openslide_read_region filling buffer with 0's for Mirax

[T. N.]

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
> 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/20200410/779f8358/attachment.html>