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metallurgical objective vs biological objective
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mjkzz



Joined: 01 Jul 2015
Posts: 557
Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 3:15 am    Post subject: Reply with quote

Thanks Rik, exactly!!!

And I did make improvements -- I bolted down both stages and camera on one piece of 8020 aluminum bar. It helped a lot that touching the knobs of either stainless micro translation stages do not cause any images shifts, even turning it to focus does not cause image shift. But both are fixed on the plate, so as can be seen, both micro stages are arranged in Y direction, this is to get more focus range.

I am focusing on the side surface of the micro stage plate, I guess as long as I get good texture, ZS can find enough good feature points to track and align, even at subpixel level.

Yes, 550D has second curtain feature, I thought about it when I set it up, but did not do it. Now I think it should help alot -- having long exposure in the dark (relative) can cause camera to lift up mirror and finish with all its mechanical stuff that can cause vibration, without strong light, very little is exposed till the final flash! Great idea!

Unfortunately, I returned the objective, so have to wait a bit more Sad
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mjkzz



Joined: 01 Jul 2015
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Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 5:20 am    Post subject: Reply with quote

Something really strange . . . the displacement keeps increasing, isn't each offset number supposed to be between two successive images? Or is it the offset from the very first image?
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rjlittlefield
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Joined: 01 Aug 2006
Posts: 18095
Location: Richland, Washington State, USA

PostPosted: Sat Sep 19, 2015 7:43 am    Post subject: Reply with quote

mjkzz wrote:
Or is it the offset from the very first image?

The calculation is done by comparing images incrementally, but the number that's calculated is cumulative from the first image. The number is what portion of the frame width (or height) the image has to be shifted, in order to line up with the first one.

--Rik
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mjkzz



Joined: 01 Jul 2015
Posts: 557
Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 8:55 am    Post subject: Reply with quote

Thanks Rik, that makes a lot of sense.

After playing a bit more, I finally attached a bellow to my 550D and it seems to improve stability because now when I touch the objective, image in live view does not shift too much. Since I returned my 40X 3.73WD objective, I am using 10X objective, so that also help reduce image shifting (less mag).

With 10X objective, I did one more tests with following setup:

550D camera
Mitsumi XEG60 driven by 1.8 degree step motor (200 steps per rev). Every rotation of knob moves stage by 0.5mm or 500um
TI8255 driver set at 1/8 micro stepping
10x objective

The following graph is the result (each point represents 8 microsteps, or 2.5um)



As can be seen, there are some slipages, each step is not as even as I like, but there is no pattern suggesting cyclis behavior. I think I can improve it by tightening up all components, reduce vibration (maybe getting a heavier stone table).

But it is so tedious to copy and paste offset numbers, I think I will write a program to grab offset data automatically. Then I will do 200 samples.
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rjlittlefield
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Joined: 01 Aug 2006
Posts: 18095
Location: Richland, Washington State, USA

PostPosted: Sat Sep 19, 2015 12:29 pm    Post subject: Reply with quote

mjkzz wrote:
but there is no pattern suggesting cyclis behavior

No short cycles, anyway. Longer term, something interesting is happening. Here is your image, plus a straight line drawn between the first and last points:



Clearly the curve is concave downward, where in theory it should be straight.

The next question is what's causing that?

One possibility is that there's something wrong with the ZS alignment process that is causing it to accumulate errors differently from one end of the stack to the other. That can be evaluated by eyeball, by putting a checkmark on "Show as adjusted"in the ZS Input Files panel, then clicking back and forth from one end of the stack to the other. If the alignment process has worked as desired, you should not see any significant shifting of the image when you do this.

(In the unlikely event that you do see significant shifting, contact me offline. I'll be interested to see why that is, and I can provide a workaround for it. The latest version of ZS supports a configuration setting that causes all Stack > Align All Frames comparisons to be made against the first image instead of the previous one. That setting is not yet exposed in the GUI, but it's simple enough to hack in by editing the zerenstk.cfg file.)

Another possibility is that there is some long-scale nonlinear behavior in the system under test. If I understand your test correctly, we're looking at 39 measurements separated by 2.5 microns, for a total of 0.0975 mm of travel, about 1/5 turn of the screw. It would be interesting to see what happens over a longer distance, say 2 or 3 turns. Of course that would require lower magnification optics, but those are easier to work with anyway.

Quote:
TI8255 driver set at 1/8 micro stepping
...
The following graph is the result (each point represents 8 microsteps, or 2.5um)

Then, if I understand correctly, each point will be one full step. If we were to see any short-term cyclic behavior, it would have to be every 2 or 4 steps, one half or full cycle of the drive currents. Knowing that fact, I can look for and find hints of such pattern in the data, but I doubt that it's really there -- we humans are really good at ""seeing" patterns even in randomness.

Quote:
it is so tedious to copy and paste offset numbers, I think I will write a program to grab offset data automatically.

