Importing files from SlideBook

[Vergara, Leoncio A.]

Good morning

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.

Thanks in advance for your help

Leoncio

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[dscho]

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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[ctrueden]

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

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[Glen MacDonald-2]

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

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