http://imagej.273.s1.nabble.com/Quantifying-Stained-Retina-tp5000880p5000901.html
I'm still a little confused about what you want to quantify. Do you want
> Hello Rob and Joel,
>
> Rob, my mentor told me she used a stain called "Pearls Blue"
>
> Joel, I'm interested in quantifiying most of the stainings visible.
> (the background staining I don't desire to quantify.)
>
> What you're stating though does correlate with what my mentor has informed
> me.
> That the onl nuclei would be the most dense.
> This would be due to the way the protien settles.
>
> Thanks for the advice Joel.
>
> Natalia
>
> On 11/19/12, JOEL B. SHEFFIELD <
[hidden email]> wrote:
> > Hi Natalia,
> >
> > There are several issues with this image, to begin with. I notice that
> if
> > I look up the histogram of the image, I see that you have ignored about
> > half of the possible range of pixel intensities when you took the
> picture.
> > (min red=154, green=71, blue=177) As a result, you are able to use only
> > about half of the range of densities to draw distinctions between
> different
> > intensities.
> >
> > Then, there are several different types of staining visible. 1. the
> stain
> > in the onl nuclei (it appears) --quite dense, and mostly uniform
> throughout
> > the nucleus, although a bit stellate. 2. Then there are the nuclei of
> the
> > inner nuclear layer, which are stained around the periphery, and perhaps
> > nucleoli, but are less intense overall. 3. Then, there are some nuclei
> in
> > the choroidal tissues. 4. Then, there is the general apparent
> background
> > stain.
> >
> > I am not sure which of these you are interested in quantitating.
> >
> > However, just for fun, I took your image, and inverted the colors, to
> > generate image b (below). I then clicked on Color Threshold, which
> > selected the image as you see it in c. This, then, has selected all of
> the
> > nuclei, but limited itself only to the bits of stain in the inl. There is
> > no selection in the cytoplasmic material. You could, I suppose, collect
> > this data, but I would stress that you would have to be careful to
> specify
> > which component you are measuring. You could, perhaps, do this by
> creating
> > an ROI around a specific region.
> >
> > Joel
> >
> >
> > On Mon, Nov 19, 2012 at 7:14 PM, Rob van 't Hof
> > <
[hidden email]>wrote:
> >
> >> So did you use another dye as well to give you the pink colours? if so
> >> maybe try only the blue stain. If your stain is based on the Prussian
> >> Blue
> >> reaction I'd expect to see very distinct blue, not the pink in your
> >> image.
> >> Have you tried a blood smear as a positive control?
> >> Rob
> >>
> >>
> >> On 19/11/2012 21:28, Natalia Chacon wrote:
> >>
> >>> I'm actually trying to measure blue. Its a dye that attaches to the
> iron
> >>> in
> >>> my cell.
> >>> I know that ImageJ is able to detect quantities of blue in my image,
> I'm
> >>> just having issues getting appropriate measurements.
> >>>
> >>> Natalia
> >>>
> >>> On Mon, Nov 19, 2012 at 3:16 PM, Rob van 't Hof
> >>> <
[hidden email]>**wrote:
> >>>
> >>> Hi,
> >>>> I can't see much blue in your sample, mostly pink/purple. is the
> >>>> material
> >>>> you want to measure the intensely stained pink roughly circular object
> >>>> that
> >>>> run diagonally (top left to bottom right) along the image?
> >>>> bye,
> >>>> rob
> >>>>
> >>>>
> >>>> On 19/11/2012 19:51, Natalia Chacon wrote:
> >>>>
> >>>> On Mon, Nov 19, 2012 at 1:36 PM, Natalia Chacon
> >>>>> <
[hidden email]>****wrote:
> >>>>>
> >>>>> I mean to quantify the amount of blue staining. Now the staining
> >>>>>
> >>>>>> correlates to the amount of iron in my sample.
> >>>>>> Here is an image of my sample.
> >>>>>>
> >>>>>>
> >>>>>> On Mon, Nov 19, 2012 at 11:33 AM, Rob van 't Hof <
> >>>>>>
[hidden email]> wrote:
> >>>>>>
> >>>>>> Hi Natalia,
> >>>>>>
> >>>>>>> A very usefull plugin for analysing stained specimens is Gabriel
> >>>>>>> Landini's colour deconvolution one (
http://www.dentistry.bham.ac.
> **
> >>>>>>> ****
> >>>>>>> uk/landinig/software/cdeconv/******cdeconv.html<
http://www.**> >>>>>>> dentistry.bham.ac.uk/landinig/****software/cdeconv/cdeconv.**html<
>
http://dentistry.bham.ac.uk/landinig/**software/cdeconv/cdeconv.html>
> >>>>>>> <
http://www.dentistry.**bham.ac.uk/landinig/software/**> >>>>>>> cdeconv/cdeconv.html<
>
http://www.dentistry.bham.ac.uk/landinig/software/cdeconv/cdeconv.html>
> >>>>>>> >
> >>>>>>>
> >>>>>>>> **).
> >>>>>>>>
> >>>>>>> This is a very powerful plugin to separate different stains.
> >>>>>>>
> >>>>>>> When you say "quantify" do mean mean measuring area covered with
> >>>>>>> stain
> >>>>>>> or
> >>>>>>> stain intensity (a contentious issue, see documentation to plugin).
