[ome-users] ND2 position meta data with bioformats 5.1.1

[Enno R. Oldewurtel]

Dear Balaji,

I just upload some nd2 files: QA Bug #11064
I, also, added txt and xlsx files with the corresponding meta-data exported
by NIS-elements.

Hope this helps! It would be great to stay updated on this issue. Many
thanks,
Enno

On Thu, May 7, 2015 at 12:23 PM, Balaji Ramalingam (Staff) <
b.ramalingam at dundee.ac.uk> wrote:

>  Dear Enno,
>
>  Thank you for reporting the issue.
> Unfortunately, we were not able to reproduce the same with the files that
> we had locally (with Bio-Formats 5.1.1/5.1.2).
>
>  As suggested, it would help us troubleshoot the issue better, if you
> could submit your file to our QA system.
> https://www.openmicroscopy.org/qa2/qa/upload/
>
>  Best,
> Balaji
>
>
>
>  __________________
>
> Mr Balaji Ramalingam
>
> Software Developer
>
> OME Team
>
> College of Life Sciences
>
> University of Dundee
>
>   From: "Enno R. Oldewurtel" <enno.oldewurtel at uni-koeln.de>
> Date: Tuesday, 5 May 2015 14:16
> To: Balaji Ramalingam <b.ramalingam at dundee.ac.uk>
> Cc: Melissa Linkert <melissa at glencoesoftware.com>, "OME-users
> ome-users at lists.openmicroscopy.org.uk" <
> ome-users at lists.openmicroscopy.org.uk>
> Subject: ND2 position meta data with bioformats 5.1.1
>
>       Dear Balaji and Melissa,
>
>  firstly thanks for your great effort regarding bioformats! Following is
> a problem, which I believe could be another bug:
>
>  last year I submitted a problem about wrong indexing of x,y data of nd2
> files (#12569: BUG: ND2 files - x,y position of the different multi
> points returned in the wrong order).
>
>  I still use matlab for loading nd2 files and retrieve metadata with
> commands like:
>
> r = loci.formats.ChannelFiller();
> r = loci.formats.ChannelSeparator(r);
> r.setMetadataStore(loci.formats.MetadataTools.createOMEXMLMetadata());
> r.setId( FileName);
> metadata=r.getMetadataStore();
>  i=positionIndex;
>  j=loci.formats.FormatTools.getIndex(r, z, channel, time)
>  x=double(metadata.getPlanePositionX(i,j).value)
>  t=double(metadata.getPlaneDeltaT(i,j).value)
>
>  Position data for x,y,z retrieved with 5.1.1 for the nd2 file I submitted
> with my previous problem, are correct now. However, time-points retrieved
> with metadata.getPlaneDeltaT(i,j) in the same manner are in the wrong order.
>
> Furthermore the position data for nd2 files acquired with several z-slices
> is wrongly indexed. I have an example nd2 files with T(1) x XY(8) x Z(4)
> dimensions. Version 5.0.3 shows the correct order of 4 z-steps at the first
> XY position, which is then repeated at the remaining 7 positions. Version
> 5.1.1 shows the x,y,z values jumping about in the wrong order.
>
>  As an aside: I noted that with 5.1.1 the number of the dimensions of nd2
> files with all four T, XY, Z and lambda dimensions are correctly
> identified. Previously I could only use bioformats with 3 different types
> of dimensions. However, as soon as an nd2 files is modified and saved in
> NIS elements, the numbers of the dimensions are not correct anymore.
>
>  I can supply example nd2 files if needed, but will need to upload them
> via the qa system.
>
>  Hope this helps, and again many thanks for maintaining and developing
> such a great product!
>
>  Best,
>  Enno
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Enno R. Oldewurtel
AG Prof. B. Maier / Biophysics Group
Biozentrum
Universitaet zu Koeln
Zuelpicher Str. 47b
50674 Koeln

enno.oldewurtel at uni-koeln.de
Tel: +49-221-470-8048
Fax: +49-221-470-6230
http://www.biophysics.uni-koeln.de/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150508/9f87068d/attachment.html>