Re: Importing files from SlideBook

Posted by Glen MacDonald-2 on Sep 06, 2013; 4:55pm
URL: http://imagej.273.s1.nabble.com/Importing-files-from-SlideBook-tp5004666p5004703.html

Hi Leonicio,
Slidebook files will open with the LOCI plugin, more or less.  Almost always 1 or 2 images in a .sld file are mangled, even though they open properly with SB.  
Our usual workaround is to export  as 16-bit TIFF. (Image->Export->All intensities as 16-bit tiff).  You can delete unneeded filename parameters.  The checkbox for XML headers creates an OME-tiff that LOCI imports with preservation of metadata.  If needed, a macro can automate remerging the channels into Composite images.

Regards,
Glen
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
[phone]
[hidden email]







On Sep 5, 2013, at 7:04 AM, Johannes Schindelin <[hidden email]> wrote:

> Hi Leonico,
>
> On Thu, 5 Sep 2013, Vergara, Leoncio A. wrote:
>
>> I was wondering if there is any way to directly import SlideBook images
>> into ImageJ keeping calibrations, etc? So far the only solution we have
>> is to export from slide book into TIFF files, but this complicates some
>> of our users.
>
> I binged the terms "slidebook" and "format" and found this link:
>
> http://dev.loci.wisc.edu/trac/software/browser/trunk/loci/formats/doc/slidebook.html?rev=2938
>
> suggesting that you can open that format with the Bio-Formats Importer:
> http://loci.wisc.edu/software/bio-formats
>
> Ciao,
> Johannes
>
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