Re: xyzt image

Posted by Straatman, Kees (Dr.) on
URL: http://confocal-microscopy-list.275.s1.nabble.com/xyzt-image-tp7580102p7580117.html

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Dear Manish,

Sorry for the confusion, I did not notice carefully via which mailing list your question was posted. I indeed referred to a program called Fiji (Fiji Is Just ImageJ) which you can download from http://fiji.sc/Fiji for free. It has many powerful option for image analysis and can read most microscope file formats. It is a distribution of a program called ImageJ, so besides information on the Fiji website the manual etc can be found on the ImageJ website (http://imagej.nih.gov/ij/) under Docs. Hopes this helps to solve your problem.

Best wishes

Kees

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Glen MacDonald
Sent: 03 April 2013 16:01
To: [hidden email]
Subject: Re: xyzt image

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I believe Kees was referring the Grouped Z-Project in Fiji/ImageJ, not something in your confocal software.  Import your Leica file into Fiji with the LOCI  plugin.  The Grouped Z-Project will create a new stack in which each frame is the z-projection of the corresponding time point.  There are several routes to save that as an AVI from Fiji/ImageJ.   It is advisable to also archive the projection movie in an uncompressed format in case you want to edit it in the future.  In fact, you can add timestamps and annotations in Fiji.  Please refer to documentation:
http://imagej.nih.gov/ij/docs/guide/index.html

Regards,
Glen
Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability Box 357923 University of Washington Seattle, WA 98195-7923  USA
[phone]
[hidden email]
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On Apr 3, 2013, at 3:44 AM, Manish Kumar <[hidden email]> wrote:

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> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Kees,
> Thanks for the reply. I have tried the option. This works with the
> confocal software, but didnt work when i export it to .avi .
>
> Rgds
> Manish
>
>
> On Wed, Apr 3, 2013 at 3:45 PM, Straatman, Kees R. (Dr.) <
> [hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear Manish,
>>
>> You can use Image > Stacks > Tools > Grouped Z-project...
>>
>> Best wishes
>>
>> Kees
>>
>> -----Original Message-----
>> From: Confocal Microscopy List
>> [mailto:[hidden email]]
>> On Behalf Of Manish Kumar
>> Sent: 03 April 2013 10:51
>> To: [hidden email]
>> Subject: xyzt image
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hello everyone,
>>
>> Is there any way to convert XYZT image to xyt. format.
>>
>> I have done live cell imaging with xyzt format and and I want to
>> export the same file to XYT.avi format. That means  I want to  
>> compile the z stack so that I can get the .avi image in xyt format.
>> I am using Leica SP5 confocal misroscope.
>>
>> Regards
>> Manish Kumar
>> Imaging facility Manager
>> IGIB,
>> New Delhi
>>