Dot-blot autodetection

[Chin, Joong Hyoun (IRRI)]

Hello,
 
I am trying to development of 'high throughput system for dot-blot genotyping'. If we see dot at the position, we can think '+', and if we cannot, those are '-'. It's useful for DNA marker-assisted selection system for plant breeding.
 
I am just trying to use ImageJ for application to dot-blot.
According to the manual in internet, we just can get the intensity of visible dots after using 'threshold' menu.
When I use 'analyze'->'analyze particles', it just count or detect visible dots. But we need the '0' value of 'invisible' dots at the expected position.
 
Maybe this is same with that of microarray. We are planning to use this option for several thousand of samples, without using eye-balling reading to minimize the error of reading.
 
I will sincerely appreciate to the big contributors.
 
Thank you and regards,
 
Chin
 
Joong-Hyoun Chin
Postdoc Research Fellow
Div. of Plant Breeding, Genetics, and Biotechnology (PBGB)
IRRI, Los Banos, Philippines

[phone]-Ext. 2954 (Home)
[phone] (Cell phone) : Recommended

 
 

[Robert Dougherty]

Chin,

I just posted a Custom ImageJ Plugin that was ordered in 2005 by Leila
Mosavi-Maulik.  In addition to the design requirements and my efforts, it
contains Wayne Rasband magic.  See
http://www.optinav.com/MicroArray_Profile.htm.  It may not be easy to
control it from a macro due to its non-generic dialog, but you could
probably process thousands of images at a time by using virtual stack
opener.

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
> Chin, Joong Hyoun (IRRI)
> Sent: Saturday, August 18, 2007 7:51 PM
> To: [hidden email]
> Subject: Dot-blot autodetection
>
> Hello,
>
> I am trying to development of 'high throughput system for dot-blot
> genotyping'. If we see dot at the position, we can think '+', and if
> we cannot, those are '-'. It's useful for DNA marker-assisted
> selection system for plant breeding.

[Chin, Joong Hyoun (IRRI)]

Dear Bob,

I am happy to see the plugin. I am really impressed.
We were looking for easy and cost-free software for dot blot and related
low-cost genotyping system.
I am working at IRRI (International Rice Research Institute) at
Philippines, and this is related with GCP (Generation Challenge
Program). We are scientists, and our objectives are related with
non-profit collaboration of international research.

My boss, Dr.Vera Cruz asked me look for the software for several
thousand of images of genotyping blot of membrane or paper filter.

I hope to confirm that we can use this plugin freely, because I visited
your homepage, and I saw you have a business with the plugin packages
related with ImageJ. We hope you to contribute with this plugin, and we
will show our thanks to you and many anonymous ImageJ developers.

Thank you and regards,

Chin


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Robert Dougherty
Sent: Sunday, August 19, 2007 2:21 PM
To: [hidden email]
Subject: Re: Dot-blot autodetection

Chin,

I just posted a Custom ImageJ Plugin that was ordered in 2005 by Leila
Mosavi-Maulik.  In addition to the design requirements and my efforts,
it
contains Wayne Rasband magic.  See
http://www.optinav.com/MicroArray_Profile.htm.  It may not be easy to
control it from a macro due to its non-generic dialog, but you could
probably process thousands of images at a time by using virtual stack
opener.

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
> Chin, Joong Hyoun (IRRI)
> Sent: Saturday, August 18, 2007 7:51 PM
> To: [hidden email]
> Subject: Dot-blot autodetection
>
> Hello,
>
> I am trying to development of 'high throughput system for dot-blot
> genotyping'. If we see dot at the position, we can think '+', and if
> we cannot, those are '-'. It's useful for DNA marker-assisted
> selection system for plant breeding.

[Robert Dougherty]

Chin,

I'm glad the plugin looks useful.  Yes, you are free to use it.  See the
open source Berkeley Software Distribution license that is quoted on the
OptiNav web site and also can be found in the plugin code.  I write ImageJ
plugins like this one for fun. (As I mentioned, Wayne Rasband helped in this
case.)  The main reason for the "Custom ImageJ Plugin" business is to find
out who is serious about needing a plugin.

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
> Chin, Joong Hyoun (IRRI)
> Sent: Sunday, August 19, 2007 10:44 PM
> To: [hidden email]
> Subject: Re: Dot-blot autodetection
>
> I hope to confirm that we can use this plugin freely, because I
> visited your homepage, and I saw you have a business with the plugin
> packages related with ImageJ.