Re: Quantifying Stained Retina

Posted by Rob van 't Hof-2 on
URL: http://imagej.273.s1.nabble.com/Quantifying-Stained-Retina-tp5000880p5000889.html

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://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<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: 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>
>>>>>>
>>>>>>   --
>>>>> _____________________________
>>>>> 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: [phone]
>>>>> email: [hidden email]
>>>>> _____________________________
>>>>>
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>>>>>
>>>>   --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>
>> --
>> _____________________________
>> 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: [phone]
>> email: [hidden email]
>> _____________________________
>>
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>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
_____________________________
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: [phone]
email: [hidden email]
_____________________________

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