svs-file

[Malgorzata Swider]

Hello,
does anyone know how to open and EDIT svs-file in ImageJ?
Thanks,
MS

[No Name-4]

We looked into this a while back. You should be able to use the
LOCI-BioFormats plugin (http://www.loci.wisc.edu/bio-formats/imagej) to
open svs and many other formats.

The only problem with this is that there seems to be a limit in the size
of svs file that can be opened. Since this format is typically used for
whole-slide scans, which for us are 200-500Mb in size, we were not able to
use it to open up and process entire slides.

What we do as a workaround is to export the slide in CWS format (a folder
of image tiles) and batch process these in ImageJ. The pain with this is
that you lose the whole slide context for the markup/overlay image(s) and
if you need to edit the ROI, this is much easier to do on the whole slide
than 10s or 100s of tiles one at a time. CellProfiler apparently has some
support for svs files but I haven't tried it myself.

It would be fantastic if there was a beter solution for this. Someone
could write a plugin using the Aperio SDK... Any thoughts from the board?

Cheers,
Jim

Jim Deeds
Novartis Institute for BioMedical Research, Inc.
Oncology Translational Research US, Building 600 / 4C-421-01
250 Mass Avenue, Cambridge, MA 02139
[hidden email]
Tel: [phone]



Malgorzata Swider <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
11/04/2010 02:02 PM
Please respond to
ImageJ Interest Group <[hidden email]>


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Subject
svs-file






Hello,
does anyone know how to open and EDIT svs-file in ImageJ?
Thanks,
MS


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[Melissa Linkert-2]

Hi,

> We looked into this a while back. You should be able to use the
> LOCI-BioFormats plugin (http://www.loci.wisc.edu/bio-formats/imagej) to
> open svs and many other formats.
>
> The only problem with this is that there seems to be a limit in the size
> of svs file that can be opened. Since this format is typically used for
> whole-slide scans, which for us are 200-500Mb in size, we were not able to
> use it to open up and process entire slides.

You should be able to open sub-sections of an SVS file using Bio-Formats if you
select the "Crop on import" option in the "Bio-Formats Import Options"
window.  This is, of course, not entirely ideal as you still lose the
context of the entire slide, but it should at least allow you to skip
the extra step of exporting SVS files to CWS.

Regards,
-Melissa

On Thu, Nov 04, 2010 at 03:47:35PM -0500, [hidden email] wrote:

> We looked into this a while back. You should be able to use the
> LOCI-BioFormats plugin (http://www.loci.wisc.edu/bio-formats/imagej) to
> open svs and many other formats.
>
> The only problem with this is that there seems to be a limit in the size
> of svs file that can be opened. Since this format is typically used for
> whole-slide scans, which for us are 200-500Mb in size, we were not able to
> use it to open up and process entire slides.
>
> What we do as a workaround is to export the slide in CWS format (a folder
> of image tiles) and batch process these in ImageJ. The pain with this is
> that you lose the whole slide context for the markup/overlay image(s) and
> if you need to edit the ROI, this is much easier to do on the whole slide
> than 10s or 100s of tiles one at a time. CellProfiler apparently has some
> support for svs files but I haven't tried it myself.
>
> It would be fantastic if there was a beter solution for this. Someone
> could write a plugin using the Aperio SDK... Any thoughts from the board?
>
> Cheers,
> Jim
>
> Jim Deeds
> Novartis Institute for BioMedical Research, Inc.
> Oncology Translational Research US, Building 600 / 4C-421-01
> 250 Mass Avenue, Cambridge, MA 02139
> [hidden email]
> Tel: [phone]
>
>
>
> Malgorzata Swider <[hidden email]>
> Sent by: ImageJ Interest Group <[hidden email]>
> 11/04/2010 02:02 PM
> Please respond to
> ImageJ Interest Group <[hidden email]>
>
>
> To
> [hidden email]
> cc
>
> Subject
> svs-file
>
>
>
>
>
>
> Hello,
> does anyone know how to open and EDIT svs-file in ImageJ?
> Thanks,
> MS
>
>
> _________________________
>
> CONFIDENTIALITY NOTICE
>
> The information contained in this e-mail message is intended only for the
> exclusive use of the individual or entity named above and may contain
> information that is privileged, confidential or exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient, or the employee or agent responsible for delivery of the
> message to the intended recipient, you are hereby notified that any
> dissemination, distribution or copying of this communication is strictly
> prohibited. If you have received this communication in error, please
> notify the sender immediately by e-mail and delete the material from any
> computer.  Thank you.