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Support for Pannoramic WRX slide format

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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Support for Pannoramic WRX slide format

Postby bzapiec » Tue May 15, 2012 4:19 pm

My lab has a 3DHisstech midi slide scanner whose slides as well as exported multi channel fluorescent images "MRX slides" are currently unsupported by Bioformats. During VIZBI Josh Moore this could eventually be rectified by contacting some of the brilliant people at OME/Glencoe to reverse engineer the format and get it supported - Melissa Linkert was named specifically as the person I should try and get in touch with. What is the procedure for this? I tried uploading a tiny sample MRX slide file (as a zip because it's really a bunch of small files) but every time the upload would finish the page would refresh and my post would disappear. If implementing support is indeed possible please let me know how I can provide the files and if I can in any way assist.

Many thanks in advance
- Bolek
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Re: Support for Pannoramic WRX slide format

Postby mlinkert » Tue May 15, 2012 4:43 pm

Hi Bolek,

My lab has a 3DHisstech midi slide scanner whose slides as well as exported multi channel fluorescent images "MRX slides" are currently unsupported by Bioformats. During VIZBI Josh Moore this could eventually be rectified by contacting some of the brilliant people at OME/Glencoe to reverse engineer the format and get it supported - Melissa Linkert was named specifically as the person I should try and get in touch with. What is the procedure for this? I tried uploading a tiny sample MRX slide file (as a zip because it's really a bunch of small files) but every time the upload would finish the page would refresh and my post would disappear. If implementing support is indeed possible please let me know how I can provide the files and if I can in any way assist.


These are datasets that contain .mrxs files, right? If so, we do have plans to support this data already, as noted in this ticket on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/4121

If you would like to be automatically notified of our progress, just let me know and I would be happy to CC you on that ticket.

We would certainly appreciate seeing any datasets that you are willing to send; I will send you information on how best to send files to the OME team in a private message.

Regards,
-Melissa
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Re: Support for Pannoramic WRX slide format

Postby bzapiec » Mon May 21, 2012 1:26 pm

HI Melissa,

Thanks for your reply - I have uploaded some sample images and would naturally love to hear if there's any progress or if I can be helpful toward attaining such. I imagine there are more pressing matters on the development list though but I know our lab would be keen to see this added. We are currently also running Aperio ScanScope FL scanners with a Spectrum database running in the back end. Setting up an Omero server for the MIDI scans and maybe even the aperio eventually as well would be pretty awesome!

thanks again!
Bolek
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Re: Support for Pannoramic WRX slide format

Postby mlinkert » Mon May 28, 2012 4:43 pm

Hi Bolek,

Thank you for sending an example dataset. We have had several people ask for this already, so it is fairly high on our list for after the upcoming 4.4 release.

Aperio data (I assume these are .svs files?) should already be supported by OMERO, but please let us know if you encounter any problems when trying it out.

Regards,
-Melissa
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Re: Support for Pannoramic WRX slide format

Postby blurpie » Mon Jul 30, 2012 8:05 am

Have you look at http://www.openslide.org yet? Could their code be ported to BioFormats?

Caveat: OpenSlide at present only supports MRXS 1.9 files. I know of at least 3 other versions that are in use: 1.8 (legacy), 2.0 (fluorescence data), 2.2 (most recent format; used by current installations w/ Win7 operating system)
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Re: Support for Pannoramic WRX slide format

Postby mlinkert » Mon Jul 30, 2012 4:41 pm

Code: Select all
Have you look at http://www.openslide.org yet? Could their code be ported to BioFormats?


We are aware of the OpenSlide project, but it is unlikely that the code there can be ported directly into Bio-Formats due to API differences. We will certainly consider using OpenSlide as a reference implementation once we have a chance to properly write support for Mirax datasets.

Regards,
-Melissa
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Re: Support for Pannoramic WRX slide format

Postby blurpie » Tue Jul 31, 2012 7:47 am

If you're looking for reference datasets, I can provide these, too.
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Re: Support for Pannoramic WRX slide format

Postby hflynn » Mon Jan 11, 2016 11:43 am

Anyone still interested in this topic may be interested to read our latest blog post which details the work we have put into this and explains why we have not yet delivered support,

Thanks,

The OME Team.
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