openslide_read_region filling buffer with 0's for Mirax

[T. N.]

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>
> Datum: 10.04.20 10:16 (GMT+01:00)
> An: 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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>> openslide-users at lists.andrew.cmu.edu
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