[ome-devel] loading files saved using bio-formats exporter in Fiji/ImageJ

Fri Feb 24 18:00:15 GMT 2017

Hi Sebastien,

I am using bio-formats on an up-to-date Fiji with bio-formats 5.3 on OSX Sierra. I just checked and there are no new updates.
I’ll send you the sample Delta Vision file off list due to its file size.

Thanks
   Heinrich

On 24 February 2017 at 14:05:58, Sebastien Besson (Staff) (s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>) wrote:

Hi Heinrich,

Your workflow looks reasonable and it is true that the metadata of the generated OME-TIFF is surprising.

An immediate thought: which version of Bio-Formats are you using? From the schema used at export
(2015-01), it looks like you are using BIo-Formats 5.1.x. Could you try upgrading to the latest version [1]
and see if the problem persists?

If this is still the case, we might need to have access to a sample file to try and reproduce the issue.

Best,
Sebastien

 [1] http://downloads.openmicroscopy.org/bio-formats/

On 23 Feb 2017, at 15:21, Heinrich Grabmayr <h.grabmayr at physik.uni-muenchen.de<mailto:h.grabmayr at physik.uni-muenchen.de>> wrote:

Hi all,

I am writing Python software that should be able to load data from various microscope manufacturers. I therefore went for the awesome OME / bioformats library. In order to access it from Python, I am using python-bioformats (https://github.com/CellProfiler/python-bioformats/tree/master/bioformats).
Now I ran into the following issue: In some cases, I would like to first preprocess the files in ImageJ (e.g. extract one series). So I do that and save using Plugins->Bio Formats->Bio Formats Exporter, as an .ome.tiff.
When I then load the file in my software, the number of slices in C and T are switched. Also, I can’t directly access metadata about channels. Apparently, the original metadata is encapsulated in a deeper layer. When I access the description of the first level of metadata, I get another omexml with approximately the original metadata - but it is rearranged in a way that makes me unable to access it the same way I access the original files (which are DeltaVision .dv files in this case). See below for example metadata of an original file and of a IJ-saved file.
However, when I load the .ome.tiff into ImageJ, the Bio-formats importer reads the correct metadata, so it should be possible to let bioformats do the work, I suspect.

Could anyone point me to a place where the Importer checks and finds the nested and correct metadata? Or tell me the solution?
I have tried to look here
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImporterMetadata.java
and here
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-bsd/utils/mipav/PlugInBioFormatsImporter.java
, didn’t find anything suspicious, and am slightly overwhelmed with the size of the project.

This is how python-bioformats gets metadata:
https://github.com/CellProfiler/python-bioformats/blob/master/bioformats/formatreader.py#L992
Thanks very much
    Heinrich

————————————— Metadata of series 0 of original .dv(DeltaVision) file with 1 series————————————
<?xml version="1.0" encoding="UTF-8" standalone="no"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01 http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd"><Instrument ID="Instrument:0"><Objective Correction="PlanApo" ID="Objective:10612" Immersion="Oil" LensNA="1.42" Manufacturer="Olympus" Model="1-U2B933" NominalMagnification="60.0" WorkingDistance="150.0" WorkingDistanceUnit="µm"/></Instrument><Image ID="Image:0" Name="DeltaVision_Test.dv"><InstrumentRef ID="Instrument:0"/><ObjectiveSettings ID="Objective:10612"/><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.10829800367355347" PhysicalSizeXUnit="µm" PhysicalSizeY="0.10829800367355347" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.20000000298023224" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="2048" SizeY="2048" SizeZ="1" Type="uint16"><Channel EmissionWavelength="676.0" EmissionWavelengthUnit="nm" ExcitationWavelength="632.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><Channel EmissionWavelength="632.0" EmissionWavelengthUnit="nm" ExcitationWavelength="575.0" ExcitationWavelengthUnit="nm" ID="Channel:0:1" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><Channel EmissionWavelength="523.0" EmissionWavelengthUnit="nm" ExcitationWavelength="475.0" ExcitationWavelengthUnit="nm" ID="Channel:0:2" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/><Plane DeltaT="0.0" DeltaTUnit="s" ExposureTime="2.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/><Plane DeltaT="2.4860000610351562" DeltaTUnit="s" ExposureTime="5.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="1" TheT="0" TheZ="0"/><Plane DeltaT="7.808000087738037" DeltaTUnit="s" ExposureTime="10.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="2" TheT="0" TheZ="0"/></Pixels></Image><StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2015-01"><XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Wavelength 3 min. intensity</Key><Value>1641.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:1" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:photosensorReading</Key><Value>3809518.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:2" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:ndFilter</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:3" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>X axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:4" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:maxInten</Key><Value>7108.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:5" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:energyConvFactor</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:6" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Z axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:7" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:minInten</Key><Value>247.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:8" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Lens ID 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Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>ImageHeight</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:21" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:timeStampSeconds</Key><Value>2.486</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:22" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Number of focal planes</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:23" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Z element length (in um)</Key><Value>0.2</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:24" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Number of Sub-resolution sets</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:25" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Y axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:26" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:photosensorReading</Key><Value>3841243.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:27" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Sub-image starting point 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Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Pixel sampling size (X)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:61" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Row axis sequence</Key><Value>2</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:62" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Wavelength 5 min. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:63" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:exWavelen</Key><Value>632.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation 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Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:expTime</Key><Value>10.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:72" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:minInten</Key><Value>1641.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:73" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Number of timepoints</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:74" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Wavelength 1 mean intensity</Key><Value>437.96347</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:75" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Wavelength 4 min. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:76" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:timeStampSeconds</Key><Value>7.808</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:77" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Image Type</Key><Value>unknown</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:78" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:ndFilter</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:79" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>Wavelength 4 max. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:80" Namespace="openmicroscopy.org/OriginalMetadata<http://openmicroscopy.org/OriginalMetadata>"><Value><OriginalMetadata><Key>NumberOfImages</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation></StructuredAnnotations></OME>

————————————— Metadata when opened with ImageJ saved using bio-formats exporter————————————

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