Once upon a time, one of our forum members wrote a "ZS Data Digger" to do that. See discussion at Explaining Zerene Stacker alignment parameters. It looks like the links have been taken down, but the program may still be available from the author.

I don't do this often enough to have bothered writing a canned program for it. Instead, I pull the console log or project file into Gnu Emacs, which is a text editor that supports capture/replay keyboard "macros". Then I record a search/delete/search/insert_newline sequence that isolates whatever parameter I want to look at, and have the text editor execute that repeatedly. Usually I'm quite impatient to get a quick look at the data, so I grab partial results by copy/paste from the ZS console log window while the Stack > Align All Frames operation is still running.

--Rik
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Bushman.K



Joined: 26 Aug 2015
Posts: 162
Location: OR, USA

PostPosted: Sat Sep 19, 2015 1:13 pm    Post subject: Reply with quote

From the mechanical side, this situation can easily be caused by uneven shape of lead screw or corresponding carriage nut.
People tended to think, that any thread is a series of continuously smooth surfaces. It is true, if we are talking about certain macro scale. But in micro (sub micron) scale, it is not always true. Any subtle vibration of machine setup can cause microscopic waviness of thread, and it can be revealed in situation like this.
So, to find out, what's going on here, I would run at least two full turns.
Then, to look for any pattern, I would rotate the graph around its origin and scale it along the Y axis.
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mjkzz



Joined: 01 Jul 2015
Posts: 557
Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 5:51 pm    Post subject: Reply with quote

Rik, I think ZS is working fine. The way I checked it is to find the "abnormal" pair of points in the dataset, load the corresponding images into Paint.Net, copy one image into a layer of another, set layer blending mode to "difference", the use arrow keys on keyboard to move the top layer, when they "coincides", the image will be black. So far, number of arrow key strokes agree with ZS calculation, so I think ZS is working fine.

I think the issue still is vibration, I saw some optical breadboards, some are made of aluminum, some are magetic stainless steel, the stainless steel one is not cheap, about 200USD for a 300x600 (mm) piece. Do you think it would help?

I also saw another kind, it looks like a sandwitch -- some kind of damping device sandwitched between two pieces of metal (one with M6 threaded holes on its surface). These are expensive.

I will do a dataset with at least 2 turns worth samples.
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mjkzz



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PostPosted: Sat Sep 19, 2015 5:58 pm    Post subject: Reply with quote

Hi Bushman, yes, there are something going on at microscopic level.

The moving part is actually a Mitsumi XEG60 dovetail micro translation stage (made in Japan, if that means anything), I trust its quality, so if something is wrong, it has to be my assembly, motor, driver, motor mounting plates, and of course, vibration due to my overall setup. Or at least I will look for problem in my setup FIRST.
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Bushman.K



Joined: 26 Aug 2015
Posts: 162
Location: OR, USA

PostPosted: Sat Sep 19, 2015 7:36 pm    Post subject: Reply with quote

mjkzz, I do trust Mitsumi, but my point is a bit different.
Here is the datasheet for this stage: http://us.misumi-ec.com/pdf/fa/2012/p1_1645.pdf

It has an assembly print, but it's not the same thing as production print, so we don't have any GD&T callouts to find out, how good certain parts are. The only thing they saying about accuracy is some number "50 micrometers", which can represent almost everything. Another thing we know about tolerances is that straightness and parallelism tolerances for this table are 30 micrometers (that's from the website, not from this PDF).

So, there is no reason to think, that level of precision of lead screw there is several tens more than level of precision for the whole assembly. It just doesn't make sense. It doesn't mean this stage is bad. It only probably means, it's not accurate in every aspect up to sub-micron level. Every technological process has own limitations and nobody will try to overcome it for product, not intended for that kind of precision. Typical stages are intended to be accurate up to 2-5 microns. Therefore, there can be any inaccuracy smaller than that (0.2-0.5 microns) and it is acceptable for its purpose.

Let me show you one thing:

This is large steel sprocket I made as my first serious CNC training project. See that sort of regular pattern on the thread surface, especially where it's a bit out of focus? This is completely okay for this size of thread (2" major diameter, 8 threads per inch). This pattern is created by thread milling process, because I set the tolerance for this operation just as it should be according to thread standard. It was possible to avoid this pattern, if I would use tighter tolerance, but it takes proportionally more time, and for production it's unacceptable. That's why you shouldn't expect to get much higher precision than any part is intended for.

Source of inaccuracy can be everywhere: lead screw, nut of lead screw, contact point between micrometer head shaft and corresponding anvil.
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mjkzz



Joined: 01 Jul 2015
Posts: 557
Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 8:48 pm    Post subject: Reply with quote

Hi Bushman, I totally agree with you, it could be anywhere Sad

Here is two turns data (well, I forgot to take 401 pix, so only 399 samples). I, as human being, could not see any pattern, I see irregularities. Each sample point represents 8 microsteps (a full step, 0.5/200 = 2.5um).



