http://imagej.273.s1.nabble.com/Batch-color-thresholder-tp5014215p5014222.html
Your images were not attached, by the way.
Selecting "macro" creates the macro code, but you still need to run it separately to obtain the desired mask.
As you say, saturation will give you an idea as to how 'pure' your yellow is, which is a good indication if you are going towards 'pale' as you say. But I cannot say without an image to look at. The risk I see is that is less saturated images, you might not be able to pick up your hue as well, decreasing the number of pixels for the saturation measurement. Perhaps using the 'brightness image' to select only the parts of the wing with bright elements and then measuring the saturation regardless or hue could work? I suggest you try both manually and see if you get the same result?
Again I'd be happy to have other's opinion on this.
Ideally if you want to go through this quantitative route, you need some sort of internal control for the intensity/colors. Usually people use a color palette taken in conjunction with the image so that in case the white balance changes or overall illumination is modified, these can be corrected before proceeding with quantification. Something like this:
Finally, if you have tried transforming your RGB image to HSB (Image->Type->HSB Stack), you will have noticed some nasty artifacts, especially in the saturation image. This is the problem with
1. JPEG compression creating artifacts due to the nature of the compression algorithm.
2. Potential oversaturation of the image by the camera to make the image more 'appealing'. This often happens unbeknownst to the user.
So please always work in RAW formats to avoid these kinds of issues. You will most likely get a significant difference in your metric, as it is probably clear cut, but the data quality could be deemed insufficient because of the JPEG compression. So it is at your own risk.
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> ram prasad
> Sent: Wednesday, September 2, 2015 10:42
> To:
[hidden email]
> Subject: Re: Batch color thresholder
>
> Hi Oli,
>
> Thank you very much for your response.
>
> When I select "Macro" from the threshold color, it gives me a macro code
> and a red coloured mask on the area of my interest. However, when I try to
> create a selection on this mask I get the error I mentioned in the first mail in
> this thread.
>
> "However the question remains on what you are trying to measure on your
> original RGB image. From what I gather if you measure inside a selection, you
> will get the average of the red green and blue channels where you want the
> 'yellow color intensity' which is not really that."
>
> I was under the impression that selecting yellow pixels with the hue slider
> should give me a selection that has only yellow pixels. That way when I
> measure saturation I should get the intensity only for the yellow pixels?
> I'd like your opinion on this one.
>
> Herewith, I have attached two images that show a difference in the intensity
> (one is yellow and the other one is pale), for your reference.
> This difference is what I would like to measure.
>
> Best,
> R
>
>
> On Tue, Sep 1, 2015 at 5:12 PM, Burri Olivier <
[hidden email]> wrote:
>
> > Hi,
> >
> > If you select "Macro" from the Threshold Color window, it will give
> > you a macro code you can run and get a mask that you can use "Create
> > Selection" on
> >
> > However the question remains on what you are trying to measure on your
> > original RGB image. From what I gather if you measure inside a
> > selection, you will get the average of the red green and blue channels
> > where you want the 'yellow color intensity' which is not really that.
> >
> > I'd like others' opinions on this, but a better approach once you have
> > your mask is to measure the Brightness component of your original
> > image converted to HSB stack (Slice 3).
> >
> > Best
> >
> > Oli
> >
> >
> > > -----Original Message-----
> > > From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf
> > > Of ram prasad
> > > Sent: Tuesday, September 1, 2015 16:08
> > > To:
[hidden email]
> > > Subject: Batch color thresholder
> > >
> > > Hi all,
> > >
> > > I would like to quantify yellow colour intensity on a number of
> > > images,
> > but I
> > > am having trouble writing a macro for that purpose.
> > >
> > > I can get as far as opening the colour thresholder and applying my
> > cut-off's
> > > but then selecting the region of interest is a bit slippery and I'm
> > hoping you
> > > guys can help me out with this.
> > >
> > > This is what I'd intended to do.
> > >
> > > 1) Create a duplicate of my image (Image -> Duplicate)
> > > 2) Open the thresholder and select yellow pixels using the hue
> > > slider
> > (Image -
> > > > Adjust -> Threshold)
> > > 3) Then create a selection (Edit -> Selection -> Create selection)
> > > 4) Restore the selection on the original image (Edit -> Select ->
> > > Restore
> > > selection)
> > > 5) Finally, measure Integrated density using (Analyze -> Measure)
> > >
> > > The problem I have with the third step is that when I try to create
> > > a
> > selection
> > > (using Edit -> Selection -> Create Selection) I get a pop-up with
> > > the
> > following
> > > message,
> > >
> > > "This command creates a composite selection from a mask or from an
> > > image that has been thresholded using Image -> Adjust ->Threshold
> > > tool. The current image is not a mask and has not been thresholded"
> > >
> > > I'm not sure why I'm getting this error here as I used Image ->
> > > Adjust
> > > ->Threshold to threshold my image.
> > >
> > > I'm attaching a sample image here for your reference. Please let me
> > > know
> > if
> > > you need more information from my side.
> > >
> > > P.S the click operation on the Select button in the thresholder
> > > dialog
> > box
> > > does not get recorded in the macro recorder that's why I'm resorting
> > > to
> > Edit -
> > > > Select -> Create selection to create a selection.
> > >
> > > Thanks,
> > > R
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
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