[ome-users] Release of Bio-Formats 6.1.0

[Sebastien Besson (Staff)]

Hi Konrad,

As you probably saw in the release announcement [1], a large portion of the Bio-Formats 6.1.0 work was targeted towards the integration of the library into OMERO 5.5 due in the upcoming week as well as adding support for the BigDataViewer format. Several in-progress fixes, including the one you raised a few months ago, were not ready for inclusion.

With the 6.1.0 release behind us, our priority for the next few weeks is to focus on the backlog of open contributions, integrating everything that passes our QA process as patch releases. The NDPI fix is still blocked on making it backwards compatible with all our Hamamatsu NDPI samples but we expect a resolution soon. As before, you can follow the work at https://github.com/openmicroscopy/bioformats/pull/3248.

We understand your frustration with this process. In OME, it’s always true we have a large and growing backlog, especially in supporting proprietary file formats. Hamamatsu NDPI is an important file format, and has many users. Our overarching view on proprietary file formats (PFFs) from commercial vendors is published [2]. We are always interested in working with these partners to ensure long-term, durable support for PFFs in Bio-Formats.

Best,
Sebastien

[1] https://www.openmicroscopy.org/2019/05/20/bio-formats-6-1-0.html
[2] http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/

On 23 May 2019, at 20:33, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de<mailto:Konrad.Koelble at uk-erlangen.de>> wrote:

Hi All,
does 6.1.0 fix the NDPI issue noticed last October?

Cheers
Konrad

Von: ome-users [ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>]" im Auftrag von "David Gault (Staff) [d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>]
Gesendet: Montag, 20. Mai 2019 17:02
An: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Betreff: [ome-users] Release of Bio-Formats 6.1.0

Dear all,
Today we are releasing Bio-Formats 6.1.0. This latest release contains the completion of Phase I of OME’s work on improved support for binary vessels. In addition to the KLB format we supported in version 6.0, we have now added a BigDataViewer reader...

We’ve also worked to improve the integration of Bio-Formats 6.1 into OMERO 5.5 (to be released Summer 2019). Finally, we’ve also reviewed and updated many of Bio-Formats dependencies to align them with the Fiji ecosystem...
File format fixes and improvements:
...
removed header key from original metadata
Hamamatsu VMS
...
________________________________________
Von: ome-users [ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>]" im Auftrag von "David Gault (Staff) [d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>]
Gesendet: Mittwoch, 17. Oktober 2018 12:06
An: OME User Support List
Betreff: Re: [ome-users] Insight uploaded BF *.ndpi fails to render in

Hi Konrad,

Thank you for reporting this bug and providing a sample file to test.
I was able to reproduce the issue and it was being caused by a bug in the Bio-Formats reader.
I have opened a PR to fix the issue which will be reviewed and tested for inclusion in a future release: https://github.com/openmicroscopy/bioformats/pull/3248

With Thanks,
David Gault

On 16 Oct 2018, at 12:53, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de<mailto:Konrad.Koelble at uk-erlangen.de>> wrote:

Hi,
recently about 10% of our brightfield *.ndpi uploads using OMERO.insight-5.4.1-ice36-b75-win
fail to render in OMERO.web 5.4.6-ice36-b87. You'll find a 2.6GB
06-T05322_1A_HEc.ndpi
as an example of such a fail2show under https://volafile.org/r/pmbwqedm

Cheers
Konrad
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