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Ticket #330 (closed defect: fixed)

Opened 2008-11-19T13:05:59-06:00

Last modified 2008-11-26T08:06:31-06:00

Cannot read OME-TIFF files saved from Image5D window

Reported by: melissa Owned by: melissa
Priority: major Milestone:
Component: plugins Severity: serious
Keywords: Cc: sgriesha@…
Blocked By: Blocking:

Description

To reproduce:

  1. "File>Open Samples>Fluorescent Cells" in ImageJ
  2. "Plugins>Image5D>Stack to Image5D" with default options
  3. Save as an OME-TIFF file using "Plugins>LOCI>Bio-Formats Exporter"
  4. Attempt to open the saved file using the Bio-Formats importer or command line tools; the following exception should occur: 
Exception in thread "main" loci.formats.FormatException: Invalid image number: 1 (series=0, imageCount=1)
  at loci.formats.FormatTools.checkPlaneNumber(FormatTools.java:484)
  at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:126)
  at loci.formats.in.OMETiffReader.openBytes(OMETiffReader.java:76)
  at loci.formats.FormatReader.openBytes(FormatReader.java:538)
  at loci.formats.FormatReader.openImage(FormatReader.java:521)
  at loci.formats.ImageReader.openImage(ImageReader.java:344)
  at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:475)
  at loci.formats.tools.ImageInfo.main(ImageInfo.java:643)

Change History

comment:1 Changed 2008-11-24T20:28:08-06:00 by melissa

  • Status changed from new to closed
  • Resolution set to fixed

Nominally fixed in r4652. The problem was that when exporting from an Image5D window, you can only export the Z slices from the first channel and timepoint (1 slice in this case). This was not reflected in the metadata that was written to the OME-TIFF file - so the resulting OME-TIFF file had only one plane, but the metadata indicated that there should be three planes.

As of r4652, the metadata is updated to reflect the number of planes actually written, so any files exported from an Image5D window will now be valid. However, it is still advised that you do not export from an Image5D window.

comment:2 Changed 2008-11-26T08:06:31-06:00 by melissa

Better fix in r4658. You should now be able to export all of the planes from an Image5D window.