macro using bio formats to open ND2 files with image series

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macro using bio formats to open ND2 files with image series

Leoncio Vergara
Hi

I am trying to write a macro to open ND2 files that contain multiple image series (locations). I was wondering if there is a way to open them using bioformats macro extensions without calling the bioformats importer plugin. I haven't been able to find an answer in the bio-formats documentation website. The macro examples deal with hyperstacks with multiple channels, time points and z planes, but only open the first series on multiple series files. I have been able to work with multiple series using macro extensions to read the number of series in the files and then use the "recorder" to get the command to call the importer, but I was wondering if there is a way to open the data set only with macro extensions.

Thank in advance for any information.

L Vergara
Houston, Texas

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Re: macro using bio formats to open ND2 files with image series

David Gault (Staff)
Hi Leoncio,

You can use the macro extensions to open the image series by using getSeriesCount and setSeries.
The below example shows how to iterate over the available series and set which series Bio-Formats will read:
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/utils/macros/basicMetadata.txt

With Thanks,
David Gault

On 9 Jul 2018, at 23:21, Leoncio Vergara <[hidden email]<mailto:[hidden email]>> wrote:

Hi

I am trying to write a macro to open ND2 files that contain multiple image series (locations). I was wondering if there is a way to open them using bioformats macro extensions without calling the bioformats importer plugin. I haven't been able to find an answer in the bio-formats documentation website. The macro examples deal with hyperstacks with multiple channels, time points and z planes, but only open the first series on multiple series files. I have been able to work with multiple series using macro extensions to read the number of series in the files and then use the "recorder" to get the command to call the importer, but I was wondering if there is a way to open the data set only with macro extensions.

Thank in advance for any information.

L Vergara
Houston, Texas

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