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

[Michael Ellis]

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-8a7a8309f327</UUID>
<TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
<UUID FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f327</UUID>
<TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1">
<UUID FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f327</UUID>
<TiffData FirstC="3" FirstT="0" FirstZ="0" IFD="3" PlaneCount="1">
<UUID FileName=“FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f327</UUID>