Re: Colocalization plugins

Posted by Slavena Trifonova on Jul 07, 2010; 12:48pm
URL: http://imagej.273.s1.nabble.com/Colocalization-plugins-tp3687701p3687703.html

Dear All,

Thank you very much for your replies,I am a beginner in this field. I used
JaCoP manual and tried it on images but still have some questions using this
colocalization measurement plugin. I would really appreciate any help. To
analyze the colocalization of the blue and the red signal which refer to Cy3
for Glucocorticoid receptor and Dapi for nucleus in lymphocytes I focused on
objects based analysis.I choose to work on centre to centre distances
suspecting that the cells are not close to the optical resolution. I don’t
know which picture format I have to use the original file-zvi or it can be a
tif file. I have also some difficulties in setting up the three tabs that
appear on the screen using JaCoP. First I don’t know how to adjust the
threshold of the two images. Second the xy and z (nm) calib -where shall I
take this numbers from and what NA means-it is not pointed out anywhere.
Another issue is how to measure the particle size with imageJ in order to
filter and select only the small lymphocytes excluding the big granulocytes?
Thank you very much for your help in advance.

Kind regards:Slavena Trifonova

> PhD student in Psychoimmunology
>
> Institute of Immunology,
>
> Laboratoire National de Santé
>
> 20A rue Auguste Lumière
>
> L-1950
>
> Luxembourg
>
> Grand Duchy of Luxembourg
>
> [phone] *** PLEASE NOTE NEW TELEPHONE NUMBER***
>
> [phone] (fax)
>
> mailto:[hidden email]
>
> http://www.uni-trier.de/ <http://www.uni-trier.de/index.php?id=159>
>
> and

> Laboratory of Immunology,
>
> Centre de Recherche Public - Santé http://www.crp-sante.lu
> <http://www.crp-sante.lu/>
>

Kind regards:Slavena Trifonova
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of John
Oreopoulos
Sent: Friday, July 02, 2010 3:42 PM
To: [hidden email]
Subject: Re: Colocalization plugins

Try the JACoP plugin which allows for thresholding of the images prior to
calculating the colocalization. This will only work however if your
structures of interest exhibit an intensity that is measurably different
than the background signals.

John Oreopoulos


On 2010-07-02, at 9:04 AM, Slavena Trifonova wrote:

> Hello,
>
>
>
> I would ask for some advices for analyzing my data with ImageJ. Shortly
what
> I did is  immunofluorecent labeling of human Glucocorticoid receptor in
> peripheral white blood cells.My aim is to study the temporal localization
of
> the receptor-(GR shuttling between nucleus and cytoplasm within the time).
> Techinically on 10 wells slides I stained white blood cells with Cy3
> conjugated Ab  for the Glucocorticoid receptor and Dapi for the nucleus. I
> am trying to find an ImageJ plugin that can help me automatically to
choose
> only the lymphocytes excluding the granulocytes from my pictures and to
> measure % of the colocalization of the red and the blue signal . I used
> Object counter 3D plug in for segmentation and determination of the
cetroids
> and intensity centers. After calculation it gives me their respective
> coordinates x,y,z.I don’t know how to use these coordinates to calculate
the

> colocalization I also wonder whether this is the best plugin for the
> analysis of my data. I read about this Vector method as well but it is
> considered for a method  obtaining a first estimation of colocalization.
>
> Thank you very much for your assistance in advance!
>
>
>
> Slavena Trifonova
>
> PhD student in Psychoimmunology
>
> Institute of Immunology,
>
> Laboratoire National de Santé
>
> 20A rue Auguste Lumière
>
> L-1950
>
> Luxembourg
>
> Grand Duchy of Luxembourg
>
> [phone] *** PLEASE NOTE NEW TELEPHONE NUMBER***
>
> [phone] (fax)
>
> mailto:[hidden email]
>
> http://www.uni-trier.de/ <http://www.uni-trier.de/index.php?id=159>
>
>
>
> and
>
>
>
> Laboratory of Immunology,
>
> Centre de Recherche Public - Santé http://www.crp-sante.lu
> <http://www.crp-sante.lu/>
>
>