[ome-devel] BioFormats Export/Import of Composite Images

[Michael Ellis]

Dear Balaji,

Thank you for the update. It seems the the ImageJ BioFormats Importer also fails to set the ImageJ pixel size in accordance with the metadata physicalSizeX/YZ parameters.

            Unit<Length> unit = UNITS.MICROMETER;
            Length physicalSizeX = new Length(1.0, unit);
            Length physicalSizeY = new Length(1.5, unit);
            Length physicalSizeZ = new Length(2, unit);

— Michael Ellis


> On 18 Oct 2016, at 15:25, Balaji Ramalingam (Staff) <b.ramalingam at dundee.ac.uk> wrote:
> 
> Hi,
> 
> Thank you for sharing your issue and the code as well.
> 
> We were able to reproduce the issue and I have added a reference to an
> existing ticket (to handle the slice labels appropriately in the
> Bio-Formats Exporter as well),
> https://trac.openmicroscopy.org/ome/ticket/13306 <https://trac.openmicroscopy.org/ome/ticket/13306>
> 
> This will get looked into at the earliest, and since you are already part
> of the cc list, you will get notified when there is a status change on the
> ticket.
> 
> Hope that helps.
> Best,
> Balaji
> 
> 
> 
> __________________
> Mr Balaji Ramalingam
> Software Developer
> 
> OME Team
> School of Life Sciences
> University of Dundee
> 
> 
> 
> 
> 
> 
> On 13/10/2016, 15:43, "ome-devel on behalf of Michael Ellis"
> <ome-devel-bounces at lists.openmicroscopy.org.uk <mailto:ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of
> michael.ellis at dsuk.biz <mailto:michael.ellis at dsuk.biz>> wrote:
> 
>> Is it possible to use the BioFormat Exporter to save a multi-slice
>> composite images, and then have the BioFormats Importer import that image
>> restoring the ImageJ slice names and slice LUTS?
>> 
>> This ImageJ script creates a 4 channel composite image, with channel
>> names and luts specified.
>> 
>> newImage("MyStack", "8-bit random", 256, 256, 4);
>> run("Make Composite", "display=Composite");
>> setSlice(1);
>> run("Set Label...", "label=Dapi");
>> run("Blue");
>> setSlice(2);
>> run("Set Label...", "label=Fitc");
>> run("Green");
>> setSlice(3);
>> run("Set Label...", "label=TxRed");
>> run("Red");
>> setSlice(4);
>> run("Set Label...", "label=Aqua");
>> run("Cyan");
>> 
>> If I use BioFormats Exporter/Importer on this image, the slice labels and
>> slice LUTS are not restored.
>> 
>> The created file certainly has the slice name information as can be seen
>> from the .ome.tif header
>> 
>> <OME UUID="urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f327"
>> 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">
>> <Image ID="Image:0">
>> <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0"
>> Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm"
>> PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0"
>> PhysicalSizeZUnit="µm" SignificantBits="8" SizeC="4" SizeT="1"
>> SizeX="256" SizeY="256" SizeZ="1" TimeIncrement="0.0"
>> TimeIncrementUnit="s" Type="uint8">
>> <Channel Color="-16776961" ID="Channel:0:0" Name="Dapi"
>> SamplesPerPixel="1">
>> <LightPath/>
>> <Channel Color="-16711936" ID="Channel:0:1" Name="Fitc"
>> SamplesPerPixel="1">
>> <LightPath/>
>> <Channel Color="-65536" ID="Channel:0:2" Name="TxRed" SamplesPerPixel="1">
>> <LightPath/>
>> <Channel Color="-16711681" ID="Channel:0:3" Name="Aqua"
>> SamplesPerPixel="1">
>> <LightPath/>
>> <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
>> <UUID
>> FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32
>> 7</UUID>
>> <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
>> <UUID
>> FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32
>> 7</UUID>
>> <TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1">
>> <UUID
>> FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32
>> 7</UUID>
>> <TiffData FirstC="3" FirstT="0" FirstZ="0" IFD="3" PlaneCount="1">
>> <UUID
>> FileName=³FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32
>> 7</UUID>
>> 
>> 
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> 
> 
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