Re: Autothreshold B&W displays inverse

Posted by Wayne Rasband on Oct 12, 2009; 8:53pm
URL: http://imagej.273.s1.nabble.com/Autothreshold-B-W-displays-inverse-tp3690826p3690830.html

On Oct 12, 2009, at 3:51 PM, Mike Cowperthwaite wrote:

> 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.

Thanks to Gabriel Landini, this bug is fixed in the 1.43i daily build.

-wayne

> 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