[ome-users] NullPointerException on line 176

[Sebastien Besson (Staff)]

Hi Konrad,

Thanks for getting back to us. The fix for this issue is targetted for our next major version of
Bio-Formats 6 which has been the primary object of our efforts over the past months. We are
expecting to have Bio-Formats 6.0.0 released in the upcoming weeks including the Hamamatsu
NDPI fix.

The first version of OMERO including Bio-Formats 6 will also contain this fix. At this stage, this
Is likely going to be OMERO 5.5 due later in the first half of 2019.

Thanks for sending another sample file. We will add it to our curated QA repository to complete
the testing. Can this representative file also be made public under CC-BY license [1] ?

Best,
Sebastien

[1] https://downloads.openmicroscopy.org/images/Hamamatsu-NDPI/


On 8 Feb 2019, at 12:26, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de<mailto:Konrad.Koelble at uk-erlangen.de>> wrote:

Hi,
since last October's HAMAMATSU NDP.scan 3.2 "update" (see below) between 10-30% of our brightfield *.ndpi uploads using
OMERO.insight-5.4.1-ice36-b75-win, Build: November 22, 2017 08:40 PM
fail to render in OMERO.web 5.4.6-ice36-b87.
This may be due to a NullPointerException on line 176, with the `markers` variable being null.

You'll find a 2.6GB
06-T05322_1A_HEc.ndpi
as an example of such a fail2show under
https://volafile.org/r/pmbwqedm

According to
https://github.com/openmicroscopy/bioformats/pull/3248
sbesson added this to the 6.0.0
(/openmicroscopy/bioformats/milestone/64)
milestone on 1 Nov 2018 (#event-1940568024)

Any progress and/or has this issue been solved in 5.4.10?

Cheers
Konrad
________________________________________
Von: Kölble, Konrad
Gesendet: Dienstag, 16. Oktober 2018 13:53
An: OME User Support List
Betreff: Insight uploaded BF *.ndpi fails to render in

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


The University of Dundee is a registered Scottish Charity, No: SC015096
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