Re: plugins for flat field correction

Posted by lechristophe on Aug 12, 2008; 8:37am
URL: http://imagej.273.s1.nabble.com/plugins-for-flat-field-correction-tp3695416p3695417.html

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
>