What software is available and widely used for macro focus stacking? In other areas photoshop, lightroom, aperture, etc are kind of industry standard options. Is there such a thing for focus stacking?
I believe you are looking for something like Helicon Focus.
I've heard from reliable sources that stacking can also be done manually in Photoshop CS 5, but I haven't done it myself.
In Photoshop CS5 or later, load your images into layers.
Select Edit > Auto Align Layers (at macro distances even on a tripod small changes in focus will alter the perspective of each shot)
Select Edit > Auto Blend Layers. This will select the sharpest parts of each layer and create a mask. The masks can be quite complex, but it does a very good job.
There is an open source program CombineZP
One solution has been omitted for this question - most people who stack actually tend to use Zerene Stacker - it's the only package that has various user generated plugins for substack slabbing. If you look through Flickr there are twice as many Zerene pics as there are for Helicon. Helicon is faster though and suits lab workers better, ZS better for photographers. Both this and Helicon are the class leaders.
I've worked with both Helicon focus and the two-part combination of a Stackshot rail paired with ZereneStacker.
I prefer Stackshot and Zerene. Once all the various parts are wired together properly (takes some effort to figure it all out) I fire up:
1) entangle tethered directly to the camera and 2) Zerene Stacker, which has a GUI interface for controlling the rail--all of which I have mounted on a tripod in front of a light tent.
Lighting is a big issue too. I won't attempt that discussion now. Use trial and error to determine the ideal manual exposure. My Nikor 105mm macro lens seems to like F8 best.
Determine closest focus point and the furthest. Click the mouse appropriately to tell Zerene where those points are. Fire away. Zerene controls it all from that point on.
Now quit everything. You now have N raw exposures in the stack all exposed and lighted identically. Edit any one raw image from the middle of the stack with rawtherapee. Save a *.pp3 file in the current directory, perhaps named as now.pp3
From a terminal window type:
mkdir tiffs [enter]
rawtherapee-cli -o tiffs -p now.pp3 -t -Y -d -c . [enter]
That performs the same rawtherapee editing steps, as defined in the pp3 file, to each raw image in the stack, converting to *.tif on the fly. That command also deposits each *.tif file in the tiffs directory made above.
Now run Zerene again on all tifs (ZereneStacker.sh *tif). Align and stack all tifs as per various GUI options.
Now save as a single stacked *.tif, named what ever you like. It's convenient to name stacked tifs as stk-filename.tif
Now run gimp on stk-filename.tif to make the final image.
Helican was full of bugs two years ago when I used it. Perhaps they have it ironed out by now. Helicon electronically twists the focus ring on the lens for each new exposure. Stackshot and Zerene leave the lens focus ring as is and physically moves the camera instead.
Zerene/Stackshot works best for me. Helicon may be better suited to larger subjects while Stackshot/Zerene is better suited to the smallest subjects.
https://www.photomacrography.net/ is a great source of information. With access to experts.