As far as we can see from the comments connecting the microscope to a computer needs an additional PCI-card. This is likely to be a Firewire port for an optional camera for image acquisition.
In that case we depend on proprietary drivers and software that are most likely not available for a Linux system unless the manufacturer decides to develop such a solution (contact them if you feel this is needed). A Firewire solution may also make the integration of proprietary Windows software via a virtual machine difficult.
An alternative would therefore be to mount a microscope camera attached to a standard USB port. It would then be much easier to get the data in either by a Linux driver or by running custom software through a virtual machine.
We have good experience with a Jenoptic ProgRes camera that can be attached to USB and gives a decent image qualitity. Unfortunately the default software that comes with this camera runs on Windows or MacOS only. There also is a Java plugin for the public domain ImageJ image processing software that may be worth a look (we have not tested this software here yet). There is also a Linux SDK and limited Linux drivers available for the Firewire camera models.