openslide-users Digest, Vol 115, Issue 6

Fri Apr 10 11:54:10 EDT 2020

I agree with Derek.
My company (www.kanteron.com) is vendor-neutral (we work with ALL scanners
in the market) and our software turns all and any scanner output into
DICOM. Some of our developers have been active/passive participants in
openslide and other FLOSS efforts.
We have customers in several countries (from Mexico to Thailand) using it
for primary diagnosis for years, with hundreds of slides per day.

When I hear "no pathologist will ever invest due to lack of return of
investment" it makes me sad. That's a pathologist comparing looking into a
microscope vs looking at a screen. BUT, how about all the other workflow
actions around it? It's all about Transaction Cost: search for a slide (by
patient name, or date), calculate how many types of staining per week, seek
a second opinion or teleconsultation, participate in a Multidisciplinary
Team (like Molecular Tumor Board), using thrid party advanced visualization
algorithms, applying ML/AI/analytics, population health, teaching... when
you consider the whole WORKFLOW (which our software provides, beyond just
image transformation, visualization and reporting), then return on
investment becomes VERY clear.

My two cents. [Relevant] self-promotion out.

Jorge Cortell
Founder & CEO
Kanteron Systems

On Fri, Apr 10, 2020 at 5:42 PM <
openslide-users-request at lists.andrew.cmu.edu> wrote:

