Re: Batch processing of .oib

Posted by ctrueden on Mar 02, 2010; 9:22pm
URL: http://imagej.273.s1.nabble.com/Re-Batch-processing-of-oib-tp3685528p3685533.html

Hi Sam,

Check out the "recursive TIFF converter" macro on the Bio-Formats web site:

https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/utils/macros/recursiveTiffConvert.txt

You will need to change the extension from "DM3" to "OIB" and tweak some of
the Bio-Formats Importer parameters on the line:
      run("Bio-Formats Importer", "id='" + inBase + path + "' view=[Standard
ImageJ] stackOrder=Default virtual");

You can determine the appropriate parameters by using the Macro Recorder,
opening one of your OIB files with the Bio-Formats Importer plugin, and then
copy/pasting the arguments into the macro. Specifically, to support the 3
channel overlay, you will probably want to check the "Merge channels to RGB"
option—something like:

run("Bio-Formats Importer", "open=[" + inBase + path + "] merge_channels
view=Hyperstack stack_order=XYCZT use_virtual_stack");

-Curtis

On Tue, Mar 2, 2010 at 1:02 PM, Sam Albers <[hidden email]>wrote:

> Hello all,
>
> Sorry for cross posting with the confocal list but it was suggested that I
> look for an answer to my problem here.
>
> I am trying to batch process some OIB files into TIFF files. I have a bunch
> of OIB file without a z-series but with 3 separate channels. I would like
> to
> produce a single TIFF file for each OIB file (i.e. overlay 3 channels into
> one). I can easily do this manually but I have hundred of images and was
> wondering if there is a way to do this more efficiently.
>
> Have anyone ever batch processed OIB files without a z-series into single
> TIFF files?
>
> I am running Ubuntu 9.10 and Imagej 1.43b and am using the latest version
> of
> LOCI.
>
> Thanks in advance!
>
> Sam
>
> --
> *****************************************************
> Sam Albers
> Geography Program
> University of Northern British Columbia
> 3333 University Way
> Prince George, British Columbia
> Canada, V2N 4Z9
> phone: [phone]
> *****************************************************
>