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BioFormats Export/Import of Composite Images

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Michael Ellis-2

BioFormats Export/Import of Composite Images

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

David Gault (Staff)

Re: BioFormats Export/Import of Composite Images

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael P Ellis

Re: BioFormats Export/Import of Composite Images

Dear David Gault,

Many thanks for your reply.

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.

Regards — Michael Ellis

> 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz <http://www.dsuk.biz/>
[hidden email]
tel: +44(0)1223 911215

The Commercial Centre
6 Green End
Cambridge
CB23 7DY

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael P Ellis

Re: BioFormats Export/Import of Composite Images

In reply to this post by David Gault (Staff)

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

David Gault (Staff)

Re: BioFormats Export/Import of Composite Images

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

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/
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

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]>> 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]>> 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]><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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz<http://www.dsuk.biz/> <http://www.dsuk.biz/>
[hidden email]<mailto:[hidden email]>
tel: +44(0)1223 911215

The Commercial Centre
6 Green End
Cambridge
CB23 7DY

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael P Ellis

Re: BioFormats Export/Import of Composite Images

David,

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?

Apart from our own karyotyping software www.karyotyper.com <http://www.karyotyper.com/>, 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?

— Michael

> 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>
> Michael Ellis (Managing Director)
> Digital Scientific UK Ltd.
> http://www.dsuk.biz<http://www.dsuk.biz/> <http://www.dsuk.biz<http://www.dsuk.biz/>> <http://www.dsuk.biz/ <http://www.dsuk.biz/>>
> [hidden email] <mailto:[hidden email]><mailto:[hidden email] <mailto:[hidden email]>>
> tel: +44(0)1223 911215
>
> The Commercial Centre
> 6 Green End
> Cambridge
> CB23 7DY
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

David Gault (Staff)

Re: BioFormats Export/Import of Composite Images

Hi Michael,

With regards updating the Bio-Formats Importer in ImageJ, there is currently no time frame I could give you for including these fixes but along with the open trac ticket I have add a Trello card to our Bio-Formats board which will be updated once the work has been scheduled: https://trello.com/c/mmQ3LC1D/30-bio-formats-plugin-slice-data-on-imageplus-objects

It certainly seems like Bio-Formats would be a suitable tool for the job. If you are looking to add arbitrary metadata into the OME-TIFF then I would recommend reading into StructuredAnnotations which can be set via Bio-Formats.
http://www.openmicroscopy.org/site/support/ome-model/developers/structured-annotations.html

If you need any further help with the Bio-Formats library specifically please feel free to follow up on the Bio-Formats mailing list and we will be happy to help.

With Thanks,
David Gault
________________
Software Developer
OME Team
School of Life Sciences
University of Dundee

On 21 Oct 2016, at 12:32, Michael Ellis <[hidden email]<mailto:[hidden email]>> wrote:

David,

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?

Apart from our own karyotyping software www.karyotyper.com<http://www.karyotyper.com> <http://www.karyotyper.com/>, 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?

— Michael

On 21 Oct 2016, at 12:04, David Gault (Staff) <[hidden email]<mailto:[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] <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] <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] <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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz<http://www.dsuk.biz/> <http://www.dsuk.biz<http://www.dsuk.biz/>> <http://www.dsuk.biz/ <http://www.dsuk.biz/>>
[hidden email]<mailto:[hidden email]> <mailto:[hidden email]><mailto:[hidden email] <mailto:[hidden email]>>
tel: +44(0)1223 911215

The Commercial Centre
6 Green End
Cambridge
CB23 7DY

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz <http://www.dsuk.biz/>
[hidden email]<mailto:[hidden email]>
tel: +44(0)1223 911215

The Commercial Centre
6 Green End
Cambridge
CB23 7DY

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html