?? On quantification of Western blot bands using ImageJ

[Zhigang]

Dear ImageJ Expert colleagues,

I would like to quantify the protein bands of western blot/SuperSignal
ChemiLuminescent (Pierce) using ImageJ.

It will be very appreciated, if you could send me the standard procedure to
get this done.

Detailed information on how to calibrate the bands in order to keep the data
in the linear range will be very helpful.

Any suggestions on reference papers using ImageJ as the method for
quantification of Western-blot data is very welcomed.

Thanks for your help

Zhigang
---------------------------
Zhigang Kang  Research Fellow
Section on Neuroendocrine Immunology and Behavior
Intergrative Neural Immune Program, NIH
5625 Fishers Lane, Room 4N15, MSC-9401,
Rockville MD 20852
Telephone:[phone]
Fax:[phone]
Email:[hidden email]
   

[Eddie Iannuccelli]

Try the Analyse->Gel menu

Here is a small tutorial forone-dimensional electrophoretic gels :
http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze
We used a linear model (in excel) with dna control bands to quantify our
dna samples from agarose gels, don't know if you can use such linear
model for your protein gel . Another tutorial here for dot blots :
http://rsbweb.nih.gov/ij/docs/examples/dot-blot/

Regards

Zhigang a écrit :

> Dear ImageJ Expert colleagues,
>
> I would like to quantify the protein bands of western blot/SuperSignal
> ChemiLuminescent (Pierce) using ImageJ.
>
> It will be very appreciated, if you could send me the standard procedure to
> get this done.
>
> Detailed information on how to calibrate the bands in order to keep the data
> in the linear range will be very helpful.
>
> Any suggestions on reference papers using ImageJ as the method for
> quantification of Western-blot data is very welcomed.
>
> Thanks for your help
>
> Zhigang
> ---------------------------
> Zhigang Kang  Research Fellow
> Section on Neuroendocrine Immunology and Behavior
> Intergrative Neural Immune Program, NIH
> 5625 Fishers Lane, Room 4N15, MSC-9401,
> Rockville MD 20852
> Telephone:[phone]
> Fax:[phone]
> Email:[hidden email]
>    
>  

--
******************************************
Eddie Iannuccelli
Laboratoire de génétique cellulaire
INRA - Castanet Tolosan
Tel: [phone] / Fax: [phone]

[Herbert M. Geller]

I am working with some very large stacks, do some processing, close the
stacks, and then start over with the next batch.

I am getting out of memory errors, when opening the second group of
stacks. When I use the memory monitor, I find that, with all windows
closed, except the memory monitor, it shows 564 MBytes used.

I am on a Dual Processor Dell, with 2.5 G of RAM, where I have allocated
1600 MBytes  and 4 threads for ImageJ.

Is there an easy way to release memory without restarting ImageJ?

--
--------------------------------------
Herbert M. Geller, Ph.D.
Developmental Neurobiology Section
National Heart Lung and Blood Institute, NIH
10 Center Drive MSC 1754
Bldg 10, Room 6D18
Bethesda, MD  20892-1754
Tel: [phone]; Fax: [phone]
e-mail: [hidden email]
Web: http://dir.nhlbi.nih.gov/labs/ldn/index.asp
---------------------------------------

[ctrueden]

Hi Herbert,

Is there an easy way to release memory without restarting ImageJ?
>

Nope, restarting ImageJ *is* the easy way. =) You can click the ImageJ
status bar to perform a garbage collection operation, which instructs Java
to free any memory that is no longer being used, but one of the plugins you
use might still be "eating" the memory even though it is done executing.

The problem is that any of the plugins you are using could allocate as much
memory as it wants anywhere it wants, and ImageJ has no direct way of
knowing what was done, nor how to free the memory.

I would suggest you try to track down which plugin (or plugins) is the
culprit. First, try opening one of your large stacks and then closing it
again with no processing. Check the memory use to make sure it drops back
down to where it was before you opened the stack.

Then repeat the process running just your first processing operation. Repeat
again with the first two operations, etc., and note the point at which the
memory doesn't drop back down. If you can figure out which plugin is causing
the problem, it will make it easier for us to debug.

HTH,
Curtis

On Thu, Apr 10, 2008 at 4:19 PM, Herbert M. Geller <[hidden email]>
wrote:

> I am working with some very large stacks, do some processing, close the
> stacks, and then start over with the next batch.
> I am getting out of memory errors, when opening the second group of
> stacks. When I use the memory monitor, I find that, with all windows closed,
> except the memory monitor, it shows 564 MBytes used.
>
> I am on a Dual Processor Dell, with 2.5 G of RAM, where I have allocated
> 1600 MBytes  and 4 threads for ImageJ.
>
> Is there an easy way to release memory without restarting ImageJ?
>
> --
> --------------------------------------
> Herbert M. Geller, Ph.D.
> Developmental Neurobiology Section
> National Heart Lung and Blood Institute, NIH
> 10 Center Drive MSC 1754
> Bldg 10, Room 6D18
> Bethesda, MD  20892-1754
> Tel: [phone]; Fax: [phone]
> e-mail: [hidden email]
> Web: http://dir.nhlbi.nih.gov/labs/ldn/index.asp
> ---------------------------------------
>