Open Microscopy Environment

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

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

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

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

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)

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

If you're looking for reference datasets, I can provide these, too.

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.