Magic Lantern is a free and open source firmware add-on that extends the functionality of many Canon DSLRs to provide automatic acquisition of focus stacks by controlling the motor inside automatic-focus lenses. Magic Lantern has many other features and can be difficult to learn, so we're providing here a quick recipe for how to use just the focus stacking feature.
Note that these instructions are specific to a Canon T1i camera (also known as the 500D). Operation on other supported cameras will be similar, but the button assignments may be different.
Just the recipe:
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Put the SD card into the camera and power on. Wait for normal controls panel to appear, augmented by Magic Lantern notations.
Press Live View button to enable Magic Lantern. Wait for Live View image to stabilize with Magic Lantern notations under it.
Press the Trash button to show Magic Lantern menus.
Press left/right arrows around the SET button to select the Focus menu.
Press up/down arrows to select “Focus StepSize” entry. Press SET button repeatedly to cycle the StepSize 1,2,3,1,2,3…
2 is typically a good setting.
Press up/down arrows to select “Focus StepDelay”. Press SET button repeatedly to cycle the StepDelay through a range of delays. 80 ms works well.
Press up/down arrows to select “Stack Focus”, then press Live View button to bring up a “Stack focus” mini-menu. Press up/down arrows to select “Step Size”. Press Play to decrease value and SET to increase value. Value of 1 (with StepSize=2) is typically a good value for f/11 with a Canon 100 mm macro lens. Press Live View to get rid of the mini-menu.
Press up/down arrows to select “Focus End Point”. Press SET to obtain LiveView image with small text overlay that says “Focus End Point: <number> steps from here”. Adjust focus using * and + buttons at upper right of camera back. (Caution: if you keep the * button depressed for more than 1 second, it will trigger autofocus. If you have trouble avoiding this, use the Play button at lower center instead of *.)
When you have the desired focus for the end of the stack, press the SET button to change the text overlay so it says “0 steps from here”.
Continue to use the * and + buttons to adjust focus to the start of the stack. When you have that set, press TRASH twice to restore the main Focus menu.
Press up/down arrows to select “Stack focus”. Then press PLAY (or SNAP, if you have that set as a trigger) to begin shooting the stack. (Caution: If you press PLAY without first selecting “Stack focus”, you'll just end up back in Live View able to set the focus start and end points.)
Magic Lantern works properly with Canon EOS Utility to automatically transfer captured images to a computer when tethered on a USB connection. This allows use of the Stack New Images (PMAX) feature of Zerene Stacker to process the stack while it is being shot.
Note: for Stack New Images, it's better to start at the front of the image when focusing this way. If you start at the back you're liable to get edge streaks. At least that's the case for the Canon 100 mm macro lens.