Monday, February 27, 2012

From the realm of the galaxies to the microcosm: A thin-section gigapan

I've been looking forward to posting this image (and linking to the corresponding GigaPan) for a long time.

(Click here for the zoomable GigaPan mosaic at

The image in today's post is a 156-panel mosaic of something called a thin section; it's a `geology thing', in contrast to the `astronomy things' that I've been imaging so far. Basically, it's a piece of rock (from Vermont, in this case) that's been ground so thin, light will shine through it. When viewed with the right kind of microscope, thin sections commonly show bright colors, along with variations in light-vs-dark from grain to grain. The area shown in this image is about 12mm by 18mm. This thin section is one of a set that have been at De Anza College for many years. Students in our introductory geology course look at these thin sections when they're learning to identify the different rock textures. I don't know when these thin sections were made, but I'd guess they date from the 1960s or 1970s

I've written a more detailed explanation in the `About This GigaPan' notes - if you're interested, you can scroll down below the panorama, and my notes are below the camera and image information.

Acquiring the image data:

Instead of a telescope, I had to use a microscope. I used a `trinocular petrographic microscope' that I got from The Microscope Store a few years back, when I was just dying to have my own petrographic microscope. The scope is `trinocular' because not only does it have a binocular viewer for viewing the magnified image with one's eyes, but it has a third port for attaching a camera.

For photographing thin sections, I used a Canon 20D DSLR camera. This is the same one I used when I started digital astro-imaging, several years back. To attach it to the microscope, I kludged an Orion 1.25" eyepiece-projection adapter, which happily fit right over the non-telescope-sized microscope eyepiece quite nicely! The image focuses on the camera sensor, and since it's a DSLR, I can check focus and framing right through the camera viewfinder.

The basic idea behind acquiring data for an image of this type is to shoot lots of adjacent frames, with some overlap. In that sense, it's like a large astronomical mosaic. However, since each frame only takes a fraction of a second to shoot, I can take hundreds of frames. The big difference between deep-sky imaging and microscopic imaging is that I have a nice bright light source (i.e. an incandescent bulb built into the scope). It's much easier to achieve a high signal-to-noise ratio that way!

The thin section is a small glass slide, and I moved the slide between frames. This was accomplished by means of a small slide positioner, which holds the slide and moves in two directions when I turn some small knobs. The positioner has a vernier scale on each axis, so I can make a precise 1.5-mm movement between adjacent frames in a given row, and then move 1mm between rows. This gives the GigaPan Stitch software enough overlap to work with.

Preliminary data processing:

I used Adobe Photoshop CS4 to batch-process the raw 16-bit CR2 files that came off of the camera. I used CS4's Camera Raw module to take out some slight chromatic aberration, and after converting the images to 8-bit JPEG format, I did a bit of sharpening and color saturation. The GigaPan stitching process seems to have desaturated the image a bit. Perhaps I should pre-saturate each image a bit more.

Assembling the mosaic:

This couldn't have been easier! I just turned GigaPan Stitch loose on the image files, and it made a mosaic, which is about 30,000 pixels wide! Simplicity itself. I ran the stitcher on a Mac Pro computer, which made short work of the operation. I had heard that GigaPans can take all night to run, but the Mac Pro banged this sucker out in under 15 minutes. Somewhere, Steve Jobs is smiling.

An Unsung Hero:

Somewhere in China is the real hero of this little technological story. The microscope I used is a Chinese-made import, and it's a mixed bag of build quality. Some things on the scope are perfectly serviceable, and other things could stand to be better. Centration of the objective lenses (something like collimating a telescope) is hard to do, and the objectives don't stay centered for very long. I took the whole objective turret apart, and saw that certain detents in a metal part appeared to have been cut into the metal rather haphazardly. The binocular viewer leaves something to be desired, too - it has some annoying internal reflections, and gives a partially-cross-polarized view even when the `analyzer' (one of the polarizing filters) is out of the optical path. However, this microscope really shines in one important area - the flatness and sharpness of the image field. Man, that thing is flat! By that I mean that there are almost no visible aberrations from the center of the field to the edge, at least in the low-power objective. And there are very few diffraction artifacts visible on high-contrast edge features, which is more than I can say for a more-expensive Japanese-made microscope at school, even when it's adjusted for Kohler illumination. (Sorry for this microscope geekery, interested readers may want to look at the Nikon or Olympus microscopy websites.)

Who knows if I'm correct in my speculations, but I can't help imagining an optical designer in China somewhere, making those objectives as perfect as possible, out of love for the craft of optical design. Somehow or another, they made those things so as to deliver a really remarkable level of performance (at least as judged by my eye), despite the relatively low price point. Whether by luck or by design, the image quality of those objectives largely makes up for the deficiencies in other parts of the microscope.

A Dream of Automation:

As I described in the `About This GigaPan' notes, I have this dream of motorizing the stage-positioner controls, so as to be able to automate the acquisition of the image data. I'd love to be busily grading papers, or surfing the web, or processing images, while the microscope and a computer are robotically churning out the data for another enormo-mosaic. It's quite a bit like my dream of having a robo-focus unit for my telescope, so that I could acquire image data automatically while doing visual observing. One can dream!

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