[ome-users] BFail.ndpi solved in Bio-Formats 6.0.1?

[David Gault (Staff)]

Hi Konrad,

Unfortunately we do not yet have a working fix for that NDPI issue (https://trello.com/c/1jxzzrWk/1-ndpi-null-pointer-exception). We have also had other reports for this issue from other users and as such we did dedicate a significant amount of time in trying to find a solution in time for the 6.0.1 release. So far we have not yet been able to find a suitable fix but we are continuing to work to solve the issue as best we can.

With Thanks,
David Gault

On 15 Mar 2019, at 09:59, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de<mailto:Konrad.Koelble at uk-erlangen.de>> wrote:

Hi All,
does 6.0.1 include the NDPI issue fix I have been moaning about (though not ONLY publicly) since last October?

Cheers
Konrad

Von: Confocal Microscopy List [CONFOCALMICROSCOPY at LISTS.UMN.EDU<mailto:CONFOCALMICROSCOPY at LISTS.UMN.EDU>]" im Auftrag von "David Gault (Staff) [d.gault at DUNDEE.AC.UK<mailto:d.gault at DUNDEE.AC.UK>]
Gesendet: Donnerstag, 14. März 2019 16:44
An: CONFOCALMICROSCOPY at LISTS.UMN.EDU<mailto:CONFOCALMICROSCOPY at LISTS.UMN.EDU>
Betreff: Release of Bio-Formats 6.0.1
...
File format fixes and improvements:
...
 *   Hamamatsu ndpi
    *   improved handling of variants where a constituent NDPI has no wavelength
...
 *   TIFF
    *   improved handling of direct tile copying to prevent invalid images
    *   improved handling of tiles in scenarios of an invalid offset or byte count of 0
...

________________________________________
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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