[ome-devel] Fwd: Clear Bio-Formats 'split channels' in a macro

[Roger Leigh]

A bug in the bioformats imagej plugin?


-------- Forwarded Message --------
Subject: Clear Bio-Formats 'split channels' in a macro
Date: Thu, 8 Jan 2015 17:40:58 -0800
From: Glen MacDonald <glenmac at U.WASHINGTON.EDU>
Reply-To: imagej at LIST.NIH.GOV
To: IMAGEJ at LIST.NIH.GOV

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
(206) 616-4156
glenmac at uw.edu

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