getting list of raw pixel values in ROI

[Don Thrall]

Relatively new ImageJ user.  Have looked for answer online but have not
been successful.

Is there a way to get a list of raw pixel values from a hand drawn ROI?  
I've tried histogram and x-y coordinate functions, but neither are quite
right.

Thanks

[Wayne Rasband]

> Relatively new ImageJ user.  Have looked for answer online but have  
> not been successful.
>
> Is there a way to get a list of raw pixel values from a hand drawn  
> ROI?  I've tried histogram and x-y coordinate functions, but  
> neither are quite right.
> Thanks

Clear the background and then use the Analyze>Tools>Save XY  
Coordinates command. Here is a macro that converts the image to 16-
bits, clears the background to 65,535, and then saves the coordinates  
and values of all the pixels that do not have a value of 65,535.

    setBatchMode(true);
    if (bitDepth==24)
        exit("Grayscale image required");
    run("Duplicate...", "title="+getTitle);
    run("16-bit");
    run("Make Inverse");
    setColor(65535);
    fill();
    run("Save XY Coordinates...");

-wayne