[ome-users] loci_tools with Nikon ND2 files - Excessive metdadata entries for time + multipoint stack

Wed Jun 26 14:12:52 BST 2013

Dear all,

I am using loci_tools.jar to read out Nikon ND2 files obtained with
NIS-Elements AR 4.00.03 (Build 775).

I record nd2 files with several timepoints and multipoints (XY). Without
time dimension assigned the metadata shows entries for each x,y,z and time
position only once, but whenever there is also a time dimension, each XY
point is treated as one series point and for each series point the x,y,z
and time information is repeated.
This repeat causes a large size increase of the metadata. I read in the
metadataList using the getMetadata() in Matlab and frequently get a
metadataList with a few million entries, causing a large increase in memory
usage. For one special experiment I had to obtain a few thousand
multipoints and neither Matlab nor imageJ managed to open this.

Is it possible to change the metadata structure obtained from nd2 files in
such a way that there are no repeats?

In case this is not possible, is there a way to extract the information
within the usual Metadata List in a different way. That way I might be able
to leave out the .getMetadata() and create the metadataList manually,
although I'd prefer to directly access a complete list of metadata.

At the bottom I give some of the metadata of a nd2 file one obtained with
time dimension turned on, causing the increase of size for a small nd2 file
with only 6 XY points.

I have two example nd2. One without the repeats of metadata, since I turned
the time dimension off, and one with it being turned on during acquisition.
I will submit those to the OME's QA system.

Many thanks for your great work and support. I hope someone can help me out
on this one.
Enno

MP2x3_Ch1_T1_timeOn.nd2 (series 1) X position    -71158.0
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Y position    59268.0
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #1
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #2
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #3
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #4
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #5
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #6
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #1    1.5470483098831027
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #2    3.1381038113413378
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #3    3.808205685772933
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #4    4.541229801683687
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #5    6.136187115310691
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #6    6.8340883906930685
MP2x3_Ch1_T1_timeOn.nd2 (series 2) X position    -71158.0
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Y position    59268.0
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #1
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #2
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #3
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #4
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #5
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #6
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #1    1.5470483098831027
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #2    3.1381038113413378
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #3    3.808205685772933
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #4    4.541229801683687
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #5    6.136187115310691
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #6    6.8340883906930685
MP2x3_Ch1_T1_timeOn.nd2 (series 3) X position    -71158.0
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Y position    59268.0
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #1
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #2
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #3
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #4
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #5
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #6
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #1    1.5470483098831027
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #2    3.1381038113413378
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #3    3.808205685772933
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #4    4.541229801683687
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #5    6.136187115310691
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #6    6.8340883906930685
MP2x3_Ch1_T1_timeOn.nd2 (series 4) X position    -71158.0
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Y position    59268.0
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #1
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #2
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #3
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #4
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #5
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #6
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #1    1.5470483098831027
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #2    3.1381038113413378
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #3    3.808205685772933
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #4    4.541229801683687
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #5    6.136187115310691
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #6    6.8340883906930685
MP2x3_Ch1_T1_timeOn.nd2 (series 5) X position    -71158.0
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Y position    59268.0
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #1
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #2
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #3
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #4
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #5
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #6
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #1    1.5470483098831027
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #2    3.1381038113413378
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #3    3.808205685772933
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #4    4.541229801683687
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #5    6.136187115310691
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #6    6.8340883906930685
MP2x3_Ch1_T1_timeOn.nd2 (series 6) X position    -71158.0
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Y position    59268.0
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #1
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #2
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #3
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #4
499.975
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #5
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #6
500.0
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #1    1.5470483098831027
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #2    3.1381038113413378
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #3    3.808205685772933
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #4    4.541229801683687
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #5    6.136187115310691
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #6    6.8340883906930685

-- 
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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