Re: calibrat to known function

Posted by Justin McGrath on Aug 19, 2007; 4:06pm
URL: http://imagej.273.s1.nabble.com/calibrat-to-known-function-tp3698569p3698572.html

I think I see what you mean.

You could try this macro (a plugin would probably do the processing
faster, but I've only used them a little).

height = getHeight();
width = getWidth();
chl = newArray(width*height);
for ( i = 0 ; i < width ; i++) {
     for ( j = 0 ; j < height ; j++ ) {
          chl[i+j*width] = ( pow( 10,getPixel( i,j )*0.015 ) - 2); //
I solved for chl a from the equation you provided.  You might want to
check my math.;
     }
}

newImage("[Chl]", "32-bit", width, height, 1);
selectWindow("[Chl]");
for ( i = 0 ; i < width ; i++ ) {
    for ( j = 0 ; j < height ; j++ ) {
         setPixel( i,j,chl[i+j*width] );
    }
}


This should work if the image is 8 bit, 16 bit or 32 bit.  The result
is a new 32-bit image (you can change it if you don't need 32 bits).
It will probably all be black unless you adjust the contrast.

How do you get images that represent chlorophyll concentration?

Justin




On 8/18/07, Anne Salomon <[hidden email]> wrote:

> Thanks for your detailed and speedy reply Harry! Unfortunately, my problem
> is still not solved. Here's why...
>
> I have made a .lut file just as you said BUT when I use it in ImageJ, the
> 1-255 pixels, although defined in color, are not defined in the value of the
> chlorophyll a they should represent i.e. pixel =(log10 (chla)+2)/0.015.So,
> when I make my image the colors are not calibrated to the function above.
> So, how do I assign each pixel (that now has the correct color based on my
> .lut file) a value of chl a given the above equation?
>
> Thanks again for your help,
> Anne
>
> ----- Original Message -----
> From: "Harry Parker" <[hidden email]>
> To: <[hidden email]>
> Sent: Saturday, August 18, 2007 2:05 PM
> Subject: Re: calibrat to known function
>
>
> > Hi Anne,
> >
> > An ImageJ LUT can be defined simply as a text file, 257 rows by 4 columns.
> > The 1st row contains text.  Each following row has 4 integers from 0 to
> > 255, separated by tabs: index, red, green, and blue values. Index is
> > incremented from 0 to 255. Then for each index give the values wanted for
> > red, green and blue. If you want grey values, red, green and blue are set
> > equal to each other.
> >
> > I created something similar using Excel to calculate the LUT numbers.
> >
> > Rename the file with the extension, ".lut", and place it in a folder named
> > "LUTs" in the ImageJ folder.
> >
> > --
> > Harry Parker
> > Senior Systems Engineer
> > Digital Imaging Systems, Inc.
> >
> > ----- Original Message ----
> > From: Anne Salomon <[hidden email]>
> > To: [hidden email]
> > Sent: Saturday, August 18, 2007 3:44:43 PM
> > Subject: calibrat to known function
> >
> > I am trying to calibrate pixel colors 1-255 of a LUT to a known function:
> > pixel=((log x+2))/0.15. How do I do this in image J?
> >
> > Thanks very much for you insight,
> > Anne
> >
> >
> >
> >
> >
> >
> > ____________________________________________________________________________________
> > Be a better Heartthrob. Get better relationship answers from someone who
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>