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

Wed Oct 19 10:52:07 BST 2016

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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