[ome-users] ND2 meta data with bioformats 5.0.4

Tue Sep 9 13:05:19 BST 2014

Hey Curtis,

thanks for the info. My stitched image has ~83 Mpix. I have used fiji to
stitch similar images before some time ago, so that should probably work.
However since my nd2 files are on the order of severals tens of GB in size,
I find it easier to do everything within matlab and only temporarily load
and stitch the bits I need. Often I do not even stitch the entire, but only
a subsection of the image. This way I can keep the original large nd2 with
all its metadata and do not have to lose disk space for copies of stitched
images.

Regards,
Enno

On Tue, Sep 9, 2014 at 1:49 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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
>>
>>
>

-- 
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/
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