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I have a requirement to be able to take a series of photos using a 5D Mk3 to be used for focus stacking using a remote. I cannot use a laptop so the solution must be hardware-based or in-camera.

Without a remote I have hardware options (for example the Promote) and an in-camera software option (using Magic Lantern's focus stacking), however the Promote's remote input is incompatible with the hardware I want to use to trigger each focus stack (A Kessler Second Shooter) and the Magic Lantern focus stacking can only be triggered from within a menu (not from the shutter button).

Is there any other option available to me?

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As far as I've seen on their website, Kessler Second Shooter does not provide any focus control mechanism, therefore you would have to improvise.

First option, workaround with the device itself: Set the lens on manual focus, move the camera on the slides using the Second Shooter's motor controls in small steps (here you need to check what's the smallest movement step offered by the controllers)

Or using extra devices, either get a motorised/computerised follow focus solution, either build something yourself.

Building a focus stacking controller

There are guides on the Internet how to use an Arduino (here things are flexible, one could build similar things with RaspberryPi or any other microcomputers and boards on the market

Motorized follow focus

You can look for something like Opteka FFR-900 Motorized Remote Focus and Zoom or Vidpro MR-400 Motorized Focus & Zoom

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