http://imagej.273.s1.nabble.com/BioFormats-Export-Import-of-Composite-Images-tp5017403p5017444.html
Many thanks. For now my aim is to add an image export capability to my own (Java) Computer assisted microscope application that will allow me to attach a variety of metadata (e.g. physical pixel size, objective magnification, filter information, timestamp, exposure time, etc.) to multi-image files ( multiple fluorescence channels, multiple z-sections, multiple times) with the minimum amount of code and with and a variety of export file format targets (metadata obviously available to targets subject to that which can be carried by the target format), and indeed the OME-TIFF will allow it all. BioFormats just has to be the best tool, right?
>, ImageJ is the next port of call for an app to look at our images and indeed if we have to, we will implement our own plugin that reads the OME_TIFF and populates, plane names, LUTS and more, but it does seem that we will be re-inventing the existing ImageJ Bioformats Importer plugin if we have to do that. Of course I would rather have it for free :-)
I am not sure whether this is an appropriate place to add this, or even if it already exists, but it would be great if BioFormats allowed for arbitrary metadata to be added to a file, this could be structured in the OME-TIFF as embedded XML that had an ID based on a unique package name style “uk.dsuk.myimagemetadata” to avoid 3rd parties tripping over one another bespoke extensions.
The advantage would be that you could seamlessly integrate company/application specific metadata along side common core metadata in the same mechanism.
Finally is there a time frame for the Image BioFormats Importer to be updated to handle slice names, physical pixel size and or LUTS?
> On 21 Oct 2016, at 12:04, David Gault (Staff) <
[hidden email]> wrote:
>
> Hi Michael,
>
> Im afraid the addGlobalMetaList function is not available through the ImageJ macros, instead the metadata will need to have been written to the file before it is imported.
> In this case as the metadata values are already stored on the image perhaps another alternative to get the data into ImageJ would be through a custom plugin using Bio-Formats.
> A good example of this to read images including populating slices and LUTs would be
https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/bio-formats-plugins/utils/Read_Image.java <
https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/bio-formats-plugins/utils/Read_Image.java>
>
> This could be modified to read the channelNames as such:
> IMetadata retrieve = (IMetadata) reader.getMetadataStore();
> String channelName = retrieve.getChannelName(imageIndex, channelIndex);
>
> Then to add them as labels for the slices:
> stack.addSlice(channelName, ip);
>
> The full Bio-Formats documentation has can be found from
http://www.openmicroscopy.org/site/support/bio-formats5.2/ <
http://www.openmicroscopy.org/site/support/bio-formats5.2/>
> Examples of using Bio-Formats in an ImageJ plugin can be found here:
http://www.openmicroscopy.org/site/support/bio-formats5.2/developers/java-library.html <
http://www.openmicroscopy.org/site/support/bio-formats5.2/developers/java-library.html>
>
> With Thanks,
> David Gault
> ________________
> Software Developer
> OME Team
> School of Life Sciences
> University of Dundee
>
> On 20 Oct 2016, at 20:01, Michael Ellis <
[hidden email] <mailto:
[hidden email]><mailto:
[hidden email] <mailto:
[hidden email]>>> wrote:
>
> Dear David Gault and Balaji Ramalingam
>
> Thank you for your suggestions about using global metadata list as suggest here:
>
>
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-October/003769.html <
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-October/003769.html>
>
> However I am unsure of the context on where addGlobalMetaList() is being called. Is this ImageJ macro code? There does not seem to be any methods in Metadata called addGlobalMetaList(). A google search reveals there is a method by this name in the FormatReader class, but I am not making use of the class when calling BioFormats library when writing my file.
>
> This leads me to ask if there is any other sources for BIoFormats documentation. There seems to be so much that is not explained. The Java docs often offer little more than a long winded version of the function name:
>
> addGlobalMeta <
http://downloads.openmicroscopy.org/bio-formats/5.2.3/api/loci/formats/FormatReader.html#addGlobalMeta(java.lang.String,%20java.lang.Object)>(String <
http://docs.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true> key, Object <
http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true> value)
> Adds an entry to the global metadata table.
>
> There seems to be very little overview and few example/
>
> Any help would be greatly appreciated.
>
> — Michael Ellis
>
>
>
> On 17 Oct 2016, at 14:39, David Gault (Staff) <
[hidden email] <mailto:
[hidden email]><mailto:
[hidden email] <mailto:
[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 <
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 <
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]><mailto:
[hidden email] <mailto:
[hidden email]>><mailto:
[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 <
http://www.openmicroscopy.org/Schemas/OME/2015-01>" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance <
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>
http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd <
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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> Michael Ellis (Managing Director)
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