calibration bar maximum value incorrect?

[Neil Fazel]

I have a 32-bit text image which I have normalized. (I found the maximum pixel value in the image, then divided all pixels in the image by that value.) Then I used Analyze -> Tools -> Calibration Bar... to overlay a calibration bar. I see that the top range of the calibration bar values is not 1, as expected; it's 0.48. The image is normalized; so the brightest pixel's value should be 1. Am I doing something wrong?

Thanks,
Neil

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

On Jun 5, 2014, at 5:13 PM, Neil Fazel wrote:

> I have a 32-bit text image which I have normalized. (I found the maximum pixel value in the image, then divided all pixels in the image by that value.) Then I used Analyze -> Tools -> Calibration Bar... to overlay a calibration bar. I see that the top range of the calibration bar values is not 1, as expected; it's 0.48. The image is normalized; so the brightest pixel's value should be 1. Am I doing something wrong?

Please provide a minimal macro that reproduces the problem, something like the following, except this example works as expected.

-wayne

   run("M51 Galaxy (177K, 16-bits)");
   run("32-bit");
   run("Enhance Contrast...", "saturated=1 normalize");
   run("Fire");
   run("Calibration Bar...", "location=[Upper Right] fill=Black label=White number=5 decimal=1 font=12 zoom=1 bold overlay");

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[Neil Fazel]

Hi Wayne,

   Thanks for the tip. I hadn't used Process -> Enhance Contrast... to normalize. But I just tried that, and the calibration bar range is correct if I do it that way.

I had done it by first using Analyze -> Measure to find the max pixel value, then by using Process -> Math -> Divide to divide all pixels in the image by the max pixel value. Then I ran the calibration bar. Shouldn't this method also work? I tried it using M51 Galaxy image, and the top range of the color bar is 0.2 instead of 1.

   run("M51 Galaxy (177K, 16-bits)");
   run("32-bit");
   run("Measure");
   run("Divide...", "value=10106");
   run("Calibration Bar...", "location=[Upper Right] fill=Black label=White number=5 decimal=1 font=12 zoom=1 bold overlay");

Best regards,
Neil

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[Henry Barwood]

Is it possible to replace the arrow with a vertical line when measuring distances?

Henry Barwood
Department of Chemistry and Physics
Troy University
Troy, Alabama  36082

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

On Jun 5, 2014, at 6:54 PM, Neil Fazel wrote:

> Hi Wayne,
>
>   Thanks for the tip. I hadn't used Process -> Enhance Contrast... to normalize. But I just tried that, and the calibration bar range is correct if I do it that way.
>
> I had done it by first using Analyze -> Measure to find the max pixel value, then by using Process -> Math -> Divide to divide all pixels in the image by the max pixel value. Then I ran the calibration bar. Shouldn't this method also work? I tried it using M51 Galaxy image, and the top range of the color bar is 0.2 instead of 1.
>
>   run("M51 Galaxy (177K, 16-bits)");
>   run("32-bit");
>   run("Measure");
>   run("Divide...", "value=10106");
>   run("Calibration Bar...", "location=[Upper Right] fill=Black label=White number=5 decimal=1 font=12 zoom=1 bold overlay");

After dividing by the maximum pixel value, call resetMinAndMax() to reset the display range. The color bar range is determined by the display range, not the pixel value range.

-wayne

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