As long as I’ve been doing microscopy, it’s been tricky to make videos that are easily playable cross-platform. A lot of microscopy software packages support only a few video output formats, possibly with codecs that either aren’t available on the machine you want to play videos from or that produce bad compression artifacts.
To avoid these problems I currently use Handbrake to transcode videos to H264 video in an mp4 container, which appears to be playable on just about any machine. It’s how I’ve produced all the videos on this blog. It also produces pretty good compression and nice looking movies. In general, I first use the microscopy software to produce an uncompressed AVI file. This is huge, but avoids introducing compression artifacts. I then open this in Handbrake and transcode it to H264 video. The default settings produce good results and converting a 10 second video only takes a few seconds. You can see some of the results in these posts.