[ome-users] ND2 meta data with bioformats 5.0.4

[Enno R. Oldewurtel]

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/
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