3D Histech on Openslide?

[schueffp at mskcc.org]

Thank you for the fast response.

I meant the first case, three-dimensional reconstructions from serial sections, generated by a 3D Histech scanner. Such that openslide has another handle in which one can adjust the z-layer.

Best,
Peter

From: Coleman Stavish [mailto:coleman at proscia.com]
Sent: Friday, January 20, 2017 3:30 PM
To: Schueffler, Peter/Sloan Kettering Institute
Cc: openslide-users at lists.andrew.cmu.edu
Subject: Re: 3D Histech on Openslide?

Hi Peter,

To be clear, do you mean three-dimensional tissue reconstructions from serial sections? Or do you mean the standard 2D WSI captured by a 3DHISTECH scanner?

If you're referring to the latter, Openslide officially supports the MIRAX (.mrxs) format that most if not all 3DHISTECH scanners output. From my experience, the 3DHISTECH software exports a single WSI as a directory of many files, one of which has the extension ".mrxs". In order for Openslide to successfully read the MIRAX image, the .mrxs file must exist in the same parent directory as the directory containing the .dat files. Further, that directory must have the same name (without the extension) as the .mrxs file. More information can be found here: http://openslide.org/formats/mirax/

Illustrated poorly, an example structure that Openslide could read would look like this:

Slide.mrxs
Slide/
  -> Data0000.dat
  -> Data0001.dat
  -> ...
  -> Index.dat
  -> Slidedat.ini

While supporting one of our clients with a 3DHISTECH scanner and software, we found that MIRAX images exported using the 3DHISTECH "batch export" feature were in some way malformed, and Openslide failed to read them. The same images exported one at a time had no problems. The only noticeable difference at first glance was that the .dat files were in a different order dependent on whether the image was batch-exported or solo-exported. This may not affect you, but I thought I would share it with the mailing list.

Best,
Coleman


Coleman Stavish
Chief Technology Officer
Proscia Inc.
coleman at proscia.com<mailto:coleman at proscia.com>
https://proscia.com

On Fri, Jan 20, 2017 at 3:00 PM, Peter via openslide-users <openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>> wrote:
Is it possible to view 3D Slides (e.g. 3D Histech from Mirax) with openslide?

If not, how could that be implemented? What would you need for that? An example slide?

Best,
Peter

Dr. Peter J. Schueffler
Postdoctoral Researcher
MSKCC, Computational Pathology Lab
485 Lexington Ave
New York, NY 10017
+1-646-888-8116<tel:(646)%20888-8116>
schueffp at mskcc.org<mailto:schueffp at mskcc.org>
www.thomasfuchslab.org<http://www.thomasfuchslab.org>


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--
Coleman

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