Subtracting Background Problem

[Naveen Krishnan]

I have sets of images that vary in overall background intensity and I was
wondering if there was a quick fix that could normalize the backgrounds of
all the images to zero (or close to zero), while removing the corresponding
artificial intensity from the cells in the images. I have used the subtract
background function of imageJ with various parameters for the rolling ball
radius but I am wondering if there is a more accurate way. I have also tried
some of the plugins on the internet for background correction but so far
with the parameters I have used I haven't seen any good results. Any help
here would be greatly appreciated.

Thanks,

Naveen

[Ralph Common]

There is a free, easy to use program called Image Arithmetic that will do
the job.  It can be downloaded from

http://www.t3i.nl/myblog/?page_id=7

Ralph Common

----- Original Message -----
From: "Naveen Krishnan" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, February 19, 2008 12:16 PM
Subject: Subtracting Background Problem


> I have sets of images that vary in overall background intensity and I was
> wondering if there was a quick fix that could normalize the backgrounds of
> all the images to zero (or close to zero), while removing the
corresponding
> artificial intensity from the cells in the images. I have used the
subtract
> background function of imageJ with various parameters for the rolling ball
> radius but I am wondering if there is a more accurate way. I have also
tried
> some of the plugins on the internet for background correction but so far
> with the parameters I have used I haven't seen any good results. Any help
> here would be greatly appreciated.
>
> Thanks,
>
> Naveen
>

[dscho]

Hi,

On Tue, 19 Feb 2008, Ralph Common wrote:

> There is a free, easy to use program called Image Arithmetic that will
> do the job.  It can be downloaded from
>
> http://www.t3i.nl/myblog/?page_id=7

And sure enough, this program is Windows-only.

Sigh,
Dscho

[Naveen Krishnan]

Were you referring to performing subtractions using the mask of a background
as image2 and the original image as image1 or do you know a better way to
subtract out the background for a large number of images using this program?

Thanks,

Naveen

On Tue, Feb 19, 2008 at 10:10 PM, Ralph Common <[hidden email]> wrote:

> There is a free, easy to use program called Image Arithmetic that will do
> the job.  It can be downloaded from
>
> http://www.t3i.nl/myblog/?page_id=7
>
> Ralph Common
>
> ----- Original Message -----
> From: "Naveen Krishnan" <[hidden email]>
> To: <[hidden email]>
> Sent: Tuesday, February 19, 2008 12:16 PM
> Subject: Subtracting Background Problem
>
>
> > I have sets of images that vary in overall background intensity and I
> was
> > wondering if there was a quick fix that could normalize the backgrounds
> of
> > all the images to zero (or close to zero), while removing the
> corresponding
> > artificial intensity from the cells in the images. I have used the
> subtract
> > background function of imageJ with various parameters for the rolling
> ball
> > radius but I am wondering if there is a more accurate way. I have also
> tried
> > some of the plugins on the internet for background correction but so far
> > with the parameters I have used I haven't seen any good results. Any
> help
> > here would be greatly appreciated.
> >
> > Thanks,
> >
> > Naveen
> >
>

[ctrueden]

Hi Dscho,

> http://www.t3i.nl/myblog/?page_id=7
>
> And sure enough, this program is Windows-only.
>

I tried installing it on Ubuntu Gutsy under WINE with a fake Windows (i.e.,
not an actual Windows install) and it seems to work fine.

-Curtis

On Feb 20, 2008 6:07 AM, Johannes Schindelin <[hidden email]>
wrote:

> Hi,
>
> On Tue, 19 Feb 2008, Ralph Common wrote:
>
> > There is a free, easy to use program called Image Arithmetic that will
> > do the job.  It can be downloaded from
> >
> > http://www.t3i.nl/myblog/?page_id=7
>
> And sure enough, this program is Windows-only.
>
> Sigh,
> Dscho
>

[Gabriel Landini]

> > There is a free, easy to use program called Image Arithmetic that will
> > do the job.  It can be downloaded from
> >
> > http://www.t3i.nl/myblog/?page_id=7

I am curious... what can this do that IJ cannot?

Cheers,
G.

[dscho]

Hi,

On Wed, 20 Feb 2008, Curtis Rueden wrote:

> > http://www.t3i.nl/myblog/?page_id=7
> >
> > And sure enough, this program is Windows-only.
>
> I tried installing it on Ubuntu Gutsy under WINE with a fake Windows
> (i.e., not an actual Windows install) and it seems to work fine.

Well, try that on a PowerPC Mac.  Or on a SPARC Solaris.  Or on HP-UX.

The whole _point_ of ImageJ being written in Java is that you can run it
almost everywhere.  And yes, the nicest clusters I know are still SPARC
clusters.

I would not even be surprised if ImageJ worked on my mobile phone.

Try that with said Windows program.

Ciao,
Dscho