Calibration- pixels/um or um/pixel

[Knecht, David]

I was having trouble setting up calibrations in Micro-manager yesterday and finally figured out why.   Set Scale in ImageJ reads out in pixels/micron.  If you take those numbers and try to enter them into Micro-manager's calibration, it asks for the data as um/pixel.  The Micro-manager folks asked if it could be changed in ImageJ to conform to their setup.  I don't know if there is any "standard" way of doing this, but it would be nice if the two used the same units to avoid confusion. However, I am sure that if it is changed in ImageJ, lots of people might have their data altered.  Is there an easy way to resolve this?   Thanks- Dave

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[Philip Ershler]

As I'm sure you know, from a microscopist's point of view, the calibration is virtually always microns/pixel. Because NIH Image and now ImageJ originally came from general purpose image manipulation pixels/micron originally made more sense. By now both calibration expressions are so deeply engrained that trying to change either would cause utter confusion. With Micro-Manager and ImageJ so tightly coupled you just really have to keep your wits about what is happening where. This is not much help, but I feel your frustration.

Philip R. Ershler Ph.D.
P.I. Confocal Microscope Core
Nora Eccles Harrison Cardiovascular Research and Training Institute
University of Utah
95 South 2000 East
Salt Lake City, UT
84112

[hidden email]

On Dec 16, 2010, at 4:25 PM, David Knecht <[hidden email]> wrote:

> I was having trouble setting up calibrations in Micro-manager yesterday and finally figured out why.   Set Scale in ImageJ reads out in pixels/micron.  If you take those numbers and try to enter them into Micro-manager's calibration, it asks for the data as um/pixel.  The Micro-manager folks asked if it could be changed in ImageJ to conform to their setup.  I don't know if there is any "standard" way of doing this, but it would be nice if the two used the same units to avoid confusion. However, I am sure that if it is changed in ImageJ, lots of people might have their data altered.  Is there an easy way to resolve this?   Thanks- Dave
>
> Dr. David Knecht    
> Department of Molecular and Cell Biology
> Co-head Flow Cytometry and Confocal Microscopy Facility
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)

[Rasband, Wayne (NIH/NIMH) [E]]

On Dec 16, 2010, at 6:25 PM, David Knecht wrote:

> I was having trouble setting up calibrations in Micro-manager yesterday and finally figured out why.   Set Scale in ImageJ reads out in pixels/micron.  If you take those numbers and try to enter them into Micro-manager's calibration, it asks for the data as um/pixel.  The Micro-manager folks asked if it could be changed in ImageJ to conform to their setup.  I don't know if there is any "standard" way of doing this, but it would be nice if the two used the same units to avoid confusion. However, I am sure that if it is changed in ImageJ, lots of people might have their data altered.  Is there an easy way to resolve this?   Thanks- Dave

Use Image>Properties instead of Analyze>Set Scale. It displays the scale in microns/pixel. It also has the advantage of a convenient and easy to remember keyboard shortcut (shift-p).

-wayne

[Knecht, David]

I am not as worried about reading out the size as setting it. I don't think you can do that with Properties In my lab and my microscopy course, I teach my students to use a stage micrometer measure a known distance to set the scale for each objective.  So I have to read out the value in ImageJ invert it and then enter that number in Micro-manager.  Dave

On Dec 16, 2010, at 11:50 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Dec 16, 2010, at 6:25 PM, David Knecht wrote:
>
>> I was having trouble setting up calibrations in Micro-manager yesterday and finally figured out why.   Set Scale in ImageJ reads out in pixels/micron.  If you take those numbers and try to enter them into Micro-manager's calibration, it asks for the data as um/pixel.  The Micro-manager folks asked if it could be changed in ImageJ to conform to their setup.  I don't know if there is any "standard" way of doing this, but it would be nice if the two used the same units to avoid confusion. However, I am sure that if it is changed in ImageJ, lots of people might have their data altered.  Is there an easy way to resolve this?   Thanks- Dave
>
> Use Image>Properties instead of Analyze>Set Scale. It displays the scale in microns/pixel. It also has the advantage of a convenient and easy to remember keyboard shortcut (shift-p).
>
> -wayne

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[Heeschen, Bill (WA)]

Regarding pixel scale:
(I receive postings in digest mode, so this inquiry may have already
been answered)

If you "Show Info..." for an image in ImageJ (Image->Show Info...), both
ways of describing spatial calibration are listed.

Pragmatically, it is easier to measure the number of pixels across an
object of known size (hence pixels/micron) than it is to try to measure
the real-world width of one pixel (micron/pixel).

Onward,

Bill
William A. Heeschen, Ph.D.
Microscopy, Digital Imaging
The Dow Chemical Company
Midland, MI  48667
[hidden email]

------------------------------

Date:    Thu, 16 Dec 2010 18:25:43 -0500
From:    David Knecht <[hidden email]>
Subject: Calibration- pixels/um or um/pixel

I was having trouble setting up calibrations in Micro-manager yesterday
and finally figured out why.   Set Scale in ImageJ reads out in
pixels/micron.  If you take those numbers and try to enter them into
Micro-manager's calibration, it asks for the data as um/pixel.  The
Micro-manager folks asked if it could be changed in ImageJ to conform to
their setup.  I don't know if there is any "standard" way of doing this,
but it would be nice if the two used the same units to avoid confusion.
However, I am sure that if it is changed in ImageJ, lots of people might
have their data altered.  Is there an easy way to resolve this?
Thanks- Dave

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

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End of IMAGEJ Digest - 15 Dec 2010 to 16 Dec 2010 (#2010-163)
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