How to callibrate scale bar?

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ndemik

How to callibrate scale bar?

Post by ndemik » 17.12.2007 21:11

I'm considering making the cross over from automontage to HF for my scientific illustration of insect specimens.

One necessity, however, is that I be able to obtain accurate scale bars relative to the magnification of the images. I'm shooting with a c-mount JVC digi cam running through a third ocular of a Lecia stereoscope with a zoom range of 7.11x-115x.

So, for example, if I'm zoomed in at 80x, I need a scale bar that accurately reflects that magnification, as opposed to if I were zoomed in at 75x or 82x or any other amount.

Anyone got ideas?

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Ariel
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Post by Ariel » 19.12.2007 09:16

Okay, depending on focus and lots of different elements (not to mention printing or viewing size), the scale will be different. What you need to do is size the scale on-screen to match the actual subject. It's a manual job, no two ways about it.

ndemik

Post by ndemik » 19.12.2007 21:23

Ariel wrote: What you need to do is size the scale on-screen to match the actual subject. It's a manual job, no two ways about it.
That seems like a major limitation compared to the calibration options available in software like Automontage. While it might not serve as an inconvenience for the artist, the scientist is generally required to show the scale of the illustration in any publication. I had been hoping to buy the pro version of HF as an alternative to Automontage, but without a simple scalebar callibration, it would be hard to justify.

Any creative work-arounds?

ndemik

Post by ndemik » 19.12.2007 21:29

Ariel wrote:Okay, depending on focus and lots of different elements (not to mention printing or viewing size), the scale will be different.
The only factor that should affect the length of the scalebar relative to the length of the subject is the magnification (zoom). The absolute size of the scalebar will vary according to printing, viewing, etc., but the size relative to the subject should always remain constant.

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Ariel
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Post by Ariel » 19.12.2007 22:29

ndemik wrote:The only factor that should affect the length of the scalebar relative to the length of the subject is the magnification (zoom). The absolute size of the scalebar will vary according to printing, viewing, etc., but the size relative to the subject should always remain constant.
You're right. Printing doesn't matter here. However, no matter what zoom, objects farther from the camera will appear smaller than objects near the camera. Are you suggesting a feature which calculates the average DOF of the shots, coupled with camera and focal length, to automatically make a scale?

I could see how that could theoretically work, but it wouldn't be accurate often enough, for the following reasons: A camera might not record the focus distance. A camera might incorrectly display the focus distance. Different cameras have different sized CCD sensors, focal lengths, and other specifications (meaning "5x zoom" on one camera with a 30-300mm lens would be significantly different from '5x zoom' on a camera with a 100-600mm lens), so it would only work with a list of specific cameras and, for SLRs, specified lenses. Using add-on lenses would also lead to incorrect results.

What you as a scientist have to do is measure the object you are working on yourself and then simply size the scale to match. Maybe the feature you are looking for can be added, but I'm not one to say. I think it is much more practical and reliable to do the measuring yourself. Or, you can do as many people do and include an actual measure in the photographs next to the subject. (You can even do just one photo with the measure and use this info to correctly scale one in the completed image.)

But seriously, I don't know if any programs exist which can do what you're looking for.

Guest

Post by Guest » 20.12.2007 04:49

Ariel wrote: But seriously, I don't know if any programs exist which can do what you're looking for.
Thanks for helping me think about some of these issues. The program I use now, Automontage (Synchroscopy) allows for presetting as many calibration sets as needed. I've added a few screen shots to illustrate the feature.

Basically, I image a micrometer at different zoom intervals, then use one of the program's measurement functions to measure a unit (i.e. 1mm). I then plug in the value of the measurement (i.e. 1mm) and the software calibrates the value to the magnification. So, if I'm zoomed in 45x, I select the preset calibration I made for that magnification, and the software gives me a calibrated scalebar.

I should also mention that I am working with a microscope zoom, not a camera zoom. The difference in focal length between the closest element of the subject and the farthest element is a matter of microns, and I don't think it significantly changes the scale.
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Guest

Post by Guest » 20.12.2007 04:53

Here's another screen shot from automontage callibration options...
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Ariel
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Post by Ariel » 20.12.2007 05:41

I see. That looks like a nice tool for micro photography where the user can pre-define microscope or zoom settings. I'll post a suggestion, maybe it will be added in the next version.

Comment on it here: http://forum.helicon.com.ua/viewtopic.php?p=3159#3159

Dan Kozub
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Post by Dan Kozub » 21.12.2007 15:27

My question: is it really necessary to calibrate _every_ zoom? I was thinking about calibration at limits and interpolating (linear) intermediary values.

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Post by Guest » 21.12.2007 21:57

If the scale bar function in HF would accept some basic parameters such as sensor size, number of pixels/frame width, and magnification it could all be done automatically.

But here is a possible work-around.

ndemilk.... if you go to my site here:
http://krebsmicro.com/
you will see a link to a spreadsheet for scale bar calculations under "Articles and Resources". One reason I put this together was for determining scale bars using HF. Since HF uses either the # of pixels, or a percentage to create the scale bar size desired, that is what the spreadsheet provides.

Since I assume with your setup you normally use the same camera, the values for pixel width and sensor size will remain the same. The only variable in you case is the magnification. So while not completely "automatic" you can very easily see the value (in pixels or percentage) you need to produce the correct size scale bar. You could even modify the spreadsheet slightly and print up a chart (or create a file) that would cover the range of your magnifications.

BTW the latest Photoshop CS3 Extended offers some capability in placing calibrated scale bars (if that is ever an option in your case).

Charles Krebs
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Post by Charles Krebs » 21.12.2007 22:18

Danylo,

I forgot to log in when I replied above. But I would like to add some additional thoughts.

While I appreciate the ability to place a scale bar in Helicon Focus, I too feel it would be much more useful if it were more "automated".

It is a simple calculation, and all that is needed from the user standpoint is the camera sensor size, the number of pixels on a side of the sensor, and the magnification at which the picture was taken.

Since for most users the camera sensor information remains the same, the program could save and display those values (of course they could be changed as needed). Then, all the user would need to input would be the magnification at which the picture was taken, and the desired size represented (ie: ".5mm", "100 micron") by the scale bar. The placed bar would then meet the users needs without the need for them to calculate values outside Helicon Focus.

For now, I think the spreadsheet I referred to above works well for those needing this info.

Charlie Krebs

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Ariel
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Post by Ariel » 21.12.2007 22:28

You know, what you can always do in the mean while is to use Helicon Filter to merge the images, and then use GIMP or something to put pre-made scales into the image.

ndemik
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Post by ndemik » 22.12.2007 01:04

Charles, thank you for pointing me towards your most illuminating website. Really brilliant work! I do think it will be possible to make a "cheat sheet" for plugging in accurately calibrated scale bars into HF.

If automating scale bar calibration seems feasible in the future development of HF, I can imagine it saving a nice chunk of time and transcription error in the long run.

Dan Kozub
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Post by Dan Kozub » 25.12.2007 17:24

Charles,

Thanks for your contribution to the discussion.

I personally do not trust formulas that includes several parameters. I think error of 10-15% is too high for me.

I think the best solution would be to calibrate the whole optical system in several points (x10,x50, x80) and then use the nearest calibration point if you need scale bar for some different magnification (x70). The program can calculate the scale bar by simple linear formula.

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Ariel
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Post by Ariel » 25.12.2007 22:42

Also, perhaps there should be different sets of calibrations, like one used for a specific lens/microscope, one used for different diopter lenses, etc.

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