Batch processing of .oib

Posted by Sam Albers on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Batch-processing-of-oib-tp4657008.html

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



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Sam Albers
Geography Program
University of Northern British Columbia
3333 University Way
Prince George, British Columbia
Canada, V2N 4Z9
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