Batch processing of .oib

[Sam Albers]

Hello all,

I am trying to batch process some .oib files into .tiff files using the hyperstack projection macro for imagej (http://bipl.umn.edu/files/hyperstack_projection.txt).

The difference with my .oib files is that they aren't stacks and thus z always equals zero. When I try to run the macros on one of my files I received the error message "This command requires a stack".

If I comment out the following from the macro I received a message that no images are open:

    // run the max intensity z projection
    //run("Z Project...", "projection=[Max Intensity]");
    
    // after the projection the file is now a stack
    // made up of the different channels
    // seperate and save
    run("Image Sequence... ", "format=TIFF save=[" + path2 + "] save=[" + path2 + "]");
   

What I would like to do is process a bunch of .oib files with 3 channels into a single composite .tiff image. However, when I look through the macros it is not entirely obvious to me which part specifies that the files must be a stack so I'm not sure which part to change.

Any help would be greatly appreciated. Sorry if this is extremely simple. Thanks in advance.

The reason that I am posting to this list rather than the imagej list is because I first heard about the hyperstack projection macro on this list.

I am running Ubuntu 9.10 and Imagej 1.43b.

Sam



--
*****************************************************
Sam Albers
Geography Program
University of Northern British Columbia
3333 University Way
Prince George, British Columbia
Canada, V2N 4Z9
phone: [phone]
*****************************************************

[Glen MacDonald-2]

Hi Sam,
The OIB is not a TIFF format.  The LOCI plugin is required to open them.  I'm sending a macro to you off list that uses the LOCI plugin to batch process importing different types of files, written to import the OIF and OIB formats, among others.  You can specify merge type, channel order, etc.

Regards,
Glen


On Mar 1, 2010, at 1:13 PM, Sam Albers wrote:

> Hello all,
>
> I am trying to batch process some .oib files into .tiff files using the hyperstack projection macro for imagej (http://bipl.umn.edu/files/hyperstack_projection.txt).
>
> The difference with my .oib files is that they aren't stacks and thus z always equals zero. When I try to run the macros on one of my files I received the error message "This command requires a stack".
>
> If I comment out the following from the macro I received a message that no images are open:
>
>     // run the max intensity z projection
>     //run("Z Project...", "projection=[Max Intensity]");
>      
>     // after the projection the file is now a stack
>     // made up of the different channels
>     // seperate and save
>     run("Image Sequence... ", "format=TIFF save=[" + path2 + "] save=[" + path2 + "]");
>    
>
> What I would like to do is process a bunch of .oib files with 3 channels into a single composite .tiff image. However, when I look through the macros it is not entirely obvious to me which part specifies that the files must be a stack so I'm not sure which part to change.
>
> Any help would be greatly appreciated. Sorry if this is extremely simple. Thanks in advance.
>
> The reason that I am posting to this list rather than the imagej list is because I first heard about the hyperstack projection macro on this list.
>
> I am running Ubuntu 9.10 and Imagej 1.43b.
>
> Sam
>
>
>
> --
> *****************************************************
> Sam Albers
> Geography Program
> University of Northern British Columbia
> 3333 University Way
> Prince George, British Columbia
> Canada, V2N 4Z9
> phone: [phone]
> *****************************************************

Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]

[Daniel James White]

Sam,

post this problem to the ImageJ list, and someone will probably answer.

if you get the Fiji distro of imageJ....
http://pacific.mpi-cbg.de/
there is a built in script editor that will help you fix this stuff  
more easily,
the docs are on the same website as the download.
Fiji is just ImageJ, batteries included.

The script editor does the image J macro language as well as nicer  
modern scripting languages like python and ruby that are much more  
powerful than the macro lang.

cheers

Dan


On Mar 2, 2010, at 7:07 AM, CONFOCALMICROSCOPY automatic digest system  
wrote:

> Date:    Mon, 1 Mar 2010 13:13:34 -0800
> From:    Sam Albers <[hidden email]>
> Subject: Batch processing of .oib
>
> --0016369205f6ce1a1a0480c3b8f1
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello all,
>
> I am trying to batch process some .oib files into .tiff files using  
> the
> hyperstack projection macro for imagej (
> http://bipl.umn.edu/files/hyperstack_projection.txt).
>
> The difference with my .oib files is that they aren't stacks and  
> thus z
> always equals zero. When I try to run the macros on one of my files I
> received the error message "This command requires a stack".
>
> If I comment out the following from the macro I received a message  
> that no
> images are open:
>
>    // run the max intensity z projection
>    //run("Z Project...", "projection=[Max Intensity]");
>
>    // after the projection the file is now a stack
>    // made up of the different channels
>    // seperate and save
>    run("Image Sequence... ", "format=TIFF save=[" + path2 + "]  
> save=[" +
> path2 + "]");
>
>
> What I would like to do is process a bunch of .oib files with 3  
> channels
> into a single composite .tiff image. However, when I look through  
> the macros
> it is not entirely obvious to me which part specifies that the files  
> must be
> a stack so I'm not sure which part to change.
>
> Any help would be greatly appreciated. Sorry if this is extremely  
> simple.
> Thanks in advance.
>
> The reason that I am posting to this list rather than the imagej  
> list is
> because I first heard about the hyperstack projection macro on this  
> list.
>
> I am running Ubuntu 9.10 and Imagej 1.43b.
>
> Sam
>
>
>
> --
> *****************************************************
> Sam Albers
> Geography Program
> University of Northern British Columbia
> 3333 University Way
> Prince George, British Columbia
> Canada, V2N 4Z9
> phone: [phone]

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 )