Clear Bio-Formats 'split channels' in a macro

Posted by Glen MacDonald-2 on Jan 09, 2015; 1:40am
URL: http://imagej.273.s1.nabble.com/Clear-Bio-Formats-split-channels-in-a-macro-tp5011146.html

Hello,
I’ve encountered  the following behavior difference in calling Bio-formats manually versus from a macro. If someone runs Bio-Formats from the plugins menu and checks ‘split_channels’, that option is not cleared if subsequently Bio-formats is called from a macro that is not intended to split channels.  

for example, run from macro to split channels:
 run(“Bio-Formats Importer”,”open=[bunchastuff] color_moded=Grayscale split_channels view=Hyperstack stack_order=default”); -> splits channels

then  run from macro to NOT split channels:
 run(“Bio-Formats Importer”,”open=[bunchastuff] color_moded=Grayscale  view=Hyperstack stack_order=default”); -> does not split channels

Now, open Bio-Formats from plugins menu, manually select ‘split channels’ -> splits channels

then run from macro to NOT split channels:
 run(“Bio-Formats Importer”,”open=[bunchastuff] color_moded=Grayscale  view=Hyperstack stack_order=default”); ->  still splits channels

Is there a way around this?

thanks,

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

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