[ome-users] ND2 meta data with bioformats 5.0.4

Tue Sep 9 12:49:46 BST 2014

Hi Enno,

> What I need to do is to retrieve the positions of the multipoints in
> an nd2 file in order to know how to stitch them together.

If your stitched image is not more than 2 Gpix, you might be able to save a
lot of trouble by stitching the images using Fiji's "Grid/Collection
Stitching" plugin (http://fiji.sc/Stitching), saving the result, then
importing that into MATLAB for further processing if needed.

Regards,
Curtis

On Tue, Sep 9, 2014 at 6:46 AM, Enno R. Oldewurtel <
enno.oldewurtel at uni-koeln.de> wrote:

> Hi Melissa,
>
> thank you for your reply. I managed to use the commands you recommended.
> It, also, helped me to look at an m-file by Sebastien Besson (
> https://gist.github.com/sbesson/6529406) to learn how to use the
> commands. However, I still have some problems. Maybe I still do not
> understand how to call the right plane with the right index.
>
>
> What I need to do is to retrieve the positions of the multipoints in an
> nd2 file in order to know how to stitch them together.
> I have nd2 files with 120 multipoints, several time-points and 2-3
> channels.
> I usually only retrieve the positions of the first time-point, since each
> multipoint should be at the same position at following times. In my first
> e-mail I outlined how to retrieve positions using the entries from
> r.getGlobalMetadata().
> Now I tried the same using the commands you gave me:
>
> r.setMetadataStore(loci.formats.MetadataTools.createOMEXMLMetadata());
> r.setID();
> metadata = r.getMetadataStore();
> planeIndex=0;
> for positionIndex=1:120
>    xPosition(i) = metadata.getPlanePositionX(positionIndex, planeIndex);
>    yPosition(i) = metadata.getPlanePositionY(positionIndex, planeIndex);
> end
>
> However, I do not get the expected positions. For clarity I attach plots
> of the x and y positions retrieved with versions 5.0.3 and 5.0.4 and also
> the expected plot retrieved via my old method with version 5.0.3 and
> another plot with wrong positions retrieved with my old method and version
> 5.0.4.
>
> I know that I should get a pattern like in the lower left plot that I
> attached. Can you help me once more how to call the correct positions? I
> understand that the positionIndex should be the index for differnt
> multipoints, but how does the planeIndex look like for different
> time-points and channels?
>
> The next bit is not as important to me, but still with regards to the PFS
> status: PFS offset and state are not quite sufficient for me. During my
> experiments the PFS often fails to correct to the proper position and
> resultingly there can be different status returns indicating if the PFS was
> switched off, still searching, not finding, or actually finding the correct
> z-position (maybe there are even more status possibilities, from the top of
> my head I know that 0,1,5 and 7 are possible values). With NIS elements I
> can take a look at those status values for each image to see what went
> wrong. It would be nice if this information was to be retrieved by
> bioformats, too. Also, I often have differnt PFS offsets, e.g. at different
> multipoints. Hence, a single PFS offset value for the entire experiment
> does not tell me too much.
>
>
> Many thanks,
> Enno
>
>
> On Tue, Sep 9, 2014 at 12:23 AM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
>
>> Hi Enno,
>>
>> > I use bioformats.jar with Matlab to read in ND2 files. Previously I
>> used a
>> > 5.0.0-DEV version of loci_tools.
>> > With bioformats I have some problems to retrieve meta data from ND2
>> files.
>> > With 5.0.3 I can successfully read x,y,z position data, but with 5.0.4 I
>> > get some discrepancies.
>> > With both bioformat versions I fail to get the time values of each
>> image.
>> > However, with loci_tools I was able to do this.
>> >
>> > Below is my current approach to read meta data from an ND2 file. Maybe
>> > someone can point out to me how to do this differently, or how to fix
>> the
>> > code I use?
>>
>> The best way to retrieve the stage position and timestamp data is as
>> follows:
>>
>> %%%
>> % positionIndex selects which multipoint to use (starting from 0)
