The Virtual Microscope

The Virtual Microscope is a Java application that supports interactive viewing of high-resolution, multi-dimensional image datasets from various microscopes. We currently support data from a Philips Environmental Scanning Electron Microscope (ESEM), and a Fluorescence Light Microscope.

Download the Virtual Microscope interface→

Interface Controls

The interface provides a simulation of our actual microscope interface(s). Controls common to all datasets include brightness, magnification (usually up to 1800x), navigation, measurement, and annotation. SEM samples include a contrast control, and some also include a focus control.

The navigation and magnification controls allow the user to explore any point of interest on the sample. This differs from other virtual microscopes that have been produced which provide only a few 'hot spots' that can be magnified and explored.


The focus control is a real focal plane adjustment instead of a blurring of the image. Our automated data capture software (see below) allows us to capture an arbitrary number of focal planes. Thus, the focus control on the Virtual Microscope allows the user to glide through those planes interactively, bringing items closer and farther into focus. This is particularly useful with thick specimens viewed in the SEM.


We have included a full set of specimen annotation tools so that experts and laypeople alike can mark up the datasets for future reference. These annotations are useful for teaching details about the data, as well as for allowing teachers to ask students to identify data features as homework. The annotations can be saved and reloaded as XML files.

Automated Data Collection

It can take thousands of images to fully describe a single specimen so that the user can explore any point at varying magnifications with multiple focal planes. As a result, some of our datasets are many gigabytes (GB) in size. In order to accurately and sanely collect this data, we have written various software programs that automatically control the instruments.

Download the data collection tools→

The Bugscope Connection

The software for our SEM is based off of a work on a previous project called Bugscope. Bugscope is an online educational outreach project that provides real-time access to our SEM over the web so that school children can look at bugs from their own backyards. We have leveraged the remote-control software we wrote for Bugscope into an automated data-collection package for the SEM. On the Light Microscope, we are using Openlab, and will be distributing our tiling scripts in case you have a similar system.

Specimen IDs

Each Virtual Microscope specimen gets its own unique specimen identification number. For those building new samples, click the button below to generate a new specimen ID. Generated IDs expire after two months, so don't grab one until you need it. When specimens are submitted, we will verify they have a valid ID automatically.

Automated Stitching/Blending

Additionally, the interface allows experts and laypeople alike to annotate specimens and/or load previously-created annotations.

Download the image stitching tools →

File Format

The file format we use to store our image datasets is described by an XML file that accompanies each dataset. We encourage others to use this file format for compatibility with the Virtual Microscope.

Download the file format XML and XSD files→