Help with viewing slides on the web

Wed Feb 7 10:29:14 EST 2018

+1 to this proposal. We’d be up for contributing some funds to support a developer as well. I’m also keeping an eye out for someone local, and if we find one, will definitely appreciate help from Benjamin.

Completely agree with Derek’s comments. I would like to see support for Z-stacks.

Amongst formats, would really like Olympus VSI. Derek is your code open source?

Typos via iPhnoe

-Ashish Sharma
Assistant Professor
Department of Biomedical Informatics
Emory University
________________________________
From: openslide-users <openslide-users-bounces+ashish.sharma=emory.edu at lists.andrew.cmu.edu> on behalf of schueffp at mskcc.org <schueffp at mskcc.org>
Sent: Wednesday, February 7, 2018 9:43:14 AM
To: openslide-users at lists.andrew.cmu.edu
Subject: RE: Help with viewing slides on the web

Yes very good idea,

don't forget the z-layers, as Derek already mentioned.

E.g.:

MRXS's z-layers (3D Histech) should maybe not be too difficult, as it is an extension of the already existing MRXS format.

Best,
  Peter

From: openslide-users [mailto:openslide-users-bounces+schueffp=mskcc.org at lists.andrew.cmu.edu] On Behalf Of Derek Magee
Sent: Wednesday, February 07, 2018 8:52 AM
To: PD Dr. M. Weihrauch <m.weihrauch at smartinmedia.com>; openslide-users at lists.andrew.cmu.edu
Subject: [EXTERNAL] RE: Help with viewing slides on the web

My 2p, with tentative, but slightly reluctant interest…

Formats openslide should probably support and doesn’t (probably non exclusive list):

Zeiss – There’s already a zeiss driver, it’s just not in the main openslide build for reasons to do with NDAs. It works well actually!

Olympus – We wrote our own (non-openslide) driver already. It’s a pretty simple format to reverse engineer (tiff based with some external binary files for the big images).

Precipoint – Again some sort of openslide driver already exists (all be it only supporting jpeg .. does anyone know if these scanners actually output anything else? Png/bmp/jp2???). The jury is out on whether this is production ready until I see some image files.

DICOM – Some work was done on this but the code is very flaky (lots of asserts rather than proper error checking that cause your code to exit, assumptions about filename conventions, reliance on existence of dicomdir file, etc.). This one I wouldn’t use in production! I’d say this needs re-writing properly.

Roche BIF – This is supported but broken (due to non uniform grid of tiles assumed to be uniform). It is on my TODO list to look at, but it took me about a day to get my head round building openslide and how the code is structured and I haven’t had time to look at it since (it’s not that high up the TODO list).

Also:

One big disadvantage with openslide currently is that it doesn’t support multi z-plane images (there is no API let alone any code). There are no plns to fix this.  Many vendors (Aperio, Hammamatsu, 3D Histech, Olympus to name a few) can produce these. In fact the lack of supports is variable as some drivers just take the first plane, and others cannot read such files at all.  I see no point (from our point of view) in putting resources into openslide supporting new formats unless this issue is sorted. We have a project that requires this for Aperio and/or Hamamatsu (at least) coming up, so this is on my mind to look at.

Derek

From: openslide-users [mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk at lists.andrew.cmu.edu] On Behalf Of PD Dr. M. Weihrauch
Sent: 07 February 2018 09:32
To: openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>
Subject: Re: Help with viewing slides on the web

Guys:

Why don't the companies, which read this list (among which is mine) throw together money, hire a full time developer for a year, who integrates all of these currently foreign slide formats that are still missing into OpenSlide (e. g. Olympus, Zeiss, Precipoint, etc pp)?

We can get someone e. g. in Germany for €60k /year  incl. all costs. If there are 6 or more companies here, each pays €10k. I'd be totally up for it.

Martin

Am 07.02.2018 um 10:06 schrieb Yves Sucaet:

Hi Jen,

It seems some work on this was done already in the past:

https://github.com/openslide/openslide/issues/168

Unfortunately, the sample files mentioned in the thread don't seem to exist

anymore and were never added to the repo at

http://openslide.cs.cmu.edu/download/openslide-testdata/ (possibly the

licensing was never resolved?).

Could you help us help you by providing some new sample files?

Thanks in advance,

Yves Sucaet

------ Original Message ------

Received: 09:23 AM CET, 02/07/2018

From: Jen Wei Ying <jenweiying at gmail.com><mailto:jenweiying at gmail.com>

To: openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>

Subject: Help with viewing slides on the web

Hello,

I’m so sorry to trouble but I’m very new at this and was wondering if

anyone could help me. I have a small bank of slides scanned using

Precipoint software. The scans are saved in .vmic format. I want to share

the slides with other members of my department using a web-based slide

viewer. We are currently sharing our case log using a WordPress platform.

Does anyone know of any way in which I can make a web-based viewer directly

from a .vmic file? I tried converting it to TIFF format using ConvertPoint,

but the resulting image file is so large that most software can’t open

it.

I would be really grateful for any help!

Thank you,

Jen

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