Sean Lauber:AMIRA - Using Snagit
Download Snagit from here: http://www.oldapps.com/SnagIT.php?old_snagit=12. Apparently it's free with a key in the comments section. Versions after 7.2.5 aren't free.
Unfortunately I can't take snap shots of snagit itself when I'm trying to use snagit to take the pictures, so I'll have to use words rather than pictures to explain this.
1. Load up Snagit. Note that the program must be opened to use snagit. In later versions you can close the program and still use it, but here the program must be minimized.
2. To take snapshots, go to INPUT then select FIXED REGION.
3. Click the "..." to open the properties and change what you need to. I like to use 300 pixels x 300 pixels for a nice square.
4. Change OUTPUT to clipboard (so you can simply paste an image into powerpoint for instance).
5. I like to set the FILTER to scale 50%. This reduces the image size 50% so it isn't so big.
6. Below FILTER I uncheck the arrow and "preview in editor" options.
7. Now just start taking pictures! I try to take pictures about every 10 slices or so (in AMIRA) and try to take pictures with and without the overlay. Make sure you're zoomed in about 2x so your 300 x 300 snapshot will just cover the lung. It should take about 6 pictures to span the lung. Figure out where you need to start to get about 6 pictures from the top to the bottom of the lung. To take comparable shots between animals, use the number of ribs as markers to guide you.