How to create impossibly huge depth of focus with microscope photography

May 22, 2018

John Aldred

John Aldred is a photographer with over 20 years of experience in the portrait and commercial worlds. He is based in Scotland and has been an early adopter – and occasional beta tester – of almost every digital imaging technology in that time. As well as his creative visual work, John uses 3D printing, electronics and programming to create his own photography and filmmaking tools and consults for a number of brands across the industry.

How to create impossibly huge depth of focus with microscope photography

May 22, 2018

John Aldred

John Aldred is a photographer with over 20 years of experience in the portrait and commercial worlds. He is based in Scotland and has been an early adopter – and occasional beta tester – of almost every digital imaging technology in that time. As well as his creative visual work, John uses 3D printing, electronics and programming to create his own photography and filmmaking tools and consults for a number of brands across the industry.

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The one certainty in photography is that the closer we get to our subjects, the shallower our depth of field becomes. If we’re shooting with a macro lens, we have the option to stop our lens all the way down to increase the depth of field. Sometimes this can be enough to give us what we need. And sometimes it can’t.

If you’re shooting down a microscope, though, then changing the aperture isn’t really an option. So you have to get a little creative. And this is where focus stacking comes in. After recently switching up to DSLRs for microscope photography, The Thought Emporium YouTube channel decided to put this video together on their microscope photography focus stacking technique.

YouTube video

The principle of focus stacking is quite straightforward. Take a bunch of photos of your subject with different parts of the shot in focus. Shoot enough that, between them, every part of it is sharp and in focus. Then blend them all together in post to create the final result.

Focus stacking isn’t just for the small stuff, though. It can be applied to the very large as well. It’s quite popular for landscape photography, for example. But there are various shooting techniques for doing it with small subjects.

  • Keep the camera and subject static and just adjust the focus on the lens
  • Keep the subject and focus static and move the camera toward or away from your subject
  • Keep the camera and focus static and move the subject toward or away from your camera

All three methods have their own quirks depending on what you’re shooting, the gear you’re using, and how the subjects are aligned. The first one is the most straightforward because your camera and subject remain parallel to each other for every image.

When you move the camera or the subject, it needs to be done perfectly in line with the plane of focus. If you rotate your camera or subject slightly between images, then you can get a completely different perspective. And when your subject is this close, that difference can become very obvious.

For a microscope, though, it’s the last option. As the camera isn’t really looking directly at the subject, but through a microscope lens, there’s no point refocusing the camera or moving it. It would do more harm than good. There’s also little point refocusing the microscope lens, either, when it’s simply to just adjust the height of the surface on which the subject resides.

Fortunately, microscopes have the perfect design for keeping the movement parallel to the lens. The slide is positioned so that the closest part of the subject is in focus and a photograph is taken. The slide is raised to move the subject closer to the lens, and push the plane of focus further “down” the subject. Another shot is made. Rinse and repeat until you’re done.

If you’re using something like a macro lens, rather than a microscope, you might want to look into picking up a macro focusing rail.

Once you’ve shot enough images to cover the entire subject’s depth, it’s just a case of loading them up in Photoshop. Load the images as separate layers on a single canvas, and tell Photoshop to Auto-Align Layers from the Edit menu. Choose “Auto” and hit OK. A short time later, Photoshop will have aligned all the layers so that the sharp parts of each match with each other.

Finally, choose Auto-Blend Layers, again from the Edit menu. Choose “Stack Images” and hit OK. This bit may take a while, but it’s worth the wait. At the end of it, you’ll see an image that should be sharp from front to back.

The only real caveat for focus stacking is that your scene needs to stay static in front of the camera. It’s not really practical if your subject changes its pose from shot to shot. In the video they suggest about 10 shots, of course, this will vary depending on the depth of field of the lens you’re using relative to its distance as well as the depth of your subject. So, you’ll want to practice and experiment.

[via Hackaday]

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John Aldred

John Aldred

John Aldred is a photographer with over 20 years of experience in the portrait and commercial worlds. He is based in Scotland and has been an early adopter – and occasional beta tester – of almost every digital imaging technology in that time. As well as his creative visual work, John uses 3D printing, electronics and programming to create his own photography and filmmaking tools and consults for a number of brands across the industry.

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2 responses to “How to create impossibly huge depth of focus with microscope photography”

  1. Anthony Woodruffe Avatar
    Anthony Woodruffe

    It buy an X-T2 with up to 999 focus stacked images.

  2. Tj Ó Seamállaigh Avatar
    Tj Ó Seamállaigh

    umm .. was that English?
    Anyway, I’ve been doing microscope photography for some time now, and you really don’t need that adapter even. It is a good thing to have it of course but not an absolute requirement. Just use any macro photography technique, place the camera on a rail and get slowly close to the eyepiece till you fill the frame (yes, it can be dangerous if you accidentally hit the lens front). My favorite method is typically the reverse-lens technique. Not using an adapter can give you an advantage as well, since you can get extra magnification (by adding extra extension tubes for example) and you can add filters as well (I like taking infrared photos for my subject). Finally, Photoshop is not really a good choice for stacking. There are other methods. I’ve found out, the hard way, that Photoshop is the least reliable work environment for this (maybe because my PS is old? Could be). My microscope is pretty old (had it since I was 14) but well, for a hobbyist like me it does provide me with excitement still.
    Attached: Infrared shot (about 45X magnification) for an ant’s head.
    https://uploads.disquscdn.com/images/6d81670a78bb50b4a1b98815ad32025b3e5ce2018c13827351ed91d5dafb232c.jpg