I have used Helicon Focus extensively with my photomicroscopy to give me huge depth of focus using focus stacking. I am now getting into using the associated Helicon Remote software which automatically controls a DSLR to again create a focus stacked image – this software is totally remarkable. I just plug my Canon 5D MkII into the USB port with Helicon Remote running – and it does it all for you! The software even works with the RAW files from the 5D MkII which is more than I can say for CS3!! Anyway – you set a low f# (you don’t need depth of field as you’re focus stacking) a low ISO for low noise, and your exposure time to suit. Using the software buttons in HR you set the near and far field focus points and let HR work out the best stack. Hit take the pictures and off it goes taking an image, shifting focus, and taking the next image until it’s completed the stack. Now comes the best bit – it now puts all the images into Helicon Focus where it focus stacks the lot.   Here is my first real go with this software – I’m going to have to go up into the loft to get the butterflies out again.
http://www.flickr.com/photos/12801949@N02/5517649340/