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Re: Autothreshold B&W displays inverse

Posted by Mike Cowperthwaite on Oct 12, 2009; 7:51pm
URL: http://imagej.273.s1.nabble.com/Autothreshold-B-W-displays-inverse-tp3690826p3690829.html

On 10-Oct-09 4:16 am, Wayne Rasband wrote:

> On Oct 7, 2009, at 8:06 PM, Mike Cowperthwaite wrote:
>
>> (Using 1.43g)
>> When using Adjust|Threshold with "B&W" display mode, the thresholded
>> image shown is the inverse of what you get when you click "Apply." This
>> is true regardless of the setting of "Dark background" checkbox.
>>
>> It is very confusing! I can't believe it's intentional. Could this be
>> fixed, please?
>
> "Apply" in the Threshold window converts the image to binary using the
> Process>Binary>Convert to Mask command. The background (non-threshold)
> color used is determined by the "Black background" setting in the
> Process>Binary>Options dialog box. You can get an exact representation
> of the "B&W" mode window by using the Image>Flatten command in v1.43h,
> or Plugins>Utilities>Capture Image in earlier versions of ImageJ.

Wayne, thanks for pointing out the Binary Options setting.  I now
understand the issue better, but I still think there's a problem that
needs fixing.  Having the image invert when you click Apply violates the
Law of Least Astonishment.

For the purposes of Make Binary, I generally want the Binary Option
"Black Background" to be ON.  This converts my (black-background)
greyscale image into white features on a black background, with a
standard, non-inverting LUT: exactly what I expect.  Changing that
setting to OFF inverts the image only by inverting the LUT; the pixel
values remain the same.  (Inverting via LUT may or may not be the best
approach here; I don't want to change this, but I would change the UI of
Binary Options somehow to explicitly mention that the setting *is* the LUT.)

So, assuming "Black Background" is ON and the result LUT will be the
standard, non-inverting LUT:

If you Threshold a greyscale image with "Dark background" checked, the
Red display is sensible (red features against a black background) and
the B&W display is not -- it shows black features against a white
background.  When I click Apply in the Red display mode, I get the
expected results: the low end is forced to black, the red turns white.
When I click Apply in the B&W display mode, I get the originally-desired
results: the white turns black and the black turns white.

The problem is the appearance used in B&W display mode, not in the
results of the Apply.  Assuming that's handled with a LUT, I think you
should just reverse the B&W Display LUT.  Basically, whatever appears
RED in Red mode should appear WHITE in B&W mode.  It's just that simple.


Separately from that, I question whether a result with an "Inverting
LUT" (i.e., Binary Option "Black Background" is OFF) should ever be
generated when Thresholding.  I think the Binary Option "Black
Background" should be internally held to ON for any thresholding action
(display *or* image conversion).

--
Mike Cowperthwaite
Lathrop Engineering, San Jose CA