Reg analysis of array

[Arivusudar Marimuthu]

Hello everyone,
 
I have an array image with uniformly arranged spots. They are similar to
microarray spots. Each spot has different intensity of signal. I am
trying to measure the spot intensities and compare each spot. To do that
I need to create a template and overlay on the spots and measure
intensities, subtract background intensities. The above process is
something similar to the function of image acquisition software for gene
expression arrays such as Genepix. How can I carry out the above
analysis using imageJ ?
 
Thanks
Arivu

[Robert Dougherty]

Arivu,

See MicoArray Profile on my site.

Bob


Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Arivusudar Marimuthu
> Sent: Tuesday, August 12, 2008 3:37 PM
> To: [hidden email]
> Subject: Reg analysis of array
>
> Hello everyone,
>
> I have an array image with uniformly arranged spots. They are similar to
> microarray spots. Each spot has different intensity of signal. I am
> trying to measure the spot intensities and compare each spot. To do that
> I need to create a template and overlay on the spots and measure
> intensities, subtract background intensities. The above process is
> something similar to the function of image acquisition software for gene
> expression arrays such as Genepix. How can I carry out the above
> analysis using imageJ ?
>
> Thanks
> Arivu

[Arivusudar Marimuthu]

Hi Bob,

Thanks for your reply. I have a problem in loading all the plugins.

Let me explain what I did. I downloaded the plugin MicroArray
profile.jar in to plugins folder.

Then I tried to run each plugin. Except for Microrray.class the other
plugins, circle arranger and microarray profiler were unable to load. I
got error while trying to run them.

Please let me know if I am doing in a right way.

Thank you very much
Arivu



 I could not load the circle arranger.class and Microarray
profiler.class plugins

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Robert Dougherty
Sent: Tuesday, August 12, 2008 10:38 PM
To: [hidden email]
Subject: Re: Reg analysis of array

Arivu,

See MicoArray Profile on my site.

Bob


Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Arivusudar Marimuthu
> Sent: Tuesday, August 12, 2008 3:37 PM
> To: [hidden email]
> Subject: Reg analysis of array
>
> Hello everyone,
>
> I have an array image with uniformly arranged spots. They are similar

to
> microarray spots. Each spot has different intensity of signal. I am
> trying to measure the spot intensities and compare each spot. To do
that
> I need to create a template and overlay on the spots and measure
> intensities, subtract background intensities. The above process is
> something similar to the function of image acquisition software for
gene
> expression arrays such as Genepix. How can I carry out the above
> analysis using imageJ ?
>
> Thanks
> Arivu

[Robert Dougherty]

Arivu,

The only plugin in the .jar file should be Microarray Profile.  The other
class files are internal things to help Microarray Profile function. You
should not try to run them, and normally you should not even see them.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Arivusudar Marimuthu
> Sent: Friday, August 15, 2008 8:03 AM
> To: [hidden email]
> Subject: Re: Reg analysis of array
>
> Hi Bob,
>
> Thanks for your reply. I have a problem in loading all the plugins.
>
> Let me explain what I did. I downloaded the plugin MicroArray
> profile.jar in to plugins folder.
>
> Then I tried to run each plugin. Except for Microrray.class the other
> plugins, circle arranger and microarray profiler were unable to load. I
> got error while trying to run them.
>
> Please let me know if I am doing in a right way.
>
> Thank you very much
> Arivu
>
>
>
>  I could not load the circle arranger.class and Microarray
> profiler.class plugins
>