<div dir="ltr"><div dir="ltr"><div><div><div><div>Dear all,<br><br></div>I am using loci_tools.jar to read out
Nikon ND2 files obtained with NIS-Elements AR 4.00.03 (Build 775).<br></div><br></div>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.<br>
</div><div>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.<br>
<br></div><div>Is it possible to change the metadata structure obtained from nd2 files in such a way that there are no repeats?<br><br></div><div>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.<br>
</div><div><br></div><div>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.<br><br></div><div>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.<br>
<br><br></div><div>Many thanks for your great work and support. I hope someone can help me out on this one.<br></div><div>Enno<br></div><div><br><br></div>MP2x3_Ch1_T1_timeOn.nd2 (series 1) X position -71158.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Y position 59268.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #1 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #2 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #3 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #4 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #5 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 1) Z position for position, plane #6 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #1 1.5470483098831027<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #2 3.1381038113413378<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #3 3.808205685772933<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #4 4.541229801683687<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #5 6.136187115310691<br>MP2x3_Ch1_T1_timeOn.nd2 (series 1) timestamp #6 6.8340883906930685<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) X position -71158.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) Y position 59268.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #1 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #2 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #3 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #4 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #5 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) Z position for position, plane #6 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #1 1.5470483098831027<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #2 3.1381038113413378<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #3 3.808205685772933<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #4 4.541229801683687<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #5 6.136187115310691<br>MP2x3_Ch1_T1_timeOn.nd2 (series 2) timestamp #6 6.8340883906930685<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 3) X position -71158.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) Y position 59268.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #1 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #2 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #3 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #4 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #5 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 3) Z position for position, plane #6 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #1 1.5470483098831027<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #2 3.1381038113413378<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #3 3.808205685772933<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #4 4.541229801683687<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #5 6.136187115310691<br>MP2x3_Ch1_T1_timeOn.nd2 (series 3) timestamp #6 6.8340883906930685<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 4) X position -71158.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) Y position 59268.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #1 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #2 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #3 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #4 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #5 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 4) Z position for position, plane #6 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #1 1.5470483098831027<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #2 3.1381038113413378<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #3 3.808205685772933<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #4 4.541229801683687<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #5 6.136187115310691<br>MP2x3_Ch1_T1_timeOn.nd2 (series 4) timestamp #6 6.8340883906930685<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 5) X position -71158.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) Y position 59268.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #1 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #2 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #3 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #4 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #5 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 5) Z position for position, plane #6 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #1 1.5470483098831027<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #2 3.1381038113413378<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #3 3.808205685772933<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #4 4.541229801683687<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #5 6.136187115310691<br>MP2x3_Ch1_T1_timeOn.nd2 (series 5) timestamp #6 6.8340883906930685<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 6) X position -71158.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) Y position 59268.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #1 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #2 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #3 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #4 499.975<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #5 500.0<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 6) Z position for position, plane #6 500.0<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #1 1.5470483098831027<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #2 3.1381038113413378<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #3 3.808205685772933<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #4 4.541229801683687<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #5 6.136187115310691<br>MP2x3_Ch1_T1_timeOn.nd2 (series 6) timestamp #6 6.8340883906930685</div>
<br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>50674 Koeln<br><br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br>
Tel: +49-221-470-8048<br>Fax: +49-221-470-6230<br><a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
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