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

Sebastien Besson (Staff) s.besson at dundee.ac.uk
Mon Nov 21 15:00:46 GMT 2016 

Dear Michael,

the way to propose changes against Bio-Formats is to open a Pull Request against the development
line - see the CONTRIBUTING [1] file at the top-level of the Bio-Formats source code repository for
more information.
You can also find general information in the OME Contributing Developer documentation [2].

Best regards,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/blob/develop/CONTRIBUTING.md
[2] https://www.openmicroscopy.org/site/support/contributing/


On 18 Nov 2016, at 17:45, Michael Ellis <michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>> wrote:

Having managed to build and test the BioFormat Image plugins now I put forward the following as a fix so the Import imports BioFormats channel names:

In particular, I put forward that line 625

    String imageName = meta.getChannelName(series,zct[1]);

This seems to do the trick!

Is there a way to submit this fix for consideration in the inclusion of the BioFormats project and if so how do I do that?

— Michael Ellis



On 18 Nov 2016, at 17:01, Michael Ellis <michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>> wrote:

Further to this reported problem with Bio-Formats importer failing to populate the ImagePlus object with a slice name based on the BioFormats channel name (see https://trac.openmicroscopy.org/ome/ticket/13306) I put forward the following:

The code for setting the line label is to be found in the function constructSliceLabel() in the file:

https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImagePlusReader.java

In particular, I put forward that line 625


    String imageName = meta.getImageName(series);

Should be changed to

    String imageName = meta.getChannelName(ndx, cCount);

That is to say, the BioFormats channel name (where present), will be happened to the constructed slice name, rather than appending the BioFormats image name.

I have tried to build my own copy of the BioFormats ImageJ plugins but have so far failed.

Is there any way this one line fix could incorporated?

I really think this is probably what was intended in the first place as it would seem to be of little value to repeat the image name for every slice when the image name is already present in the ImagePlus as the image title.

— Michael Ellis


On 19 Oct 2016, at 10:52, Balaji Ramalingam (Staff) <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>> wrote:

Hi,

Thank you for the update again.

We have been reviewing the body of work on the Bio-Formats import/export front, which includes populating the ImagePlus object appropriately.

I have updated the ticket again, with your latest comments.
This will get looked into at the earliest.

Thanks again,
Best,
Balaji

__________________
Mr Balaji Ramalingam
Software Developer
OME Team
School of Life Sciences
University of Dundee

From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>> on behalf of Michael Ellis <michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>>
Reply-To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Date: Tuesday, 18 October 2016 at 15:50
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Cc: ImageJ Interest Group <IMAGEJ at LIST.NIH.GOV<mailto:IMAGEJ at LIST.NIH.GOV>>
Subject: Re: [ome-devel] BioFormats Export/Import of Composite Images

Dear Balaji,

Thank you for the update. It seems the the ImageJ BioFormats Importer also fails to set the ImageJ pixel size in accordance with the metadata physicalSizeX/YZ parameters.

            Unit<Length> unit = UNITS.MICROMETER;
            Length physicalSizeX = new Length(1.0, unit);
            Length physicalSizeY = new Length(1.5, unit);
            Length physicalSizeZ = new Length(2, unit);

— Michael Ellis


On 18 Oct 2016, at 15:25, Balaji Ramalingam (Staff) <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>> wrote:

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<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of
michael.ellis at dsuk.biz<mailto: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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Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz<http://www.dsuk.biz/>
michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>
tel: +44(0)1223 911215

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The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-devel mailing list
ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz<http://www.dsuk.biz/>
michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>
tel: +44(0)1223 911215

The Commercial Centre
6 Green End
Cambridge
CB23 7DY

_______________________________________________
ome-devel mailing list
ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

Michael Ellis (Managing Director)
Digital Scientific UK Ltd.
http://www.dsuk.biz<http://www.dsuk.biz/>
michael.ellis at dsuk.biz<mailto:michael.ellis at dsuk.biz>
tel: +44(0)1223 911215

The Commercial Centre
6 Green End
Cambridge
CB23 7DY

_______________________________________________
ome-devel mailing list
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