display multi dimension stack

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display multi dimension stack

Qi Zhang
Dear all,

I have acquired 6D images via micro-manger (XY+ Z +
Channel(DAPI+GFP+PhaseContrast) + Positions + time). Is there a simple way
to display it as a stack (color, z and time) of montages (based on
position)? I have tried hyper stack but it only combines two stack in
either horizontal or vertical way, i.e. I have to loop this several times
if I have more than 2 positions. I also tried 5D Image, but not quite
understand how to open a stack and assign it as 5D image.

The way MM store the images are one folder for every position. Is there a
plug-in that can directly convert multi-D images acquired by MM to hyper
stack?

Thanks in advance.

Qi
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Re: display multi dimension stack

dscho
Hi,

On Wed, 11 Apr 2012, Qi Zhang wrote:

> I have acquired 6D images via micro-manger (XY+ Z +
> Channel(DAPI+GFP+PhaseContrast) + Positions + time). Is there a simple
> way to display it as a stack (color, z and time) of montages (based on
> position)? I have tried hyper stack but it only combines two stack in
> either horizontal or vertical way, i.e. I have to loop this several
> times if I have more than 2 positions. I also tried 5D Image, but not
> quite understand how to open a stack and assign it as 5D image.
>
> The way MM store the images are one folder for every position. Is there
> a plug-in that can directly convert multi-D images acquired by MM to
> hyper stack?

ImageJ 1.*'s hyperstack is inherently limited to a maximum of 5
dimensions. This is something we addressed in the ImageJ 2.* version
(where the sky -- or at least something close to it -- is the limit with
regards to the number of dimensions). But since ImageJ 2.* is still in
beta phase, I fear you will have to work around that limitation for now.

Ciao,
Johannes
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Re: display multi dimension stack

ctrueden
In reply to this post by Qi Zhang
Hi Qi,



I have acquired 6D images via micro-manger (XY+ Z +

> Channel(DAPI+GFP+PhaseContrast) + Positions + time). Is there a simple way
> to display it as a stack (color, z and time) of montages (based on
> position)? I have tried hyper stack but it only combines two stack in
> either horizontal or vertical way, i.e. I have to loop this several times
> if I have more than 2 positions. I also tried 5D Image, but not quite
> understand how to open a stack and assign it as 5D image.
>
> The way MM store the images are one folder for every position. Is there a
> plug-in that can directly convert multi-D images acquired by MM to hyper
> stack?
>

Have you tried the latest version of Bio-Formats (post March 15) with your
data? It should handle multi-position Micro-Manager data, reading in each
position as a separate image window.

If you want to display as a montage, you can use Fiji's excellent Stitching
plugins. Make sure your Fiji is fully up to date (Help > Update Fiji) and
then run: Plugins > Stitching > Grid/collection stitching. For Type choose
"Positions from file" and then for Order choose "Defined by image
metadata." Click OK, then click Browse next to "Multi series file" and
select your dataset's metadata.txt file. Change any other stitching options
you desire, click OK, and wait for the magic to create your montage.

If you have any trouble, you can report a bug using Fiji's "Report a Bug"
feature in the Help menu.

Regards,
Curtis


On Wed, Apr 11, 2012 at 2:34 PM, Qi Zhang <[hidden email]> wrote:

> Dear all,
>
> I have acquired 6D images via micro-manger (XY+ Z +
> Channel(DAPI+GFP+PhaseContrast) + Positions + time). Is there a simple way
> to display it as a stack (color, z and time) of montages (based on
> position)? I have tried hyper stack but it only combines two stack in
> either horizontal or vertical way, i.e. I have to loop this several times
> if I have more than 2 positions. I also tried 5D Image, but not quite
> understand how to open a stack and assign it as 5D image.
>
> The way MM store the images are one folder for every position. Is there a
> plug-in that can directly convert multi-D images acquired by MM to hyper
> stack?
>
> Thanks in advance.
>
> Qi
>