Re: Colocalization question

Posted by Gitta Hamel on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Dyes-for-apoplastic-pH-in-leaf-tissue-tp5505884p5509927.html

Commercial response

Hello Teng-Leong,

As I understand your question, you would like to calculate the Pearson coefficient on a predefined ROI which is based on a threshold of 1 channel. Our Huygens software contains an option "Colocalization Analyzer" which can calculate the Pearson coefficient after setting a (different) threshold on both channels and take only those voxels into account that are above these thresholds.

Something else that might be interesting for you is the Object Analyzer option. This module make it possible to create an ROI and clip your data to this ROI. You can than put this information in the Colocalization Analyzer which than computes the Pearson coefficient over your ROI only, which is, as I understood it, exactly what you want. Secondly you can apply object based colocalization in the Object Analyzer itself.

You can read more about this Colocalization Analyzer on http://www.svi.nl/CoLocalization.
More about this Object Analyzer is written on http://www.svi.nl/ObjectAnalyzer

If you would like to try out these modules or if you would like to talk more about this matter, please contact us for further information.

With best wishes,

Gitta Hamel

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Gitta Hamel
Managing Director
Scientific Volume Imaging bv
Developers of the Huygens software
The Netherlands
www.svi.nl
[hidden email]
tel: ++ 31 35 6 42 16 26
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Teng-Leong Chew wrote:

Hi all,

Pardon me for opening up a can of worms of colocalization issue.

I wonder if anyone has experience in thresholding a biological
object using a channel (say, green actin in a contractile ring)
and use only that selected ROI to quantify Pearson coeefficient
between green and a red-labeled protein? Bottom line question
is: how much of the red protein co-localizes to green within
the object and not the whole cell?

We have Volocity, MetaMorph and ImageJ.

Thanks in advance for your help.

Regards,
Leong