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>    1. Re: openslide_read_region filling buffer with 0's for Mirax
>       (Derek Magee)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 Apr 2020 15:40:45 +0000
> From: Derek Magee <D.R.Magee at leeds.ac.uk>
> To: "PD Dr. med. M. Weihrauch" <m.weihrauch at smartinmedia.com>,
>         "jcupitt at gmail.com" <jcupitt at gmail.com>
> Cc: "openslide-users at lists.andrew.cmu.edu"
>         <openslide-users at lists.andrew.cmu.edu>
> Subject: Re: openslide_read_region filling buffer with 0's for Mirax
> Message-ID:
>         <
> DB6PR03MB3109C2A65348A52EC720BE9AE0DE0 at DB6PR03MB3109.eurprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="windows-1252"
>
> "no pathologist will ever invest due to lack of return of investment"
>
> For info we've digitised out entire clinical workflow in Leeds UK (1000+
> slides/day) using ~6 Leica-Aperio scanners (they will be replaced by 3
> higher capacity ones soon). There are a number of other institutions around
> the world that have done the same (Granada in Spain, Coventry in UK, The
> whole of Sweden, Some institutions in the Netherlands etc.). Most are using
> either Leica-Aperio or Hammamatsu scanners, and propriety formats. There
> are a few Phillips clinical sites coming online also. There is even the odd
> institute using DICOM. This is definitely the way forward for image
> standardisation. We're in a lot of discussions  with various parties
> regarding DICOM for Digital Pathology and I can tell you it's  a matter of
> when, not if, this will be supported by all the major scanner vendors as a
> native format. If people are interested (probably when the COVID thing is
> all over)  we have been sharing our experiences of this via various courses
> and publications. If people are in!
>  terested I can put you in touch with the appropriate people.
>
> BTW Metasystems (German company) have had a robot slide loader for 15
> years I'd say. It works with a regular microscope with a motorised stage. I
> think you'd be impressed with that also. It approaches the throughput of a
> dedicated slide scanner these days, and the system is only around E10-20K
> (not including the microscope)
>
> Derek
> ________________________________
> From: openslide-users <openslide-users-bounces+d.r.magee=
> leeds.ac.uk at lists.andrew.cmu.edu> on behalf of PD Dr. med. M. Weihrauch <
> m.weihrauch at smartinmedia.com>
> Sent: 10 April 2020 14:42
> To: jcupitt at gmail.com <jcupitt at gmail.com>
> Cc: openslide-users at lists.andrew.cmu.edu <
> openslide-users at lists.andrew.cmu.edu>
> Subject: AW: openslide_read_region filling buffer with 0's for Mirax
>
>
> The truth is (for Germany) that most scanners sold are still for isolated
> research projects. Digital pathology as a ?complete digitalization? of a
> diagnostic pathology institute is not yet happening. However, the ?game? is
> slowly starting now and there will be pressure coming from the doctors as
> soon as they want to interact with colleagues hitting a brick wall of
> vendor formats.
>
> I know that some of the vendors already have a hard time selling their
> scanners due to bad (non-open) formats.
>
>
>
> There are some great developments though (not yet marketing). One engineer
> husband of a dermatopathologist now builds his own scanners with a Kuka
> robot arm in between loading them. When I first saw this, I could not speak
> for 10 minutes ? it really was like this first iphone moment.
>
>
>
> After having scruitinized all available scanners on the market he quickly
> saw that NONE of them was ready for digitalizing 1,000 slides per day. Most
> scanner vendors do the same mistake: all 1,000 slides queue in front of
> only one objective. Or you buy 3 scanners (a 250,000?) to speed up the
> process, which no pathologist will ever invest due to lack of return of
> investment. Thus, he took his wife?s fate into his own hand and started
> constructing scanners. I really hope his small company will succeed.
>
>
>
> This is super intriguing and I can share a video to anyone interested (you
> can email me personally).
>
>
>
> He is using ? and John you will love this ? the SZI format ??
>
>
>
> Hope, things will change for the better, my company is working hard on
> that.
>
>
>
> Best
>
>
>
>
>
> Martin
>
>
>
>
>
>
>
> Von: openslide-users <openslide-users-bounces+m.weihrauch=
> smartinmedia.com at lists.andrew.cmu.edu> Im Auftrag von jcupitt at gmail.com
> Gesendet: Freitag, 10. April 2020 15:20
> Cc: openslide-users at lists.andrew.cmu.edu
> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax
>
>
>
> If people made good openslide support a "must have" feature when choosing
> a scanner, vendors might contribute code for their formats to the project,
> and perhaps even pay something towards maintenance.
>
>
>
> Unfortunately, it has not become a common requirement, and openslide is
> slowly becoming less relevant. I suspect vendors are (privately) delighted
> :(
>
>
>
> John
>
>
>
>
>
>
>
>
>
>
>
> On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch <
> m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com>> wrote:
>
> I just had a look at their SDK: There is C# and C++ parts, but everything
> is ?.sln? = Visual Studio based. I guess, it?s all for Windows really.
