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taxonomy and ethology
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Focus Stacking and Other Matters

January 20, 2012

Tonight I've put up the first of the many digital habitus photos I will eventually be adding. These new photos will be replacements for the current shots, which I originally made with my regular (film) macro camera. This time, I replaced the photos for a number of eastern Laphria that I thought particularly bad, namely, the photos for both males and females of L. affinis, L. cinera, L. divisor, L. royalensis, and L. vorax, as well as for the male of L. sacrator.

I'd like to think the old shots served their function of providing an idea of what the species look like. Nevertheless, I know they had (and still have) several big flaws. First, the plane of focus was narrow. I had tried to get it aligned with the dorsum of the thorax and abdomen and in the same plane with the wings if possible. In some cases this worked well. But in others the dangling legs and often the tips of the wings were blurry.

Second, I had removed the background by first scanning the slide (I had the photos processed as 2x2 slides). Then I adjusted the gamma with Photoshop 4.0 until the shadows disappeared. This process often took some of the wing margins with it. It also resulted in blown out highlights, and imparted a washed out look to the overall result. Still, I thought the "sans background" results preferable to the originals.

The new shots fix the blurriness by using a software-generated composite of multiple frames, taken in sequence with a stacking rail, each having a slightly different focus. For the shots I've taken so far, I've been using from 15-25 frames. The software I'm using is called "Helicon Focus." It's a propriety package that costs about $200. I usually avoid proprietary software if there is anything open-source that will do the job. In this case I tested several programs I thought might do focus-stacking. They either did something slightly different, were too complicated to use, or flat-out didn't work with large numbers of frames. So I bought Helicon.

In addition to a stacking rail on a copy stand, I'm using a Nikon D90, a 180mm Sigma macro with a 2X converter, and a circular flash. Each frame is taken at ASA-200, F-32, and 1/50th second.

So far I've included everything in the photo, including the top of the insect pin. In the future I may elminate the frames with just the pin. Or even edit the pin out altogether with the GIMP.

BTW, I use the GIMP now for everything. "GIMP" stands for "GNU Image Manipulation Program." It's an open-source Photoshop replacement and it's free. So you can run it on any number of computers without paying. There's even a version for a USB stick. I'm using the latest, 2.6.11.

I still remove the backgrounds, but I've changed how. I'll post a separate illustrated tutorial on exactly what I do later. My new method doesn't involve altering the gamma. So there are no drop-outs or wash-outs.

The new shots aren't perfect. Namely, I took some of them using four halogen spot lights, fixed in sockets that are part of the copy stand. These lights produced golden highlights, which after editing in some cases qualify as blow-outs. They almost look as if someone dabbled patches of golden paint on the top of the thorax and abdomen. I'll probably eventually retake those shots, using daylight bulbs, or with some sort of diffuser, or both. Meanwhile, I've posted them anyway. They are better than what they replaced.

When I've got my macro technique down, I'll post a tutorial on what I am doing and how, again with photos. I also may re-scan and edit some of my better original 2x2 slides, if I think they can be salvaged.

On a more general note, this site is going to be an amalgam of old and new. As an example of the old, I will be posting plates with terminalic drawings for the females of all the species and subspecies in Choerades and the two new genera. I made a plate for each of the 39 taxa. These plates were done nearly 30 years ago with pen and ink on Strathsmore board. People don't make these drawings any more, partly because they don't know how (it's complicated), partly because they don't have the necessaary modicum of artistic ability, partly because they don't want to take the required time, and partly because they don't realize that photographs are not an adequate substitute. But mainly they don't because they know that no matter how good you are at it, it won't contribute towards getting a job or grant. As for the adequacy of photographs, they can certainly do a lot; this site relies on them heavily; and the new illustrated keys that are characteristic of, say, the Canadian Journal of Arthropod Identification are superb. But for all their advantages photographs can't substitute completely for terminalic drawings. The trick will be to mix-and-match drawing and photography, using each where it works best. Last, the drawings I will be posting have since been modified with the GIMP. The explanatory text, for example, was originally done with a LeRoy Lettering Set I bought in 1979 for $300. It looks awful now. I've either replaced or will replace it with computer-generated fonts.

I must still make some drawings of the terminalia for the males of Choerades (the plates for the males of the 20 taxa in the two new genera were included in my PhD. dissertation). I've been meaning to do these Choerades plates for years. They will require that I spend maybe a week of real time per plate, and as there are 19 North American species and subspecies in the genus, at a minimum there will be maybe ten plates. It's not the kind of thing that's easy to find continuous chunks of quality time to spend on, when you are making your living doing something else, and have a family to boot. When I do get to them, it's likely I'll make them the old way, by hand. Then I'll scan and edit the result with the GIMP or Inksacpe. "Inkscape" is the open-source replacement for Adobe Illustartor. I have Illustrator Ver. 8. I also have a Wacom drawing tablet. I've never quite gotten used to using either.

There's a lot more I could write but this post is getting lengthly. It may take a while to get all the old habitus photos re-done.