Neurosurgery video

I am the media specialist for the Department of Neurosurgery at the University of Utah. Part of my job entails going into the OR and taking pictures of the case setups and then taking intraoperative video captured from the camera on the surgical microscope.

Currently we are using a win2000 computer that upon capture automatically encodes the video as WMV. This really erks me because my editing station and storage database are on macs. I can edit the WMV using 3rd party flip4mac but it is really bad. I am currently working on replacing all of this but that is a different forum.

Here is my question. I want to trans code these videos to a better codec for storage on my database. Something that will allow me to easily edit it but also keep my videos files as small as possible. Any help would be greatly appreciated.