>
>
>
> God, when will all the vendors get real and implement one single common
> file format ? radiology made that happen 100 years ago? It?s like a jungle
> getting crazier by each day. It also seems like they are all competing, who
> can come up with an even worse format (Roche *.bif anyone? Different
> overlapping tile sizes of tiles with >1,000 pixels and an XML, which tells
> you how to rearrange that mess on the screen? / 3dHistech or Olympus with
> many files per slide, etc)?
>
> With better, faster and especially cheaper scanners, we could be 5 years
> in the future already.
>
>
>
> Sorry for letting off steam here ? totally off-topic ??
>
>
>
> Martin
>
>
>
> Von: Dr. M. Weihrauch <martin.weihrauch at uni-koeln.de<mailto:
> martin.weihrauch at uni-koeln.de>>
> Gesendet: Freitag, 10. April 2020 14:27
> An: T. N. <ca95129 at hotmail.com<mailto:ca95129 at hotmail.com>>; PD Dr. med.
> M. Weihrauch <m.weihrauch at smartinmedia.com<mailto:
> m.weihrauch at smartinmedia.com>>; openslide-users at lists.andrew.cmu.edu
> <mailto:openslide-users at lists.andrew.cmu.edu>
> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax
>
>
>
> I don't know. Their demo is in C#, but I doubt they are running .NET Core.
>
>
>
> I'll check once I havd the chance.
>
>
>
>
>
>
>
> Von meinem Samsung Galaxy Smartphone gesendet.
>
>
>
>
>
> -------- Urspr?ngliche Nachricht --------
>
> Von: "T. N." <ca95129 at hotmail.com<mailto:ca95129 at hotmail.com>>
>
> Datum: 10.04.20 13:35 (GMT+01:00)
>
> An: "PD Dr. med. M. Weihrauch" <m.weihrauch at smartinmedia.com<mailto:
> m.weihrauch at smartinmedia.com>>, openslide-users at lists.andrew.cmu.edu
> <mailto:openslide-users at lists.andrew.cmu.edu>
>
> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax
>
>
>
> Does the SDK from 3DHistech work on Linux?
>
> Thanks.
> thomas
>
> On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote:
>
> 3dHistech can also give you there SDK. it is somewhat buggy, but reads all
> files..
>
>
>
> best
>
>
>
> Martin
>
>
>
>
>
>
>
> Von meinem Samsung Galaxy Smartphone gesendet.
>
>
>
>
>
>
>
> -------- Urspr?ngliche Nachricht --------
>
> Von: "T. N." <ca95129 at hotmail.com><mailto:ca95129 at hotmail.com>
>
> Datum: 10.04.20 10:16 (GMT+01:00)
>
> An: openslide-users at lists.andrew.cmu.edu<mailto:
> openslide-users at lists.andrew.cmu.edu>
>
> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax
>
>
>
> I don't work with C interface, I just use the tools under Linux and
> recently  have problem with the Mirax files generated by the new 3DHistech
> scanner. The new file format does contain some extra information that
> OpenSlide rejects or doesn't understand. I read in other mailing lists that
> people have successfully use 3DHistech converter (free download from
> 3DHistech site) to convert from MIRAX format to MIRAX format (same format
> conversion) and can successfully use the converted file with OpenSlide. The
> converter basically removes the extra overlapping information from the
> file, This is an extra step that needs to be done on the scanner PC. Is
> there possibility that OpenSlide library can be updated to avoid this
> conversion step, eg, skipping the overlapping information in the new Mirax
> format.
>
> Regards,
> Thomas
>
> On 4/9/2020 11:21 PM, Terry Wilson wrote:
>
> I am using the C interface to the windows version of OpenSlide.  I have
> successfully used it to for a number of different formats, however, the
> same code does not appear to be working for Mirax slides.  I am able to
> open the slide and see the various properties, however, anytime I try
> calling openslide_read_region, it always just fills in the buffer with
> 0's.  According to the documentation that is an indication of some error,
> however, calling openslide_get_error immediately after just returns a null
> error object.
>
>
>
> I saw an older post from someone on this mailing list who seemed to have
> the exact same problem I am having with Mirax slides ... unfortunately they
> seemed to eventually get it working but had no idea what they changed to
> get it to work.  So I am looking for some suggestions on what to try.  I
> have tried retrieving all the data for the entire level 0 using a tile size
> of 512x512 and they all seem to come back with 0's.  I tried getting an
> entire higher level (level 6) with one call but same result.  I have also
> tried various different Mirax slides (including some of the demo ones from
> the OpenSlide site) The code is pretty simple:
>
>
>
> // Try reading a single tile
>
> // x, y values start at 0,0 and increase based on the tile size
>
> int size = 512;
>
>
>
> uint32_t *data = new uint32_t[size * size];
>
> openslide_read_region(openslide, data, x, y, 0, size, size);
> const char* err = openslide_get_error(openslide);
> if (err != NULL)
> {
>     printf("error detected");
> }
>
> I used openslide_get_property_names / openslide_get_property_value to dump
> out all the various metadata values for the slides ... is there some value
> in this metadata that I need to be accounting for (I assumed that the
> OpenSlide library was already doing that)? Any suggestions on how to
> trouble shoot this problem would be greatly appreciated.
>
>
>
> Regards,
>
>
>
> Terry
>
>
>
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