (Figure 1), termed the Workbench, in which choices are made from 'drop down' menus for specimen preparation, staining reagents and type of microscopy. Students are aided in their choices by information pages, which explain the VCBL, describing each microscope system and its simulation, and providing a basic introduction to cell biology with annotated examples and references to more comprehensive primary resources.

Figure 1.

Figure 1. The "Workbench" environment is central to the VCBL. Students make point-and-click decisions about which specimens, reagents, and microscopes are to be used in each experiment.

From the Workbench, students launch the microscope simulator that they wish to use to examine their specimens. Each of these interfaces allows the user to manipulate the principal controls on the instrument and is intended to provide a feel for the capabilities of that microscope. Since most students are familiar with light microscopy, a good starting point for their observations is the conventional light microscope simulator (Figure 2).

Figure 2.

Figure 2. The light microscope interface showing a cell with microtubules labeled by a green fluorescent reagent.

The user can change objective lenses and adjust brightness, as well as selecting advanced modes such as fluorescence, phase and interference-contrast microscopy. The confocal microscope simulation (Figure 3) includes three-dimensional reconstructions of the specimen, including rotating views, which are shown as movies.

Figure 3.

Figure 3. Confocal scanning laser microscopes provide highly detailed views of cells and their components, such as the microtubule network shown here. The VCBL allows students to select combined multicolour views of the same cell to show colocalisation of cellular components. The VCBL also allows students to visualise three-dimensional views of specimens.

Similarly, the transmission electron microscope interface (Figure 4) includes a variety of lens and aperture choices. At the end of each virtual experiment, students may return to the Workbench to set up another specimen/stain combination, or alternatively, run the self-assessment module.

Figure 4.

Figure 4. Transmission electron microscopes are expensive, difficult to set up and not user friendly. This simulation provides realistic images for interpretation, and manipulation of the principal controls, while bypassing much of the technical learning curve.

Each of these simulations uses an extensive picture gallery providing multiple images of the chosen specimens, at different magnifications and photographed in a number of modes. These images were produced directly from microscope imaging systems (except electron microscopy where an intermediate negative was used). Since they represent actual views obtained from each instrument they allow students to develop interpretative skills that can be transferred to a 'real world' laboratory environment.

Two alternative approaches are provided for working through the available material in the VCBL. Since the VCBL allows students to independently design and carry out experiments, it is readily integrated into problem-based learning protocols. However, it can also be used with more structured learning approaches allowing students to negotiate through the material using a step-by-step guide that is provided in a window which stays on top of the simulations as a constant reference source (Figure 5). These approaches are not mutually exclusive.

Figure 5.

Figure 5. Problem-based learning can begin immediately, using the information package attached to the "Project Problem" (centre screen) which introduces the problem to be solved. Structured learning is also facilitated by the step-by-step "Guide" window (top left), which cross references entries in the information package. Student experiments and their notes are logged in the "Lab Book" (lower left).

Comparison with other strategies

When we initiated this project the existing CD-ROM based teaching aids were essentially electronic textbooks with mainly still images and the occasional movie clip. The present project differs significantly from these in that it not only provides a gallery of images but also laboratory simulations involving various microscopes and bench techniques. We are aware of one other microscope simulation, The Virtual Microscope1 that was developed by the Department of Earth Sciences and the Institute of Educational Technology at the Open University to introduce students to microscopy of geological specimens. There is also a commercially available interactive program, the Microscopy-Tutor, as an aid in teaching the basic concepts of bright field light microscopy2.

Continuing development

The project was designed to allow the incorporation of additional cell biology problems which can be added in a modular fashion. Additional modules on RNA and protein trafficking are planned. It is envisaged that newer technologies such as the DVD format will allow a more extensive collection of images, animations and movies to be accommodated on a single disc. In addition, this project could be installed on a server to allow Internet access by students either on campus or at remote locations. Finally, this project should be considered as a paradigm for the teaching of any techniques or processes that utilise expensive equipment or require costly infrastructure such as X-ray crystallography, nuclear magnetic resonance and mass spectrometry.


We would like to thank Sue Hamilton of this Department for her invaluable advice and enthusiasm for this project. We are grateful to Athol Reid (Biochemistry) for his help with obtaining microscope images and collating the data sets. Thanks are also due to members of The University of Queensland's Educational Multimedia Services Unit especially, Beth Cavallari, Adrienne Winzar, Tim Dunn and Cathy Stephens for art work, software development and media design.


  1. http://met.open.ac.uk/vms/vms.html
  2. http://www.ravenpress.com/media/m1208.htm

Return to Contents

UniServe Science News Volume 12 March 1999

[an error occurred while processing this directive]

Page Maintained By: PhySciCH@mail.usyd.edu.au
Last Update: Monday, 30-Apr-2012 15:38:56 AEST
URL: http://science.uniserve.edu.au/newsletter/vol12/kidd.html