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

[Balaji Ramalingam (Staff)]

Hi,

Thank you for uploading the file.We were able to reproduce the same locally.

I have filed a ticket for the same,
https://trac.openmicroscopy.org/ome/ticket/12880
And have added you to the CC list.
Notifications will be sent to your email id, when there is a status change on the ticket.

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<mailto:enno.oldewurtel at uni-koeln.de>>
Date: Friday, 8 May 2015 09:48
To: Balaji Ramalingam <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>>
Cc: Melissa Linkert <melissa at glencoesoftware.com<mailto:melissa at glencoesoftware.com>>, "OME-users ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: ND2 position meta data with bioformats 5.1.1

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<mailto: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<mailto:enno.oldewurtel at uni-koeln.de>>
Date: Tuesday, 5 May 2015 14:16
To: Balaji Ramalingam <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>>
Cc: Melissa Linkert <melissa at glencoesoftware.com<mailto:melissa at glencoesoftware.com>>, "OME-users ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto: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<mailto:enno.oldewurtel at uni-koeln.de>
Tel: +49-221-470-8048
Fax: +49-221-470-6230
http://www.biophysics.uni-koeln.de/

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