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: 250 960-6777
> *****************************************************



Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
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