Posted by
michael shaffer on
URL: http://imagej.273.s1.nabble.com/applying-a-binary-as-a-selection-tp3703129p3703134.html
Joachim Wesner writes ...
> I think what he is looking for, expressed in the most general
> way, would be the possibility to:
>
> 1) Generate a ROI mask from a binary image (this two-level
> image created from any input image, using any algorithm that
> might create a two level result)
>
> 2) Have the possibility to apply/copy this mask to another
> image for use with any arbitrary analysis (The initial image
> contents in 1) and 2) might be the same, but need not)
>
> So basically a binary image -> ROI mask plugin, practically
> the opposite of the "Edit/Selection/Create Mask", which
> converts a ROI to a black and white image.
That's pretty much it. I'm a bit surprised this capability isn't in
ImageJ(?), and was sure I was asking a stupid question. Given the following
task, let me ask if there isn't a different way ...
Suppose I have an image that contains regions of 6 brightness levels
(including detector noise). But I am only interested in 2 phases that are
very close in brightness. Furthermore, a number of bi-level thresholding
algorithms might work with separating these 2 important phases, so the
problem is to remove everything else and allow the bi-level thresholding to
"see" only the pixel values of concern. What is more, I need to process
many of these images and a macro is therefore necessary.
Am I correct is assuming the thresholding plug-in will work only with
pixels within a ROI? If so, I then only need a versatile method of creating
this ROI.
Thanx for your responses ...
michael shaffer :o)
> On Sunday 09 April 2006 12:23, michael shaffer wrote:
> > Pardon my ignorance, but I fail to see how these methods would
> > expose
> to
> > the binary thresholding ONLY selected pixels. For example, other
> softwares
> > have demonstrated that simply converting non-selected
> pixels to black
> > or white biases the histogram the thresholding works with(?)
>
> I probably misunderstood what you want to do.
> Can you explain a bit better what do you mean by:
>
> > However, I first need to threshold regions that are both darker and
> > brighter (step#1, e.g., other phases and surface defects)
> than what is
> > to
> be
> > exposed to the binary thresholding (step#2).
>
> Is it "masking"?
> I do not think that IJ can do that straight away for
> thresholding (please correct me if I am wrong).
>
> You can, however, divide the procedure into:
> (assume white is "yes", black is "no")
> threshold regions which are darker, save it to an image
> threshold regions which are brighter, save it to another image
>
> then:
> darker ADD (or OR) brighter = regions which are brighter or darker.
>
> and subtract it from the original image (so you are left with
> the areas which are not-brighter-or-darker, i.e. the non-zero areas)
>
> Now you want to threshold this result. Depending on the
> histogram method, you may have to force the thresholding
> procedure to ignore the black pixels.
> (You
> will have to include this in the code yourself).
>
> BTW, this would be a handy option to have in the built-in
> threshold plugin (Ignore black, and Ignore white check boxes
> which just set to 0 the histo[0] and histo[255] before
> submitting the histogram to the thresholding routine.
>
> I hope it helps,
>
> G.
>
>
>
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