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Re: Bioformats importer in macro

Posted by ctrueden on May 10, 2017; 9:11pm
URL: http://imagej.273.s1.nabble.com/Bioformats-importer-in-macro-tp5018696p5018697.html

Hi Ed,

> Is there a parameter that will open all series?

Yes, the "Open all series" option.

This records to macro something like:

   run("Bio-Formats", "open=" + myFile + " autoscale color_mode=Default
open_all_series rois_import=[ROI manager] view=Hyperstack
stack_order=XYCZT");

If you need to customize which series get opened in a dynamic way, you can
use the Bio-Formats Macro Extensions to get the number of series via
the Ext.getSeriesCount(seriesCount) command. From that, you could
concatenate a string variable in a loop to build up which series get
included.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
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On Wed, May 10, 2017 at 4:00 PM, Ed Siefker <[hidden email]> wrote:

> I would like to import a multi scene .czi file into ImageJ with a macro.
> I can't predict the number of series in the file.
>
> When using the GUI there is a "select all" function.  Looking at the
> macro recorder, it passes a parameter for each series.  Since I can't
> predict the number of series, I can't pass a parameter for each.
>
> Is there a parameter that will open all series?
> -Ed
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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