Clear Bio-Formats 'split channels' in a macro

[Glen MacDonald-2]

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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[Jason Swedlow-2]

Hi Glen-

Thanks for your email-- this might be a bug in Bio-Formats.  Can you
address this question the Bio-Formats developers at

http://www.openmicroscopy.org/community/

Cheers,

Jason


On Fri, Jan 9, 2015 at 1:40 AM, Glen MacDonald <[hidden email]>
wrote:

> 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]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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