Re: Importing files from SlideBook

Posted by ctrueden on Sep 05, 2013; 4:35pm
URL: http://imagej.273.s1.nabble.com/Importing-files-from-SlideBook-tp5004666p5004681.html

Hi Leoncio,

> you can open that format with the Bio-Formats Importer

Indeed, Bio-Formats does support the SlideBook format:

https://www.openmicroscopy.org/site/support/bio-formats4/formats/3i-slidebook.html

However, please take note of the following blurb from the Bio-Formats web
site:

"We strongly encourage users to export their .sld files to OME-TIFF using
the SlideBook software. Bio-Formats is not likely to support the full range
of metadata that is included in .sld files, and so exporting to OME-TIFF
from SlideBook is the best way to ensure that all metadata is preserved.

The reason is that SlideBook is a closed and proprietary, extremely
complex, often-changing format. The Bio-Formats and 3i teams both recommend
exporting to OME-TIFF instead of importing .sld files directly into ImageJ.

That said, we certainly appreciate that performing this extra export step
can be burdensome. If your workflow is negatively impacted by this
necessity, I encourage you to raise the issue with 3i, so that they can
better support your requirements.

By the way, in case you didn't know: the Bio-Formats plugins come bundled
with the Fiji distribution of ImageJ (http://fiji.sc/). Installing Fiji is
the easiest way to start using Bio-Formats.

Regards,
Curtis


On Thu, Sep 5, 2013 at 9:04 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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>

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