Colocalization

[Antje-2]

Hello,

I was playing around with the ICA (Intensity Correlation Analysis) of
the WCIF bundle.
I've analyzed images of cells taken with a confocal microscope.
Now, I've seen that the resulting vePDM-values differ if I choose only
one cell or analyze the whole image. I guess this has something to do
with the calculation of the "mean" signal, which then might differ.
But, I'm afraid that this value also differs, depending on the density
of cells... (what would screw up my analysis)
Does anybody have an idea how to handle this? Is there anybody, who did
serious colocalization analysis of a larger amount of data?


Antje





       
               
___________________________________________________________
Der frühe Vogel fängt den Wurm. Hier gelangen Sie zum neuen Yahoo! Mail: http://mail.yahoo.de

[Stuart Anderson-3]

Greetings ImageJers!

I'm using ImageJ to process video frames from a web camera built into a simple
optical pectrometer.  It's working well, but the overall process is a bit clunky
and I'd like to streamline it as much as possible.

I have two questions:

1) Frame acquisition.  So far I've been manually capturing the frames using
either BTV (on the mac) or VRtainment (on the PC).  The camera is the IceCam, a
cheap USB web cam.

Does anyone know whether, and if so, how, I could capture the frames directly
into ImageJ?

2) Intercept on Set Scale.  The way the camera is arranged in the spectrometer
results in a linear relationship between the pixel numner in the image and the
wavelength of the light.  So far I've been using teh 'plot profile' and 'list'
options to generate columns of 'pixel #' and 'intensity', and copy/pasting into
Excel for subsequent processing, but I'd like to be ding this in ImageJ, too, if
possible.

The 'set scale' command allows me to specify the slope of the pixel-wavelength
relationship, but not the intercept (which pixel corresponds to the zero order
beam).  I can do this by moving the left edge of the selected rectangular
region, but I'd prefer to calculate it from the locations of the spectral lines
in the image and implement it through a 'set scale' dialog that has an intercept
option (or something like that).

Does anyone know of a way to specify not only the ratio of user units to pixels,
but also an offset between pixel zero and the zero of the user units?

Any and all suggestions welcome - thanks so much for your collective wisdom!

Stu

*************************************************
Stuart M. Anderson
Associate Professor of Physics
Augsburg College
2211 Riverside Avenue
Minneapolis, MN  55454

Tel: [phone]
Internet: [hidden email]

*********************************************************************
"So, you were surprised to find that the holey grail is a saxophone?"
*********************************************************************

[Itsaso Garcia]

Hi!
I also make colocalization analysis in confocal micrographies, and i
use the plugin "colocalization thresholds". After learning a little bit
about the colocalization describing parameters, i think one can obtain
a lot of information with this plugin. I don´t know about ICA, though.
I would reccomend you to read the papers by: Costes SV et al, Biophys J
2004; 86(6): 3993-4003; and Manders E. et al, Journal of Microscopy
1993; 169:375-382.
I hope this helps, good luck!

Itsaso Garcia-Arcos

P.S: Happy Christmas and New Year to everyone!

> Hello,
>
> I was playing around with the ICA (Intensity Correlation Analysis) of
> the WCIF bundle.
> I've analyzed images of cells taken with a confocal microscope.
> Now, I've seen that the resulting vePDM-values differ if I choose only
> one cell or analyze the whole image. I guess this has something to do
> with the calculation of the "mean" signal, which then might differ.
> But, I'm afraid that this value also differs, depending on the density
> of cells... (what would screw up my analysis)
> Does anybody have an idea how to handle this? Is there anybody, who

did

> serious colocalization analysis of a larger amount of data?
>
>
> Antje
>
>
>
>
>
>
>
> ___________________________________________________________
> Der frühe Vogel fängt den Wurm. Hier gelangen Sie zum neuen Yahoo!

Mail: http://mail.yahoo.de
>


--
********************************
Itsaso Garcia-Arcos
Department of Physiology, Medical School,
University of the Basque Country. UPV/EHU
********************************

[Fabrice Cordelières]

Hi,

Susanne Bolte and I recently wrote a tutorial review in Journal of
microscopy about co-localisation analysis methods, and the paper was
released.... yesterday
(http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2818.2006.01706.x)!
This tutorial review comes with a plugin that is already on IJ website
(JACoP: Just Another Colocalisation Plugin,
http://rsb.info.nih.gov/ij/plugins/track/jacop.html).
I hope this will help (I really do: this was the aim of writting such a
paper ;-))

Fabrice

 
Fabrice Cordelières, PhD
 
Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
Bâtiment 112 - Centre universitaire
91405 Orsay Cedex
FRANCE
 
Tél. : [phone]
Fax. : [phone]

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Itsaso
Garcia
Envoyé : jeudi 21 décembre 2006 16:44
À : [hidden email]
Objet : Re: Colocalization

Hi!
I also make colocalization analysis in confocal micrographies, and i
use the plugin "colocalization thresholds". After learning a little bit
about the colocalization describing parameters, i think one can obtain
a lot of information with this plugin. I don´t know about ICA, though.
I would reccomend you to read the papers by: Costes SV et al, Biophys J
2004; 86(6): 3993-4003; and Manders E. et al, Journal of Microscopy
1993; 169:375-382.
I hope this helps, good luck!

Itsaso Garcia-Arcos

P.S: Happy Christmas and New Year to everyone!

> Hello,
>
> I was playing around with the ICA (Intensity Correlation Analysis) of
> the WCIF bundle.
> I've analyzed images of cells taken with a confocal microscope.
> Now, I've seen that the resulting vePDM-values differ if I choose only
> one cell or analyze the whole image. I guess this has something to do
> with the calculation of the "mean" signal, which then might differ.
> But, I'm afraid that this value also differs, depending on the density
> of cells... (what would screw up my analysis)
> Does anybody have an idea how to handle this? Is there anybody, who

did

> serious colocalization analysis of a larger amount of data?
>
>
> Antje
>
>
>
>
>
>
>
> ___________________________________________________________
> Der frühe Vogel fängt den Wurm. Hier gelangen Sie zum neuen Yahoo!

Mail: http://mail.yahoo.de
>


--
********************************
Itsaso Garcia-Arcos
Department of Physiology, Medical School,
University of the Basque Country. UPV/EHU
********************************

[lechristophe]

There's a paper, even better a "tutorial review" by Fabrice Cordelières
(author of several excellent ImageJ plugins and eminent member of our
community) in the last issue of Journal of Microscopy :

A guided tour into subcellular colocalization analysis in light microscopy
S. BOLTE, F. P. CORDELIÈRES

http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2818.2006.01706.x?ai=sp&ui=2b12f&af=H

It introduces JaCoP (Just another Colocalization Plugin) which proposes
several methods for assessing colocalization.


Hope this helps,

Christophe Leterrier

Antje wrote:

> Hello,
>
> I was playing around with the ICA (Intensity Correlation Analysis) of
> the WCIF bundle.
> I've analyzed images of cells taken with a confocal microscope.
> Now, I've seen that the resulting vePDM-values differ if I choose only
> one cell or analyze the whole image. I guess this has something to do
> with the calculation of the "mean" signal, which then might differ.
> But, I'm afraid that this value also differs, depending on the density
> of cells... (what would screw up my analysis)
> Does anybody have an idea how to handle this? Is there anybody, who did
> serious colocalization analysis of a larger amount of data?
>
>
> Antje
>
>
>
>
>
>    
>        
> ___________________________________________________________ Der frühe
> Vogel fängt den Wurm. Hier gelangen Sie zum neuen Yahoo! Mail:
> http://mail.yahoo.de
>