AW: openslide_read_region filling buffer with 0's for Mirax

Fri Apr 10 09:02:29 EDT 2020

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>
Gesendet: Freitag, 10. April 2020 14:27
An: T. N. <ca95129 at hotmail.com>; PD Dr. med. M. Weihrauch <m.weihrauch at smartinmedia.com>; 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.

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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.

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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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