Re: Quantifying Stained Retina

Posted by carlo bianco on
URL: http://imagej.273.s1.nabble.com/Quantifying-Stained-Retina-tp5000880p5000886.html

Hello Natalia,
The deconvolution made by prof Landini is excellent, if you work with well known
stains (histo/ihc) if you must face and manage
 other colors, I suggest you the segmentation plugin,


http://bigwww.epfl.ch/sage/soft/colorsegmentation/
best regards
carlo




________________________________
 Da: Rob van 't Hof <[hidden email]>
A: [hidden email]
Inviato: Lunedì 19 Novembre 2012 18:33
Oggetto: Re: Quantifying Stained Retina
 
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). 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/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
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Centre for Molecular Medicine
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Western General Hospital
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