Inkscape

Inkscape is an open source SVG package.
It is easy to download and seems quite easy to use at least from a basic point of view.
I think time getting to know this is well spent.

I would like to make a zoomable cell with some scale associated with it.

I think SVG is probably the right format to do this with.

I have just worked through the basic tutorial:
http://inkscape.org/doc/basic/tutorial-basic.html

I will probably have to do it again to be sure that I can use it but it's a good start.

Within the tutorials is also the possibility of bitmap tracing.
I am not sure exactly what this is but it looks interesting.
http://inkscape.org/doc/tracing/tutorial-tracing.html
This might be very useful for turning electron micrographs into zoomable images.