Okay I have all that stuff you recommended in 'focus stacking equipment', now what do I do with it?

There are two decisions you need to think about before trying to put your rig together;

1. Vertical or Horizontal
2. Move the camera or move the subject

The answer to (1) depends on what kit you have available and what you are prepared to purchase. One option is to make a horizontal rig and then make a stand which you can vertically mount your entire rig onto, thus converting it from horizontal to vertical, but if you choose this 'mixed' method bear in mind that some focusing mechanisms will only work properly in one orientation without modifications.

The answer to (2) depends on whether your 'movement rig' can take the weight of your camera (This will be more of an issue if the camera is mounted vertically!), and whether you can easily mount the camera on it. I generally move the subject, but this is very much a matter of personal choice. Two of the stackers I most admire move the camera - One uses a microscope focus block, the other using a Mill-table.

Vertical rig

The first component you need is something to hold the camera pointing straight down - something like a copy stand, the Olympus OM Macrophoto stand VST-1, a Nikon Multiphot stand, a Zeiss Tessovar stand, or a 'homebrew' arrangement comprising a base and a perpendicular 'riser'.

If you decided to move the camera, then your focusing mechanism needs to be between the stand and the bellows

Once you have your 'stand' you need to mount your bellows onto it, pointing downwards. You can then mount your camera on top of the bellows and a lens underneath.

If you decided to move the subject then you need to fix your specimen holder/movement rig underneath the lens. It's a good idea to allow some kind of X-Y movement in your specimen holder to allow for ease of composition.

Horizontal rig

The first thing to do is bolt the bellows unit and specimen holder to your base (If you decided to move the camera then obviously your camera movement device needs to be fitted between your base and your bellows). Quite how you do this depends on the kit you've accumulated, I'll show the steps I took to put my first proper rig together...

The Olympus bellows has a focus rail built in, although I found if I mounted the bellows directly to the base then the control for the focus rail was too tight to the base to comfortably use, so I made this little 'riser' to raise the bellows up from the base:

I simply screwed this down to the base with the two screws visible in the image above (As you can see I made four holes for fixing the riser to the base but two screws holds it in place very well!). I then drilled the mounting holes for the bellows through the base and the riser block.

With two screws from below which hold the bellows in place, the camera end of the rig looks like this:

Or a wider view:

Note I only use this focus rail for extremely low magnification work. It's simply not got fine enough control to allow high magnification stacking. It's extremely useful to have this easy rough focus available though!

Now to fix down the specimen holder. The really important thing at this stage is to ensure everything is lined up properly so that when you use your focussing mechanism to move the camera or the subject, that it moves directly towards the target (ie if you are going to move the subject as I do then it must move directly towards/away from the center of the lens). If everything is not aligned properly then when you move the focus mechanism, the subject will move to one side of the frame.