3D Histech on Openslide?

Coleman Stavish coleman at proscia.com
Fri Jan 20 15:30:09 EST 2017

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

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:

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

  -> 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


Coleman Stavish
Chief Technology Officer
Proscia Inc.
coleman at proscia.com

On Fri, Jan 20, 2017 at 3:00 PM, Peter via openslide-users <
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 <(646)%20888-8116>
> *schueffp at mskcc.org <schueffp at mskcc.org>*
> *www.thomasfuchslab.org <http://www.thomasfuchslab.org>*
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