Posted by
Vergara, Leoncio A. on
Mar 17, 2011; 4:11am
URL: http://imagej.273.s1.nabble.com/JACoP-tp3685369p3685371.html
If I understood your question, this is very basic knowledge.
xy calibration is asking for the dimension of the pixels in your images. Usually pixels are square. Your confocal software should be able to tell you the pixel size. Pixel size depends on the magnification but is mainly determined by the scanning pattern, number of pixels in x and y and zoom factor.
z calibraton is basically the z-step you used when capturing a z-series (aka z-stack) in your confocal. If you are only capturing single planes, you can probably ignore that dimension.
the x, y and z dimensions determine the size of the voxels in volumetric datasets.
Sorry if I misunderstood this part of your question.
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From: ImageJ Interest Group [
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Sent: Wednesday, March 16, 2011 10:27 PM
To:
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Subject: JACoP
Hello
I am using JACoP for colocalization , but it asks me for xy calibration and
z calibration . i am not sure what values do i punch in there. it ask in nm.
by default it shows 67nm for xy calibration and 200 for z calibration. i
dont know what these values mean. i use confocal SP5 laser microscope and
excitation wavelength of 488 and 561. Can somebody tell me what these xy
calibration values should be and what do they mean.
Also it there is a column for x shift. what does that mean. i punched in
some random numbers but it did not make any difference.
Gauri
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