Metalurgical microscope CNC

I now own what is possibly the worlds first combination CNC milling machine and metalurgical microscope.
I've realized among things, I just like looking at dies to admire the work put into them. Unfortunately, its a lot of work to take the many thousands of pictures required to get a good level of detail on even something like a 386. Plus, if you want the whole circuit, you need to repeat this for many layers.
Fortunately, I have some background in robotics and since I'm planning on getting a better microscope in the next few months, I don't feel bad being a little more aggressive with my current setup. A Unitron N, the model I have, is suppose to look something like this (image from http://microscopesonline.info/):
The z-axis gear got partially stripped at one point when I was trying to fit a shim as mine was missing. One thing in particular I hated though was the upside down sample mounting. I usually used post-its or similar to hold the dies to a drilled out petri dish. Which of course brings to the next annoyance that its also annoying to even get something mounted onto the stage at all.
Not too scared to be a little aggressive then at my half loved contraption, I got this after a few modifications:
See a crude video of it working here.
Some time ago I ditched the polaroid setup since I wasn't going to use that in any form. Next, I mounted the microscope upside down on some t-slot aluminium to make it much more convenient to view samples. Next, I wanted CNC control and I didn't really like the XYZ set-up anyway, so I replaced the XY with my Sherline 2000 CNC XY stage. Turns out, the CNC head can also still fit, but I didn't have it there during early testing.
The Z axis was a bit trickier. An earlier picture that shows the basic idea:
Also you can see I had to tape the eyepieces in so they wouldn't fall out. At first I tried to figure something out with my rotary table since it was the only other heavy duty CNC equipment I (thought I) had. I also had a Z stage for optical work, but the thumb screw was very hard to turn and adapting a servo would be difficult. The dimensions were also awkward to actuate it using the rotary table. I eventually realized I had a CNC micrometer from half of a UV-VIS spectrometer I found and scrapped at RPI. The brackets were close enough to easily adapter to the XY t-slot with an l-bracket. The sample tray base is a largish l-bracket which I've attached several different holders on to experiment. Ultimately I'll probably replace it was a kinematic mirror mount so I can correct tilt errors easily. An early test was to instead use a largish petri dish for the same purpose, but I found that Z axis movement tended to move things around too much. I should still try to couple it tighter to the main axis to reduce vibration, but it doesn't seem suitable enough unfortunately. Finally, the original set-up depended on gravity to remain stable. To compensate, I have it tightened with a rubber band:
The rubber band goes around the brass part which was suppose to be pressed against the shaft by the weight of the equipment mounted to it. As its been turned on its side, this is no longer true. At some point I might see if I can make some more proper spring loaded replacement.
One issue came up was that although you still can view through the eyepiece, its pretty awkward. With the camera over one and not wanting to re-adjust, it becomes difficult. So, I wanted to get the view onto a computer screen which is probably nicer on the eyes anyway. A 1/8" audio style jack breaks out composite where I convert it to an RCA type plug so it can go into my composite -> VGA converter box. The VGA then goes to an LCD display that was affixed to the t-slot. The second display behind the first, possibly not obvious in the above image, was arbitrarily fixed there to get a display up on a media server nearby and get the screen off of the floor.
The camera is mounted on t-slot aluminium as well. My Canon SD630 doesn't have a remove capture cord port and USB only supports PTP, so there is no built in way to do remote capture. So, I removed the top cover and soldered some wires onto the capture button. There are two spots: focus and snap. Shorting snap by itself is not enough to take a picture, focus must be depressed first. A DB25 breakout box runs to some optoisolators to short the signal. I figured out the correct polarity by using a volt meter on the leads coming from the camera button.
Electronics hardware is very simple. DB25 goes to a breakout board and then continues onto the stock Sherline driver box. I made a simple adapter to use the Vexta motor on the a axis with the Sherline box. The camera driver circuitry is very minimal:
The unused IC there is a CD4050 buffer I was going to use on the parallel port. I got lazy and didn't wire it up as the parallel port was already putting out near 5V.
Finally, there are several pieces to the software. At the core, I'm running EMC2. I set the step speeds and acceleration low so as to try to discourage the sample from vibrating. The camera is actuated from M7/M8 (coolant mist/flood) and then reset with M9 (coolant off). I use dwell instructions to give the camera enough time to take pictures, the necessary length of which I'm still working out.
The second part of the set-up is the software that generates the g-code. I wrote a Python program that you can find on my pr0ntools github repo. Its very crude currently, but may be sufficient. It assumes you are scanning a rectangle. One point is assumed to be the origin and the other is supplied on the command line. In order to make a plane, I assume the most level plane you could form from those. I'm currently always starting scans from one side on the theory it might make backlash issues less, but I'm not sure if it matters.
The test wafer I used looks like this:

An interesting piece in its own right, from what I can tell it came from an Intel Journey Inside the Computer educational kit. Of course, I didn't scan the entire wafer, but just one chip. While the plastic distorts the image, it does make a good test as its easy to level and rotate.
From a combination of my lenses are kinda dirty (probably can fix this or upgrade to modern optics, think it uses DIN components), not washing the wafer holder, and the plastic layer, the first pictures came out relatively nice. Why it may not produce quality images like the visual6502 team or Flylogic team does, it should serve to efficiently create a number of relatively high resolution shots to my hearts content. As I get a better microscope, I might also look into CNC retrofitting it, but more likely I'll focus on improving this one as better microscopes are current beyond my budget as a high risk project.