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

[Balaji Ramalingam (Staff)]

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

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 on behalf of
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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