openslide_read_region filling buffer with 0's for Mirax

Fri Apr 10 10:55:26 EDT 2020

Hi,

I agree that the format situation is a mess.
SZI is indeed great. Have you considered extending it to use WEBP? It could save half the space. Or other jpeg replacement.

Regards,
Jan Hudecek

From: openslide-users [mailto:openslide-users-bounces+j.hudecek=nki.nl at lists.andrew.cmu.edu] On Behalf Of PD Dr. med. M. Weihrauch
Sent: vrijdag 10 april 2020 15:43
To: jcupitt at gmail.com
Cc: 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.

-------- Ursprüngliche 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.

-------- Ursprüngliche 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

_______________________________________________

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
_______________________________________________
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20200410/a27a5698/attachment-0001.html>