3D Histech on Openslide?

[Derek Magee]

I’m not sure if this is relevant, but HeteroGenius MIM supports working with 3D stacks and can read individual mrxs slides (via openslide), allowing 3D annotation/visualisation and export:

http://www.medicalimagemanager.com/static/MIM/features/3d/index.html

let me know if you want more information. We have a lot of experience working with 3D stacks here in Leeds.

Yours

Derek Magee

From: openslide-users [mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk at lists.andrew.cmu.edu] On Behalf Of Peter via openslide-users
Sent: 20 January 2017 20:41
To: coleman at proscia.com
Cc: openslide-users at lists.andrew.cmu.edu
Subject: RE: 3D Histech on Openslide?

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<mailto: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>


=====================================================================

Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.

_______________________________________________
openslide-users mailing list
openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>
https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users



--
Coleman

=====================================================================

Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20170123/282b94fd/attachment-0001.html>