>> % planeIndex selects the image in the chosen multipoint (starting from 0)
>> metadata = r.getMetadataStore();
>> xPosition = r.getPlanePositionX(positionIndex, planeIndex);
>> timestamp = r.getPlaneDeltaT(positionIndex, planeIndex);
>> acquisitionStart = r.getImageAcquisitionDate(positionIndex);
>> %%%
>>
>> 'xPosition' will be the stage position along X; the Y and Z positions
>> can be retrieved using similar calls to getPlanePositionY and
>> getPlanePositionZ.  'timestamp' is the time in seconds from the
>> beginning of acquisition ('acquisitionStart').  See also:
>>
>>
>> http://downloads.openmicroscopy.org/bio-formats/5.0.4/api/ome/xml/meta/MetadataRetrieve.html
>>
>> http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Plane
>>
>> getGlobalMetadata and getSeriesMetadata are provided for informational
>> purposes, but are not necessarily guaranteed to have the same key/value
>> mappings between releases.
>>
>> > Also, is it possible to retrieve the PFS status of each image plane
>> from an
>> > ND2 file?
>>
>> PFS status is not included in the OME data model; from the files we
>> have, it looks like the "PFS, State" and "PFS, Offset" keys in the
>> global metadata table will show the state and offset.  If that doesn't
>> work,
>> though, please let us know.
>>
>> Regards,
>> -Melissa
>>
>> On Thu, Sep 04, 2014 at 06:09:16PM +0200, Enno R. Oldewurtel wrote:
>> > Dear all,
>> >
>> > I use bioformats.jar with Matlab to read in ND2 files. Previously I
>> used a
>> > 5.0.0-DEV version of loci_tools.
>> > With bioformats I have some problems to retrieve meta data from ND2
>> files.
>> > With 5.0.3 I can successfully read x,y,z position data, but with 5.0.4 I
>> > get some discrepancies.
>> > With both bioformat versions I fail to get the time values of each
>> image.
>> > However, with loci_tools I was able to do this.
>> >
>> > Below is my current approach to read meta data from an ND2 file. Maybe
>> > someone can point out to me how to do this differently, or how to fix
>> the
>> > code I use?
>> > Also, is it possible to retrieve the PFS status of each image plane
>> from an
>> > ND2 file?
>> >
>> >
>> > I used to retrieve e.g the x-position of a specific plane from an ND2
>> file
>> > in the following way:
>> >
>> > raw=r.getGlobalMetadata();
>> > x=raw.get('X position for position #00083');
>> > This is for an ND2 file with 82 timepoints, 2 channels and 120
>> multipoints,
>> > i.e. the highest index was #09840 (for some reason I had to assume
>> > 82*120*2channels as the highest index for zero padding, starting from
>> > #09841 to #19680 all values are identical)
>> >
>> > However, with bioformats 5.0.4 this gives me the x-value of the first
>> > time-point instead of the 83rd. Similarly, in another experiment with 65
>> > timepoints, the string 'X position for position #00066' gives me again
>> the
>> > value of the first time-point instead of the 66th.
>> >
>> > Is this a bug in the new 5.0.4 version? I think this happened to me
>> before
>> > with some loci_tools version, but in a later version my approach worked
>> > again. For bioformats 5.0.3 I can retrieve the mentioned x positions
>> just
>> > fine.
>> >
>> > I also need to retrieve the time data for each image. I used to work
>> with
>> > loci_tools (daily built from 6th September 2013) with
>> > rawSeries=r.getSeriesMetadata();
>> > t=rawSeries.get('timestamp #0001')
>> > (less zero-padding was needed, as this time the highest index was
>> > 82*120=9840, also getSeriesMetadata is used since getMetadata takes very
>> > long to load)
>> >
>> > This worked fine, but since there were some bug fixes for ND2 files and
>> > r.setID() runs significantly faster, I would like to stay with
>> bioformats
>> > instead of loci_tools.
>> >
>> >
>> > Best regards,
>> > Enno
>> >
>> >
>> > --
>> > 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/
>>
>> > _______________________________________________
>> > ome-users mailing list
>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
>
> --
> 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/
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140909/de3b9089/attachment.html>