plugins for flat field correction

[aparna sadananda]

Hi all,
I have two questions:

1) Is there a plugin for flat field correction?
2) I am looking at axonal transport in a system of nerves, in vivo. The
axons in solution are quite squiggly and hence not very easy to analyze for
particle movement. I want to select each axon by making line ROI. Then,
using the intensity values along the axon reconstruct the image so that
there are straight lines representing the axon. This would then be useful
for tracking the movement of particles along the straight lines. Is
there some plugin that could do this?

Thanks in advance,
Aparna

[lechristophe]

Hi Aparna,

For flat-field correction, there are a number of options available, see here :
http://imagejdocu.tudor.lu/imagej-documentation-wiki/how-to/how-to-correct-background-illumination-in-brightfield-microscopy

As regards straightening, ImageJ now has a Edit>Selection>Strtaighten
command that straighten any line selection, see here :
http://rsbweb.nih.gov/ij/notes.html
you need to upgrade to 1.41i or 1.41j to get this fucntion.
I don't know it will straighten a whole stack, but Eva Kocsis'
original plugin does it :
http://rsbweb.nih.gov/ij/plugins/straighten.html

Just a remark : if you wnat to measure movement along a straightened
trajectory, why not use a kymograph ? see here :
http://www.embl.de/eamnet/html/kymograph.html

Cheers,

Christophe Leterrier

On Mon, Aug 11, 2008 at 08:35, aparna sadananda
<[hidden email]> wrote:

> Hi all,
> I have two questions:
>
> 1) Is there a plugin for flat field correction?
> 2) I am looking at axonal transport in a system of nerves, in vivo. The
> axons in solution are quite squiggly and hence not very easy to analyze for
> particle movement. I want to select each axon by making line ROI. Then,
> using the intensity values along the axon reconstruct the image so that
> there are straight lines representing the axon. This would then be useful
> for tracking the movement of particles along the straight lines. Is
> there some plugin that could do this?
>
> Thanks in advance,
> Aparna
>

[Bertrand]

The new url for the topic "how to correct background illumination in brightfield microscopy" is http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_background_illumination_in_brightfield_microscopy&s[]=background