The Virtual Microscope 6.2.2

The Virtual Microscope is a Java application that supports interactive viewing of high-resolution, multi-dimensional image datasets from various microscopes.

The Virtual Microscope is a tool that supports data from a Philips Environmental Scanning Electron Microscope (ESEM), and a Fluorescence Light Microscope.

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.

Focus
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.

Annotations
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 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.

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 dont grab one until you need it. When specimens are submitted, we will verify they have a valid ID automatically.