<div dir="ltr"><div>Dear all,<br><br></div><div>I am using loci_tools.jar to read out
Nikon ND2 files obtained with NIS-Elements AR 4.00.03 (Build 775). The
images are Multipoint (i.e. several xy positions) and multi-channel
images.<br>
The error occurs on both windows 7 and ubuntu 12.04. On windows I use Java 6 Standard Edition Build 1.6.0_29-b11.<br><br></div><div>Trying the Trunk build of today I cannot read in the nd2 files anymore (see error message at very bottom of email).<br>
<br>Using the 4.4.6 (stable release) loci_tools.jar, I can open ND2
image files. If I obtain images with time and multipoint dimension, the
multipoints are put into individual series (i.e. getSeriesCount gives
the number of Multipoints), however when there is no time dimension, the
multipoints are identified as z-planes instead. At the bottom I put a
short extract of metadata from ND2 files with 6 multipoints, 1 Channel
with time dimension (T=1) and without T not specified during
acquisition.<br>
<br></div><div>Now the main reason, why I write is the wrong
identifcation of some nd2 files. For acquisition I specified 8
multipoints in one row with 3 channels. I acquired for each time point
an individual nd2 file, but loci_tools sometimes seems to find only 7x3
images, while normally it finds 8x3 planes, even though the settings all
stayed the same. When reading in the nd2 files with NIS Elements or
with NIS Viewer, I can see all 8 multipoints, also in the cases where
loci_tools fails to do so (see screenshot attached).<br>
</div><div>I attach the metadata for 00_30m001.nd2 with the missing 8th
plane and 00_30m235.nd2, where loci_tools correctly identified 8 planes
(even though they are shown as z-planes and not series planes).<br><br></div>
<div>Furthermore I tested previous versions of loci_tools.jar. Older
versions correctly identify 8 planes in both nd2 files, but newer ones
not anymore. Following is the summary of this:<br></div><div>Version - comment<br>
</div><div>4.4.1 - works<br></div><div>4.4.2 - works and identifies series as t-planes<br></div><div>4.4.3 - not available<br></div><div>4.4.4 - not available<br></div><div>4.4.5 - not available<br></div><div>4.4.6 - does not work on some nd2s and identifies series as z-planes<br>
</div><div><br></div><div>I am happy to supply the original nd2 files,
however 00_30m001.nd2 and 00_30m235.nd2 exceed the size quota of a
single email (together they are just under 65MB large) . Let me know, if
and where I can send emails with smaller zipped parts to or how else I
can transfer them to you.<br>
</div><div><br></div><div>Many thanks and kind regards,<br>Enno<br><br></div><div>first bit of metadata of nd2 with 6 multipoints and time on:<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) BitsPerPixel 16<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) DimensionOrder XYCZT<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 1) IsInterleaved false<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) IsRGB false<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) LittleEndian true<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) PixelType uint16<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeC 1<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeT 1<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeX 960<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeY 720<br> MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeZ 1<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) BitsPerPixel 16<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) DimensionOrder XYCZT<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) IsInterleaved false<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) IsRGB false<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) LittleEndian true<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) PixelType uint16<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeC 1<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeT 1<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeX 960<br>
MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeY 720<br> MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeZ 1<br><br><br></div><div>first bit of metadata of nd2 with 6 multipoints and time off:<br> BitsPerPixel 16<br> DimensionOrder XYCZT<br>
IsInterleaved false<br> IsRGB false<br> LittleEndian true<br> PixelType uint16<br> Series 0 Name MP2x3_Ch1_T1_timeOff.nd2 (series 1)<br> SizeC 1<br> SizeT 1<br> SizeX 960<br> SizeY 720<br> SizeZ 6<br>
<br></div><div><br></div><br>Error Message opening ND2 file with latest trunk build:<br>java.lang.<div>NumberFormatException: multiple points<br> at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1084)<br>
at java.lang.Double.valueOf(Double.java:475)<br> at java.lang.Double.<init>(Double.java:567)<br> at loci.formats.in.ND2Handler.parseKeyAndValue(ND2Handler.java:637)<br> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:523)<br>
at loci.formats.FormatReader.setId(FormatReader.java:1333)<br> at loci.formats.DelegateReader.setId(DelegateReader.java:267)<br> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br> at loci.plugins.in.Importer.run(Importer.java:79)<br> at loci.plugins.LociImporter.run(LociImporter.java:81)<br> at ij.IJ.runUserPlugIn(IJ.java:183)<br>
at ij.IJ.runPlugIn(IJ.java:150)<br> at ij.IJ.runPlugIn(IJ.java:139)<br> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:249)<br> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)<br> at ij.IJ.runUserPlugIn(IJ.java:183)<br>
at ij.IJ.runPlugIn(IJ.java:150)<br> at ij.IJ.runPlugIn(IJ.java:139)<br> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:410)<br> at ij.io.Opener.openImage(Opener.java:287)<br> at ij.io.Opener.openImage(Opener.java:306)<br>
at ij.io.Opener.open(Opener.java:137)<br> at ij.io.Opener.openAndAddToRecent(Opener.java:223)<br> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)<br> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)<br>
at java.lang.Thread.run(Thread.java:619)<br><br></div><div><br></div><a href="http://www.biophysics.uni-koeln.de/" target="_blank"></a>
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