Re: Calibration with Image J

Posted by Wayne Rasband on Nov 07, 2005; 3:13pm
URL: http://imagej.273.s1.nabble.com/Calibration-with-Image-J-tp3704525p3704526.html

ImageJ supports density calibration of 16-bit images, but only using
straight line functions.

Here are the steps needed to calibrate an image so that pixels values
are in the range -1.5 m/s to 1.5 m/s:

1. Generate a histogram of the image and note that the range of values,
e.g., 1 - 4094
2. Open the Analyze>Calibrate dialog
3. Enter  "Straight Line" as the "Function:"
4. Enter "m/s" as the "Unit:"
5. Enter 1 and 4094 in the first column (raw values) and -1.5 and 1.5
in the second (values in m/s)
6. Press "OK".
7. Generate another  histogram and note that the range is now -1.5 -
1.5.

-wayne

On Nov 2, 2005, at 6:17 AM, Soljanlahti Sami wrote:

> Hi,
>
> I have been trying to measure velocity of the blood flow
> from phase encoded MRI images. On these images the different
> shades represent different velocities. In our case black
> represent a flow velocity of 1.5 m/s and white -1.5 m/s. On
> our last project we used NIH image but now don´t have Macs
> anymore at our institution and we changed to Image J. I have
> done the calibration for the measurements the same way I did
> with NIH image. First I draw a white and a black spot to one
> of the images. Then I measure the mean grey value of these.
> Then I use the calibrate command from analyze menu. I use
> the straight line function.
>
> My problem is that although white should represent one end
> of the scale of pixel values in the picture and black the
> other there seems to be a lot more values beyond this range.
> In other words when I measure my white spot it represents
> mean gray value of 2558 and the black one represents 0. On
> the calibration function the scale goes up 65535 which in
> thery is the maximum of different shades in a
> 16-bit-picture. When I try to measure my pictures after
> calibration the values are not even between 1.5 and -1.5.
>
> If I change my images to 8-bit ones the calibration seems to
> work but my images don´t look like they should anymore. So I
> think that the problem has something to do with colour depth
> of the images (is it the right term when talking about
> black& white images?).
>
> I don´t know if I managed to describe my problem properly
> but I thank you in advance for any suggestions that would
> solve the problem.
>
> Yours,
>
>            Sami Soljanlahti, MD
>            Helsinki Medical Imaging Center
>            Helsinki, Finland