Archive | August 21, 2012

Focus stacking of live subjects

Treehopper (Ceresa sp.) from Woburn, MA [Canon 7D, Canon MP-E 65mm, 3 speedlights Canon 580EXII; 7 images, taken at f16; combined in Helicon Focus]

I first became aware of the technology known as focus stacking in 2002 or so, when a new company called Syncroscopy came to our museum at Harvard to demonstrate its new software “Auto-Montage.” It was designed to combine several shallow-focus images taken with a video camera attached to a microscope into one, seamlessly focused photo. The quality of the resulting images was far from perfect, but the technology held a lot of promise, and in the following years it has improved dramatically.

Psychodid fly (Clogmia albipunctata) from Woburn, MA [Canon 7D, Canon MP-E 65mm, 3 speedlights Canon 580EXII; 9 images, taken at f11; combined in Helicon Focus]

Given sharp, aberration-free optics you could produce images that rival those taken with a scanning electron microscope (SEM), but in full color. It is also significantly cheaper than the SEM, and allows for non-destructive photography (specimens need to be coated with a thin layer of gold for SEM imaging, destroying their original coloration.) It also allows for high definition imaging of specimens preserved in alcohol and other fluids, something that was not possible with the SEM. Not surprisingly, the technology has quickly become incredibly popular among insect taxonomists and other biologists, and now it is hard to find a taxonomic paper that includes illustrations prepared any other way.

Roeseli’s katydid (Metrioptera roeselii) from Concord, MA [Canon 7D, Canon MP-E 65mm, 3 speedlights Canon 580EXII; 2 images, taken at f14; combined in Helicon Focus]

It took significantly longer for nature photographers to embrace the focus stacking technique. For one, the early focus-stacking software was incredibly expensive (Auto-Montage cost around $4,000, and a full image stacking system that included a video camera and a computer could set you back about $40,000.) But soon competing, cheaper products started appearing on the marked, some even as freeware (e.g., CombineZ.)

But the real problem was the fact that it always took at least a few seconds to shoot a series of shallow-focus images, which meant that if the object (or the camera) moved then the resulting images would be difficult to align and combine. Therefore, dedicated focus-stacking systems use precision rails that guide the camera towards the subject; often these are motorized and can be moved in increments as tiny as a few microns. And yet, with a bit of practice (and some luck) it is possible to get very nice focus-stacked images of live subjects, even if you hand-hold your camera.

A bark louse (Psocoptera) from Mozambique [Canon 7D, Canon MP-E 65mm, 3 speedlights Canon 580EXII; 12 images, taken at f10; combined in Helicon Focus]

The focus stacking software has over the years become more sophisticated, and most packages can now correctly align misaligned photos, and ever correct for tilting and shifting of the subjects. They will also fix differences in the exposure levels between individual shots. I have been using both Helicon Focus and Photoshop CS5 stacking features to obtain my images, and both pieces of software can automatically correct image misalignment.

My process of shooting focus-stacked images of live insects and other animals is relatively simple. First, I hand-hold the camera. I do not use a focusing rail because I soon realized that any gains in stability and alignment of images taken while using the rail is paid for by a significant slowdown in the process of taking the images. It is easier and faster for me to simply rest my camera on a tripod or the edge of a table, and move it forward or backward in tiny increments without taking my eye off the viewfinder.
I usually shoot 4-10 images at f8 to f16 in a very quick succession, using external strobes. It is important that the flashes are powered by high capacity batteries that recycle immediately, otherwise some may not fire or fire with a lower power, resulting in uneven exposure of subsequent images. Lithium AA are the best, but they overheat quickly, and you must wait for them to cool off between bursts of shooting. It usually takes me 2-4 seconds to complete a stack of shallow-focus shots.

Tachinid fly (Tachinidae) from Mozambique [Canon 7D, Canon MP-E 65mm, 3 speedlights Canon 580EXII; 6 images, taken at f14; combined in Helicon Focus]

The animal, of course, must remain motionless, or nearly so, throughout the process. Surprisingly, it is easier to shoot a series of shots of an agile, fast animal than a slow moving one. This is because fast animals tend to move in spurts, and freeze between movements. Wasps, flies, katydids, tiger beetles etc., are much easier to shoot than snails or dung beetles, which are much slower, but never really stop moving. It will often take me 10-45 minutes to catch the perfect moment when the animal is motionless, but it always happens sooner or later.

Component images used to produce the stacked-focus image of a tachinid fly.

I shoot for focus stacking mostly using a featureless white or black background, but it is also possible to do it in the wild. I sometimes use a 180mm macro lens to get a series of shallow-focus images of an insect or a plant in wind-free, overcast conditions, and stack them later.

I don’t use too much focus-stacking in my photography, mostly because it is quite time consuming, but when I do it often results in remarkably sharp, striking images. The examples here were all taken this year, using a hand-held camera, and all show live insects, which were free to move (and in the case of the psychodid fly, it took advantage of this fact and flew away the moment I took the last shot.)