Author Topic: Bright field Quantification  (Read 10926 times)

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Offline rocky.balboa

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Bright field Quantification
« on: June 11, 2009, 03:31:46 PM »
I am looking to quantify the DAB (brown staining) on tissue sections taken on a Brighfield microscope. Can anyone suggest me a software for quantifying the intensity in the tissue sections.

Bright field Quantification
« on: June 11, 2009, 03:31:46 PM »

Offline hokie

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Re: Bright field Quantification
« Reply #1 on: June 13, 2009, 07:44:59 PM »
That's a pretty open ended question. What sorts of information do you need?

There is an image processing package from the NIH as well as lots of commercial packages.
Do more, less well. ~Ewald Weibel

Offline rocky.balboa

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Re: Bright field Quantification
« Reply #2 on: June 15, 2009, 04:10:19 PM »
I tried the Image J software package from NIH. Are there any specific plugins to quantify the staining ? If so please do let me know.

Thank you.

Offline Cardio

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Re: Bright field Quantification
« Reply #3 on: June 15, 2009, 05:24:58 PM »
I am looking to quantify the DAB (brown staining) on tissue sections taken on a Brighfield microscope. Can anyone suggest me a software for quantifying the intensity in the tissue sections.

Its called a counter ;) WE use image J and made a macro to count 20X pics. It won't work with DAB however because everything is converted to grayscale. I imagine if your are trying to score Dab staining you will need to set a threshhold of some sorts to cancel out the background stain of DAB. IF you change this macro (its in notepad) to size and color you want it may work for you. Just copy in notepad then drag into image j. You will need to change the 40 and 2000 to the appropriate range of the + staining.
To test the macro take a 20X pic and go through the steps without the macro. Image J-Drag pic into it- Go to process, select binary (this makes it grayscale, you may need to change this). Then click on analyze- click analyze particles. Select pixel range and check off show results.
while (nImages>0) {
   run("Threshold");
   run("Analyze Particles...", "minimum=40 maximum=2000 bins=20 show=Outlines display exclude");
   run("Close");
   selectImage(nImages());
   run("Close");
   }


Good luck
« Last Edit: June 15, 2009, 05:58:12 PM by Cardio »

Offline rocky.balboa

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Re: Bright field Quantification
« Reply #4 on: June 15, 2009, 06:40:30 PM »
Thanks for helping out. I tried the method as suggested, but could'nt get very good quantification. I was using Aperio's ImageScope software and was trying to quantify the staining. I think we need to have the Color Deconvolution algorithm to quantify DAB staining. If someone can help me find this algorithm or a site to purchase this algorithm (tried on Aperio never found), I would be thankful.


Offline PAS64

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Re: Bright field Quantification
« Reply #5 on: July 18, 2009, 09:08:50 PM »
http://

I am sure Aperio should have the intensity tool, I have been using ImagePro (Media Cybernetics)   and NIS element( Nikon) to do my DAB analysis. However, intensity analysis is tricky you may find a lot of variation from assay to assay(0 black and 254 white in a 8 bit image).  I usually go by area or number of DAB positve cells

Good luck

Re: Bright field Quantification
« Reply #5 on: July 18, 2009, 09:08:50 PM »