Re: Using the Bioformats importer to open .ims files in a macro

Posted by David Gault (Staff) on Sep 19, 2018; 9:31am
URL: http://imagej.273.s1.nabble.com/Using-the-Bioformats-importer-to-open-ims-files-in-a-macro-tp5021199p5021201.html

Hi Jacqueline,

You can find some examples of Bio-Formats macros at https://docs.openmicroscopy.org/bio-formats/5.8.2/users/imagej/#macros-and-plugins
To select the other resolutions you will need to set the Series, using Ext.setSeries(seriesNum) as in https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/utils/macros/basicMetadata.txt

With Thanks,
David Gault

On 19 Sep 2018, at 01:59, Jacqueline Ross <[hidden email]<mailto:[hidden email]>> wrote:

Hi everyone,

Our slide-scanner has an option to save files as .ims (Imaris) format. This allows us to open the files in ImageJ at different resolution levels.

I'm trying to write a macro that will open the files at "Resolution Level 2" rather than Level 1 (which is the highest) and just can't seem to get this to work.

Has anyone done this already and is willing to share the code?

It would be similar for those opening Leica .lif files where you can select the Series number.

Thanks!

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit (BIRU)
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Telephone: Ext 87438; DDI:  [phone]

Website:    http://www.auckland.ac.nz/biru




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


The University of Dundee is a registered Scottish Charity, No: SC015096

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