Set up for an Image Parameter

[Morinaga185]

Dear all,

How should I set up "xy_pix", one of the Image Parameters?
The default setting is "xy_pix=0.653 * 2", but I don't understand how this value is derived.
What is the appropriate value for the "xy_pix" when using 5472x3840 pixel, 72 bit images?

Thanks.

[JintK1111]

this means what is your image's 1 pixel size is biologically.

If you're using Zen software (Zeiss), there would be a value of one pixel in 'info' section of each picture file.

Or, I don't know but you can calculate by using what parameter you used (taken picture in 10x, 20x, etc., x(pixel) = y(um)) by desired software.

[GompfH]

I found this information after emailing the manufacturer of the microscope/software. In the Keyence BZ Analyzer software, you can get that info when you insert a scale bar and click on the calibration button.

I think what Morinaga is also asking is why is it "* 2" in the default setting? I also have this question. If we're supposed to put a value in for um/px what is the doubling for? Or does that refer to it being two channels in the default?

[JintK1111]

Dear GompfH

xy_pix = A * B here means that

A (i.e. 0.645) = 1 pixel of microscope software
B (i.e. 0.5) = exporting bin number (for 0.5, it means 2x2 bin 50%, 0.2 5x5 20% or so)

This may set according to ZEN (Zeiss) software, where the institute this developed (KAIST) usually uses for confocal imaging. I don't know well about other software's image exporting tool so you may adjust by the application you use.

if you export 1 pixel as 1 pixel in imagefile, this would make very big file so they suppose that you may export image in 50% or so to use many file to reconstruct image.