[ome-users] loci_tools with Nikon ND2 image files - Wronlgy identifying z instead of t or series; Missing index/plane
Melissa Linkert
melissa at glencoesoftware.com
Tue Apr 23 01:10:26 BST 2013
Hi Enno,
> 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.
Thank you for the bug report. We have received numerous other reports
of .nd2 files not opening correctly; all outstanding .nd2 issues should
be fixed with the upcoming 4.4.7 release of Bio-Formats.
We can double-check that your files are working as well if you upload
one or two of them to OME's QA system:
http://qa.openmicroscopy.org.uk/qa/upload/
Regards,
-Melissa
On Wed, Apr 17, 2013 at 03:46:43PM +0200, Enno R. Oldewurtel wrote:
> 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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