[ome-users] Bio-Formats CZI stitching issue

[David Gault (Staff)]

Hi Stephane,

Thank you for reporting the issue and providing a sample file. With the uploaded QA file and the latest Bio-Formats release I was able to reproduce the issues with only the metadata for the first series using spatial positions.
I have opened a new Trello card on the Bio-Formats inbox for tracking this issue: https://trello.com/c/XzUvcdPf/220-czi-incorrect-positions

With Thanks,
David Gault

On 9 Feb 2018, at 15:20, Stephane Dallongeville <stephane.dallongeville at pasteur.fr<mailto:stephane.dallongeville at pasteur.fr>> wrote:

Dear Bio-Formats team,

I got an error when i try to open a CZI dataset through TileStitcher.
I uploaded the dataset as 2.czi on your sample database.

The error i obtain is the following one :

<<
java.lang.NullPointerException
    at ome.units.quantity.Length.compareTo(Length.java:150)
    at ome.units.quantity.Length.compareTo(Length.java:35)
    at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:290)
    at java.util.ComparableTimSort.sort(ComparableTimSort.java:157)
    at java.util.ComparableTimSort.sort(ComparableTimSort.java:146)
    at java.util.Arrays.sort(Arrays.java:472)
    at loci.formats.TileStitcher.setId(TileStitcher.java:290)
    at plugins.kernel.importer.LociImporterPlugin.openReader(LociImporterPlugin.java:897)
    at plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:814)
>>

It looks like the Plane X,Y position informations from Metadata are not correctly retrieved for series #1, #2, #3 (time based position instead of spacial position) but series #0 is ok, because of that positions become not anymore comparable which make that exception to appear.

Note that I tested with last Bio-Formats version.

Best,

--
Stephane Dallongeville
Unité d'Analyse d'Images Biologiques
CNRS UMR 3691
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15 (FRANCE)

Tel: +33 (0)1 45 68 87 01
Fax: +33 (0)1 40 61 33 30

http://www.bioimageanalysis.org/

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180212/91d08200/attachment.html>