calibration question

[Cammer, Michael]

In the status bar when we drag the cursor over a pixel numbers such as
769 (33767)
are reported.  These are 16 bit images with only 12 bits of values.

How can we get rid of the number in parenthesis (without something complicated like converting to 32 bits, back to 16, and diving by 16)?

Thank you!





_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: [phone]

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[Michael Schmid]

On Sat, April 4, 2015 17:15, Cammer, Michael wrote:
> In the status bar when we drag the cursor over a pixel numbers such as
> 769 (33767)
> are reported.  These are 16 bit images with only 12 bits of values.
>
> How can we get rid of the number in parenthesis (without something
> complicated like converting to 32 bits, back to 16, and diving by 16)?

Hi Michael,

the value "769 (33767)" looks strange. Do you have signed integers in the
original file? Then it would be "769 (33537)" or "999 (33767)". If it you
read signed numbers from the file, and you have no negative values, simply
subtract 32768 and set the function in Analyze>Calibrate to 'none'.

If you have positive and negative numbers, there is no other way than
either converting to float (32 bits) or living with the display showing
the calibrated (signed) and raw values. That's because ImageJ has no
'true' signed-integer data type for images, it uses unsigned 16-bit values
and the calibration to convert these values to signed values.

Michael

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[Cammer, Michael]

Thank you for the explanation.  I was trying to do background subtractions but was getting unexpected results.  The measurements were returning the calibrated values (including negative values) but the math was on the signed image.  Converting first as per below solved all the problems.  Thank you!!

I played with your suggestions.

run("32-bit");
setMinAndMax(0, 65535);
run("16-bit");
setMinAndMax(0, 4095);

or

run("Subtract...", "value=32768");
run("Calibrate...", "function=None unit=[Gray Value] text1=[ ] text2= show");
setMinAndMax(0, 4095);

appear to solve the problem.

Regards,
Michael

_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Michael Schmid [[hidden email]]
Sent: Saturday, April 04, 2015 12:17 PM
To: [hidden email]
Subject: Re: calibration question

On Sat, April 4, 2015 17:15, Cammer, Michael wrote:
> In the status bar when we drag the cursor over a pixel numbers such as
> 769 (33767)
> are reported.  These are 16 bit images with only 12 bits of values.
>
> How can we get rid of the number in parenthesis (without something
> complicated like converting to 32 bits, back to 16, and diving by 16)?

Hi Michael,

the value "769 (33767)" looks strange. Do you have signed integers in the
original file? Then it would be "769 (33537)" or "999 (33767)". If it you
read signed numbers from the file, and you have no negative values, simply
subtract 32768 and set the function in Analyze>Calibrate to 'none'.

If you have positive and negative numbers, there is no other way than
either converting to float (32 bits) or living with the display showing
the calibrated (signed) and raw values. That's because ImageJ has no
'true' signed-integer data type for images, it uses unsigned 16-bit values
and the calibration to convert these values to signed values.

Michael

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