Re: calibrate to known function

Posted by Anne Salomon on Aug 20, 2007; 5:16pm
URL: http://imagej.273.s1.nabble.com/calibrat-to-known-function-tp3698569p3698573.html

Thanks Justin and Harry,

I'll try your suggestions and script.

I got the chl a images from NASA's Ocean Color website. It provides high
resolution satellite images of global ocean chl a data. You need permission
to get access to their 1.1 km resolution data. Permission requires a brief
request letter.

Thanks again,
Anne


----- Original Message -----
From: "Justin McGrath" <[hidden email]>
To: <[hidden email]>
Sent: Sunday, August 19, 2007 8:06 AM
Subject: Re: calibrat to known function

>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
>> >
>> >
>> >
>> >
>> >
>> >
>> > ____________________________________________________________________________________
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>>
>