3D Histech on Openslide?

[Coleman Stavish]

To my knowledge, Openslide cannot read data from alternate focal planes or
handle z-stack images (see: https://github.com/openslide/openslide/issues/31).
>From that discussion, it seems like a non-negligible work would be required
to add that sort of functionality to the API. However, I don't think the
public Openslide dataset has any multiplane MIRAX images, so if you are
able to contribute one publicly, I'm sure the project would appreciate it.

Coleman

On Fri, Jan 20, 2017 at 3:41 PM, <schueffp at mskcc.org> wrote:

> 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
>
> https://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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>
> --
>
> Coleman
>
> =====================================================================
>
> Please note that this e-mail and any files transmitted from
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> responsible for delivering this message to the intended recipient,
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-- 
Coleman
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