http://imagej.273.s1.nabble.com/BioFormats-Export-Import-of-Composite-Images-tp5017403p5017406.html
I have looked little further into this and have a suspicion that some other meta data values that could be usefully observed by the ImageJ BioFormat’s Importer, such as pixel physical dimension might also be being ignored. I will do some more tests and post any findings.
From my own (selfish) perspective, I would hope that slice names, slice colour table and pixel physical dimension are honoured.
> On 17 Oct 2016, at 14:39, David Gault (Staff) <
[hidden email]> wrote:
>
> Hi Michael,
>
> Following up on this from the response on the Bio-Formats developer mailing list below:
>
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-October/003769.html>
> The information which is being exported and stored in the OME header is indeed correct, the issue is that when importing the file the channel names are not being populated back onto the Image Window and instead you are seeing names such as “c1/4”, “c:2/4”, “c3/4”, “c:4/4”. The ticket which has been opened (
https://trac.openmicroscopy.org/ome/ticket/13306) looks to address this labeling of ImagePlus windows within the Bio-Formats plugin.
>
> The suggested solution from the mailing list link above (using global metadata list) is not perfect but would allow you to retain this information when importing the image into ImageJ. Hopefully this can be useful as a workaround until the issue of importing slice labels is resolved.
>
>
> With Thanks,
> David Gault
> ________________
> Software Developer
> OME Team
> School of Life Sciences
> University of Dundee
>
>
> On 14 Oct 2016, at 10:57, Michael Ellis (DSUK) <
[hidden email]<mailto:
[hidden email]>> 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-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>
>
> — Michael Ellis
>
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