Organisation of z stacks during 3D time-lapse in Leica LCS.

[Matthew Pearson-3]

Hi all,

I am running some 3D time-lapse experiments looking at mitochondrian dynamics on our Leica SP2.  Taking the z stacks is fine.  However, all of the individual stack images appear in the gallery, but all images from every stack appear together with no clear separation between time points and I can't find a way of highlighting say images from one stack and making a projection of the stack.  Can you select one stack from a series in the gallery view?  Ultimately I would like to run a movie which will consist of say 30 frames each frame being a projection of each time point.

I could probably do all this in the bio-formats plugin for imageJ, but i'm not sure that this software will be able to organise all the of the time-lapse data into individual stacks i.e. time points and channels.  Also when i import a z stack into bioformats and try to Image-Z project.. an error message appears, does anyone know why this would be?

Thanks for the advice!

Matt.

[Kimmo K Tanhuanpaa]

On Thu, 16 Oct 2008, Matthew Pearson wrote:

Hi,

> Ultimately I would like to run a movie which will consist of say 30 frames
> each frame being a projection of each time point.

Open your series, go to process - extended focus - maximum projection
-> projection direction z - apply
and you'll get such a movie. Providing you have the lisence for that part
of LCS.

Cheers,

Kimmo
_____________________________________________________________________
     Mr. Kimmo Tanhuanpää, PhD (Biochemistry)
  Head of Light Microscopy Unit,
  Institute of Biotechnology, University of Helsinki
     http://www.biocenter.helsinki.fi/bi/lmu/

[mahogny]

Matthew Pearson wrote:

>
> Hi all,
>
> I am running some 3D time-lapse experiments looking at mitochondrian
> dynamics on our Leica SP2.  Taking the z stacks is fine.  However, all
> of the individual stack images appear in the gallery, but all images
> from every stack appear together with no clear separation between time
> points and I can't find a way of highlighting say images from one
> stack and making a projection of the stack.  Can you select one stack
> from a series in the gallery view?  Ultimately I would like to run a
> movie which will consist of say 30 frames each frame being a
> projection of each time point.
>
> I could probably do all this in the bio-formats plugin for imageJ, but
> i'm not sure that this software will be able to organise all the of
> the time-lapse data into individual stacks i.e. time points and
> channels.  Also when i import a z stack into bioformats and try to
> Image-Z project.. an error message appears, does anyone know why this
> would be?

I don't know about the leica software but Endrov (www.endrov.net) can
handle the data the way you want it; it's optimized for 3d time
lapse+channels. if IJ cannot handle it then it's an option. there is a z
projection feature but it's not realtime yet.

yours sincerely,
Johan Henriksson


>
> Thanks for the advice!
>
> Matt.
>
>


--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net