http://imagej.273.s1.nabble.com/Batch-color-thresholder-tp5014215p5014241.html
Apologies for my delayed response. Here is a dropbox link to the images,
The macro code worked!! Thank you very much. I find this very surprising
running mine in batch. I kept getting that error and I didn't even bother
using it for batch processing. So, all this time I was one foot away from
Please have a look at the images and let me know what you think. Thanks
> Hi again,
>
> Seems the list will not attach more images? Maybe provide them via dropbox
> or some other similar service.
>
> Here is an example macro.
>
>
https://gist.github.com/lacan/05a8f7ab507560e51a1c>
> I just copy pasted the macro code and added the lines 1-3 and 47-52
>
> Just have one of your images open and run it.
>
> Best
>
> Oli
>
>
>
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> > ram prasad
> > Sent: Wednesday, September 2, 2015 12:47
> > To:
[hidden email]
> > Subject: Re: Batch color thresholder
> >
> > Hi Oli,
> >
> > I'm not sure why the images were not attached because I can see it in my
> > original email to the group. Anyway, herewith I'm attaching the images
> again.
> >
> > I have only three colours in my image -blue,yellow and black- and blue
> and
> > black are a bit far apart in the hue scale. So, I think I can be a bit
> relaxed with
> > my hue settings and this should take care of that potential risk arising
> from
> > less saturated images don't you think?
> >
> > Also, I haven't had any luck with obtaining the desired selection and
> I'm not
> > sure where I am going wrong. Would you be kind enough to write me a
> > macro so that I can see what I'm doing wrong? That would be very helpful.
> >
> > Thank you very much.
> >
> > Best,
> > Ram
> >
> > On Wed, Sep 2, 2015 at 11:32 AM, Burri Olivier <
[hidden email]>
> > wrote:
> >
> > > Hi Ram,
> > >
> > > 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:
> > >
http://scientific.datacolor.com/products/macro-calibration-target/> > >
> > > 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.
> > >
> > > Best
> > >
> > > Oli
> > >
> > >
> > >
> > > > -----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> > > > >
> > > >
> > > > --
> > > > ImageJ mailing list:
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> > > --
> > > ImageJ mailing list:
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> >
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