> >>>>>>>
> >>>>>>> You did not add an example image, so i don't know exactly what you
> >>>>>>> want
> >>>>>>> to do. If you add an example image, people like me could create a
> >>>>>>> basic
> >>>>>>> macro to show you how to do this kind of stuff.
> >>>>>>>
> >>>>>>> bye,
> >>>>>>> Rob
> >>>>>>>
> >>>>>>>
> >>>>>>> On 19/11/2012 17:07, Natalia Chacon wrote:
> >>>>>>>
> >>>>>>> Hello everyone,
> >>>>>>>
> >>>>>>>> I'm a new user of the ImageJ program.
> >>>>>>>> I'm currently working on a project where I have to quantify the
> >>>>>>>> amount
> >>>>>>>> of
> >>>>>>>> blue staining in an image.
> >>>>>>>>
> >>>>>>>> I've already found an article that is similar to what I'm doing,
> >>>>>>>> except
> >>>>>>>> its
> >>>>>>>> quantifying a red stain instead of a blue one.
> >>>>>>>> (Link provided here:
> >>>>>>>>
>
http://rsbweb.nih.gov/ij/docs/******examples/stained-sections/******<
>
http://rsbweb.nih.gov/ij/docs/****examples/stained-sections/****>
> >>>>>>>> index.html<
http://rsbweb.nih.**gov/ij/docs/**examples/**> >>>>>>>> stained-sections/**index.html<
>
http://rsbweb.nih.gov/ij/docs/**examples/stained-sections/**index.html>
> >>>>>>>> >
> >>>>>>>> <
http://rsbweb.nih.**gov/ij/**docs/examples/stained-**> >>>>>>>> sections/index.html<
http://**rsbweb.nih.gov/ij/docs/**> >>>>>>>> examples/stained-sections/**index.html<
>
http://rsbweb.nih.gov/ij/docs/examples/stained-sections/index.html>
> >>>>>>>> >
> >>>>>>>> )
> >>>>>>>>
> >>>>>>>> While this process will work from me, it seems I can't
> >>>>>>>> *Adjust>Threshold* so
> >>>>>>>>
> >>>>>>>> that I can quantify the blue!
> >>>>>>>>
> >>>>>>>> Please Advise.
> >>>>>>>> Thanks,
> >>>>>>>> Natalia
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> ImageJ mailing list:
> >>>>>>>>
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>
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> >>>>>>>> <
http://imagej.nih.**gov/ij/list.**html<
>
http://imagej.nih.gov/ij/list.**html>
> >>>>>>>> >
> >>>>>>>> <
http://imagej.nih.gov/**ij/**list.html<
>
http://imagej.nih.gov/**ij/list.html>
> >>>>>>>> <
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>
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> >>>>>>>> >
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>>
> >>>>>>> _____________________________
> >>>>>>> Dr. Rob van 't Hof
> >>>>>>> Reader
> >>>>>>>
> >>>>>>> Centre for Molecular Medicine
> >>>>>>> MRC IGMM
> >>>>>>> University of Edinburgh
> >>>>>>> Western General Hospital
> >>>>>>> Crewe Road, Edinburgh EH4 2XU
> >>>>>>> United Kingdom
> >>>>>>>
> >>>>>>> Phone: (+44)-131-6511031
> >>>>>>> email:
[hidden email]
> >>>>>>> _____________________________
> >>>>>>>
> >>>>>>> --
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>
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http://imagej.nih.**gov/ij/list.**html<
>
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> >>>>>>> >
> >>>>>>> <
http://imagej.nih.gov/**ij/**list.html<
>
http://imagej.nih.gov/**ij/list.html>
> >>>>>>> <
http://imagej.nih.**gov/ij/list.html<
>
http://imagej.nih.gov/ij/list.html>
> >>>>>>> >
> >>>>>>>
> >>>>>>> --
> >>>>>>
> >>>>> ImageJ mailing list:
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> >>>>> >
> >>>>>
> >>>>> --
> >>>> _____________________________
> >>>> Dr. Rob van 't Hof
> >>>> Reader
> >>>>
> >>>> Centre for Molecular Medicine
> >>>> MRC IGMM
> >>>> University of Edinburgh
> >>>> Western General Hospital
> >>>> Crewe Road, Edinburgh EH4 2XU
> >>>> United Kingdom
> >>>>
> >>>> Phone: (+44)-131-6511031
> >>>> email:
[hidden email]
> >>>> _____________________________
> >>>>
> >>>> --
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> >>>>
> >>>> --
> >>> ImageJ mailing list:
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> >>>
> >>>
> >> --
> >> _____________________________
> >> Dr. Rob van 't Hof
> >> Reader
> >>
> >> Centre for Molecular Medicine
> >> MRC IGMM
> >> University of Edinburgh
> >> Western General Hospital
> >> Crewe Road, Edinburgh EH4 2XU
> >> United Kingdom
> >>
> >> Phone: (+44)-131-6511031
> >> email:
[hidden email]
> >> _____________________________
> >>
> >> --
> >> ImageJ mailing list:
> >>
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http://imagej.nih.gov/ij/list.html> >
> >>
> >
> >
> >
> > --
> >
> >
> > Joel B. Sheffield, Ph.D
> > Department of Biology
> > Temple University
> > Philadelphia, PA 19122
> > Voice: 215 204 8839
> > e-mail:
[hidden email]
> > URL:
http://astro.temple.edu/~jbs> >
> > --
> > ImageJ mailing list:
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>
> --
> ImageJ mailing list:
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Joel B. Sheffield, Ph.D