This graph is plotted as following:

First obtain a dataset of displacement between two images, name it D.
Then obtain AVG(D) and STDEV(D) on this dataset.
Then plot (d - AVG(D)) / STDEV(D)

This will show how each data in D deviate from its average by number of standard deviation.



BTW, I just finihed my Windows program that extracts offset data from ZS log file (first copied to a notepad and saved as .log file). If enough people are interested in this program, I will finish it up (currently, the log file name is hard coded) to let user select a log file. It outputs CSV file (with .csv appended to the log file).


Last edited by mjkzz on Sat Sep 19, 2015 9:37 pm; edited 1 time in total
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Bushman.K



Joined: 26 Aug 2015
Posts: 162
Location: OR, USA

PostPosted: Sat Sep 19, 2015 9:22 pm    Post subject: Reply with quote

mjkzz, could you share the resulting data as CSV (and/or log by itself with short description, how to locate that offset in it - I'm not familiar with its format)?
I would really like to apply my data analysis skills and help you.
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mjkzz



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Posts: 557
Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 9:39 pm    Post subject: Reply with quote

OK, here it is, first column is xoffset and second is yoffset, the graph I plotted is d = sqrt(x*x + y*y).

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Last edited by mjkzz on Sat Sep 19, 2015 10:35 pm; edited 1 time in total
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mjkzz



Joined: 01 Jul 2015
Posts: 557
Location: California/Shenzhen

PostPosted: Sat Sep 19, 2015 9:49 pm    Post subject: Reply with quote

Here are steps I did to obtain these data set:

1. Take N images
2. Load these N images into ZS
3. In ZS, menu Stack->Align All Frames and wait until it finishes.
4. In ZS, menu Options->View Console Log
5. Right click mouse on console log and select "Select All" and do Ctrl-C (copy)
6. Open Notepad and paste data into it

For manual work, you can search on term xoffset, the yoffset data is next to it, then copy and paste them into spreadsheet. First put your cursor at the beginning of the Notepad, then do Ctrl-F to enter xoffset, then Hit F3 key to find next set.

I used the program I wrote now as to copy and paste 400 data sets is not fun.
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Bushman.K



Joined: 26 Aug 2015
Posts: 162
Location: OR, USA

PostPosted: Sat Sep 19, 2015 10:08 pm    Post subject: Reply with quote

mjkzz, thank you, I will look at these data by myself tomorrow.
But there is an obvious problem with it: about a half of points are in exponential form (-5.90E-05, for example), therefore offset precision is lost. So, it only makes sense to work with those points, where both numbers are in normal decimal form.

I was talking about sharing raw log file from ZS, because I'm guessing there can be some relatively simple regular expression pattern to extract required data from raw log, so I wanted to test it.
Personally, I'm not using ZS.
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Chris S.
Site Admin


Joined: 05 Apr 2009
Posts: 2798
Location: Ohio, USA

PostPosted: Sat Sep 19, 2015 10:09 pm    Post subject: Reply with quote

Watching this discussion, I've wondered if I should share my thoughts that working with a screw drive for high magnification stacking is simply a bad idea. Could it be made to work well with a lot of experimentation and very high-grade components? Maybe. But I have some high-quality screw-drive devices, including Velmex UniSlides and a Velmex BiSlide, and top-of-the-line translation stages from Newport and other solid manufacturers; I would definitely not wish to stack with them using microscope objectives.

Rik, and perhaps others, have demonstrated that a Cognisys StackShot rail (a screw-drive device) can be used with a 40x objective. Still, this rail is not the tool of choice for these high magnifications (though it deserves real respect at lower magnifications).

As a metaphor, I've driven a Ford Escort (an inexpensive passenger car) at 130mph. I've also driven a Chevrolet Corvette (arguably, a street-legal race car) at 130 mph. With these two cars, the experiences at high-speed are very different; the Escort gives the feeling that one is at the ragged edge of control, while the Corvette gives the feeling of "all systems normal, could do this anytime."

For photomacrography, substituting "high magnification" for "high speed," our Corvette is a microscope focus block. Harvest such a block from an old microscope, put a stepping motor on it, and you're good to go at even the highest magnifications. So I get the feeling that all this work on a screw drive is a waste of time, unless one is more interested in advancing screw drive implementation than in the photography of small things.

Screw drives do have their place. At modest magnifications, they can perform stacking movement very well. They are also very useful for rough positioning of your motorized focus block. My motorized focus block currently sits on a Velmex UniSlide, aligned on a parallel axis of translation. This UniSlide is tremendously useful for positioning the focus block wherever I want it--quickly, accurately, and repeatably. But would I stack with it? No.

My focus block unflinchingly delivers precise, repeatable steps at least as small as 0.25 micron. I haven't bothered testing below this increment, because none of my optics (and I routinely work at 100x) require even this much precision, let alone more.

Cheers,

--Chris

--edited typos


Last edited by Chris S. on Mon Sep 28, 2015 11:17 pm; edited 2 times in total
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