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Bioformats importer in macro

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Bioformats importer in macro

Ed Siefker
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

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Re: Bioformats importer in macro

ctrueden
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
Did you know ImageJ has a forum? http://forum.imagej.net/


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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Re: Bioformats importer in macro

Aryeh Weiss
On 11/05/2017 0:11, Curtis Rueden wrote:

> 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.
Here is an example of what Curtis suggested:

// The Bio-Formats extensions enable us to get the image dimensions,
number of series
// and other metadata without actually opening the images.
run("Bio-Formats Macro Extensions");
Ext.setId(inputPath);

Ext.getSeriesCount(seriesCount);
print(seriesCount);

Ext.getSizeX(sizeX);
Ext.getSizeY(sizeY);
Ext.getPixelType(pixelType);

// j is a loop variable -- I was opening each series in a loop to
individually process each series
run("Bio-Formats Importer", "open=["+inputPath+"] autoscale
color_mode=Default view=Hyperstack stack_order=XYCZT series_"+d2s(j,0));

inputId = getImageID();    // always grab the ID and title of the opened
image


Best regards
--aryeh

> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> 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
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>


--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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