Re: concatenate on open with bio-formats

[Daniel James White]

Hi Arun,

all you need to do to concatenate the time series together into a time series 2 channel hyperstack
is open the file with the bio-formats importer,
and tuen on the
concatenate series when compatible
check box.

then select the appropriate series from the ones available
(eg 1-17 but not the others)

then it will all open in one hyper stack, with sliders for channel, z and time

good luck!

Dan







On May 5, 2011, at 6:34 PM, Arun Sampathkumar wrote:

> Cool, thats great.
> Ok i will share the folder with you, you need to open series 1 to 16. They contain two different channels.  These are Z series images over time. The rest of the series (17-31) are Z projection of individual time points.
> Thanks in advance for the help
>
> Arun
> ________________________________________
> From: Daniel James White [[hidden email]]
> Sent: Thursday, May 05, 2011 4:08 PM
> To: Arun Sampathkumar
> Subject: Re: [ipf] FIJI help
>
> dropbox
>
> D
>
>
> On May 5, 2011, at 2:18 PM, Arun Sampathkumar wrote:
>
>> Hi Daniel
>> Thanks for getting back to me. There is a problem, the files are around 600MB minimum. Are you aware of any server that allows transfer of such big files.
>>
>> Cheers
>> Arun
>> ________________________________________
>> From: Daniel James White [[hidden email]]
>> Sent: Thursday, May 05, 2011 1:55 PM
>> To: Arun Sampathkumar
>> Cc: Image Processing Facility; LMF
>> Subject: Re: [ipf] FIJI help
>>
>> Hi Arun,
>>
>> I am a colleague of Johannes here at MPI-CBG
>>
>> On May 5, 2011, at 10:38 AM, Arun Sampathkumar wrote:
>>
>>> Dear Johannes
>>> I am a Post doc from the group of Dr. Staffan Persson at the Max Planck Institute of Molecular plant physiology. Guess he met you recently in Berlin during the Max planck leadnet meeting. We have some 4D data sets as Slidebook (SLD) files and at the moment i have hit a wall when it comes to opening them in Fiji. With LOCI i am able to see all the time series saved within the SLD file. But I can find out a way to put it together as a 4D data set and its only possible to view them separately.
>>>
>>> Please let me know if you know a set parameter, by which i can view the entire data set all at once. I will be very thankful if you can help me out with this.
>>
>> if you can give ius a sample file,
>> se can figure it out and tell you exactly what to click to get the images into a hyperstack
>> with sliders for time and whatever other dimensions are there.
>>
>> cheers
>>
>> Dan
>>
>>
>>>
>>> yours truly
>>> Arun Sampathkumar
>>>
>>> Post Doc
>>> Max Planck institute of molecular plant physiology
>>> Potsdam
>>
>> Dr. Daniel James White BSc. (Hons.) PhD
>> Senior Microscopist / Image Visualisation, Processing and Analysis
>> Light Microscopy and Image Processing Facilities
>> Max Planck Institute of Molecular Cell Biology and Genetics
>> Pfotenhauerstrasse 108
>> 01307 DRESDEN
>> Germany
>>
>> [phone] (German Mobile)
>> [phone] (Work phone at MPI-CBG)
>> [phone] (Fax MPI-CBG LMF)
>>
>> http://www.bioimagexd.net       BioImageXD
>> http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
>> http://www.chalkie.org.uk               Dan's Homepages
>> https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
>> dan (at) chalkie.org.uk
>> ( white (at) mpi-cbg.de )
>>
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> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> [phone] (Work phone at MPI-CBG)
> [phone] (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net       BioImageXD
> http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
> http://www.chalkie.org.uk               Dan's Homepages
> https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
>
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Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )