[ome-users] loci_tools with Nikon ND2 image files - Wronlgy identifying z instead of t or series; Missing index/plane

Wed Apr 17 14:46:43 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). The images are Multipoint (i.e.
several xy positions) and multi-channel images.
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.

Trying the Trunk build of today I cannot read in the nd2 files anymore (see
error message at very bottom of email).

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.

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).
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).

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:
Version - comment
4.4.1 - works
4.4.2 - works and identifies series as t-planes
4.4.3 - not available
4.4.4 - not available
4.4.5 - not available
4.4.6 - does not work on some nd2s and identifies series as z-planes

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.

Many thanks and kind regards,
Enno

first bit of metadata of nd2 with 6 multipoints and time on:
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) BitsPerPixel    16
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) DimensionOrder    XYCZT
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) IsInterleaved    false
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) IsRGB    false
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) LittleEndian    true
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) PixelType    uint16
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeC    1
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeT    1
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeX    960
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeY    720
 MP2x3_Ch1_T1_timeOn.nd2 (series 1) SizeZ    1
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) BitsPerPixel    16
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) DimensionOrder    XYCZT
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) IsInterleaved    false
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) IsRGB    false
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) LittleEndian    true
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) PixelType    uint16
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeC    1
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeT    1
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeX    960
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeY    720
 MP2x3_Ch1_T1_timeOn.nd2 (series 2) SizeZ    1

first bit of metadata of nd2 with 6 multipoints and time off:
 BitsPerPixel    16
 DimensionOrder    XYCZT
 IsInterleaved    false
 IsRGB    false
 LittleEndian    true
 PixelType    uint16
 Series 0 Name    MP2x3_Ch1_T1_timeOff.nd2 (series 1)
 SizeC    1
 SizeT    1
 SizeX    960
 SizeY    720
 SizeZ    6

Error Message opening ND2 file with latest trunk build:
java.lang.
NumberFormatException: multiple points
    at
sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1084)
    at java.lang.Double.valueOf(Double.java:475)
    at java.lang.Double.<init>(Double.java:567)
    at loci.formats.in.ND2Handler.parseKeyAndValue(ND2Handler.java:637)
    at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:523)
    at loci.formats.FormatReader.setId(FormatReader.java:1333)
    at loci.formats.DelegateReader.setId(DelegateReader.java:267)
    at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
    at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
    at loci.plugins.in.Importer.showDialogs(Importer.java:141)
    at loci.plugins.in.Importer.run(Importer.java:79)
    at loci.plugins.LociImporter.run(LociImporter.java:81)
    at ij.IJ.runUserPlugIn(IJ.java:183)
    at ij.IJ.runPlugIn(IJ.java:150)
    at ij.IJ.runPlugIn(IJ.java:139)
    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:249)
    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
    at ij.IJ.runUserPlugIn(IJ.java:183)
    at ij.IJ.runPlugIn(IJ.java:150)
    at ij.IJ.runPlugIn(IJ.java:139)
    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:410)
    at ij.io.Opener.openImage(Opener.java:287)
    at ij.io.Opener.openImage(Opener.java:306)
    at ij.io.Opener.open(Opener.java:137)
    at ij.io.Opener.openAndAddToRecent(Opener.java:223)
    at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
    at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
    at java.lang.Thread.run(Thread.java:619)

<http://www.biophysics.uni-koeln.de/>
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