need some help with imageJ

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need some help with imageJ

OBEID Patricia 154904
Hello,
I have a problem with files in ImageJ from Metamorph.
My manipulation involves the acquisition of several z (n = 22) for the same position x, y and on several times (n = 61).
Files generated by Metamorph are actually a stack of 22z for a given time.
The Concatenator allows me to concatenate a stacks in groups of 18. So I have 3 "movies" from 18 a stacks and a fourth of seven stacks.
I would like to create a HyperStack of all that I can see for each z what happens over time.
When I try to create HyperStack I have a black file, image empty for t = 61; z = 22 and c = 1 !!!
Could you give me some tracks to reach my goal to please.
I thank you very much in advance.
Kind regards,
Patricia
_______________________________________
Patricia OBEÏD
Animateur Informatique Biomics
CEA Grenoble
DSV / iRTSV / BGE U1038/ Biomics / Bât 4020
17 rue des Martyrs
38054 GRENOBLE Cedex 9

Email : [hidden email]<mailto:[hidden email]>
Tél : (+33)4 38 78 47 12
Fax : (+33)4 38 78 59 17
https://twitter.com/BiomicsLab



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Re: need some help with imageJ

Jerome Mutterer-3
Hi Patricia.
The following works:
First convert both of your hyperstacks to normal stacks using the
"hyperstack to stack" command. At this point you can check if there are no
missing image planes (n==z*t*c). Then use the concatenate command, and
convert back the result concatenated stack to an hyperstack using  the
"stack to hyperstack" reciprocal command, specifying the right
dimensionality.

Jerome.

On 31 October 2014 07:48, OBEID Patricia 154904 <[hidden email]>
wrote:

> Hello,
> I have a problem with files in ImageJ from Metamorph.
> My manipulation involves the acquisition of several z (n = 22) for the
> same position x, y and on several times (n = 61).
> Files generated by Metamorph are actually a stack of 22z for a given time.
> The Concatenator allows me to concatenate a stacks in groups of 18. So I
> have 3 "movies" from 18 a stacks and a fourth of seven stacks.
> I would like to create a HyperStack of all that I can see for each z what
> happens over time.
> When I try to create HyperStack I have a black file, image empty for t =
> 61; z = 22 and c = 1 !!!
> Could you give me some tracks to reach my goal to please.
> I thank you very much in advance.
> Kind regards,
> Patricia
> _______________________________________
> Patricia OBEÏD
> Animateur Informatique Biomics
> CEA Grenoble
> DSV / iRTSV / BGE U1038/ Biomics / Bât 4020
> 17 rue des Martyrs
> 38054 GRENOBLE Cedex 9
>
> Email : [hidden email]<mailto:[hidden email]>
> Tél : (+33)4 38 78 47 12
> Fax : (+33)4 38 78 59 17
> https://twitter.com/BiomicsLab
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
12, rue du Général Zimmer
67084 Strasbourg Cedex
T 0367155339
www.ibmp.cnrs.fr

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