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

Michael Ellis michael.ellis at dsuk.biz
Fri Jun 23 12:01:08 BST 2017 

Dear Bioformats folk,

Re: Pull Request #2670 https://github.com/openmicroscopy/bioformats/pull/2670

Back on November 22nd 2016 I submitted a pull request for a change to be made to the BioFormats ImageJ ImageReader plugin. It seems to have been closed and as far as I can see… forgotten.

The change requested is important to me but also, I believe, is in the best interest of the community at large. Even considering the backwards compatibility issues raised with the suggested change (1), iIstill believe the change is in the interest for all who may use the BioFormats ImageJ ImageReader plugin.

Since the change was rejected for the release of the 5.x release can anyone tell me where and how I can track the progress of this PR in the context of 6.x project.

— Michael Ellis

> On 23 Nov 2016, at 20:38, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
> 
> Hi Michael,
> 
> thanks for submitting your proposed contribution. We will be reviewing it and will get back
> to you directly via the Pull Request.
> As we are currently focused on our API additions to Bio-Formats 5.3.0 [1], please bear with
> us if our answer takes a few days. 
> 
> Best regards,
> Sebastien
> 
> [1] http://blog.openmicroscopy.org/data-model/future-plans/2016/11/01/bf-status/ <http://blog.openmicroscopy.org/data-model/future-plans/2016/11/01/bf-status/> 
> 
>> On 22 Nov 2016, at 13:46, Michael Ellis <michael.ellis at dsuk.biz <mailto:michael.ellis at dsuk.biz>> wrote:
>> 
>> Thanks for the information. I think I have complied with the necessary instructions and now generated a pull request 
>> 
>> https://github.com/openmicroscopy/bioformats/pull/2670 <https://github.com/openmicroscopy/bioformats/pull/2670>
>> 
>> And it looks like some further automated tests are now running 
>> 
>> https://travis-ci.org/openmicroscopy/bioformats/builds/177969138 <https://travis-ci.org/openmicroscopy/bioformats/builds/177969138>
>> 
>> What happens next?
>> 
>> For the record my commit text is as follows:
>> 
>> ———————————————————————————————————
>> Include BioFormats channel name, where present, into the ImagePlus slice label.
>> 
>> constructSliceLabel() previously created the slice label based upon the BioFormats time, position, z position and channel position and then appended the image name, where present. For example a generated slice name might look like:
>> 
>> "c:1/4 z:2/3 t:1/3 - ExImageName"
>> 
>> This meant that the image name was replicated for every channel and in any case is redundant since the image name is also present in the ImagePlus image title (displayed in the ImagePlus window title).
>> 
>> Additionally any channel names specified in the BioFormats file was simply ignored.
>> 
>> This fix does two things
>> 
>> 1. If the BioFormat image file has a non empty channel name defined for a channel, the slice label uses this in preference to the c:i/j channel position specifier. This seems reasonable as it provides extra information and ImageJ displays the relative channel position anyway.
>> 
>> 2. Omits the appending of the image name to every image slice (avoiding needless replication of information that is already present with ImagePlus.getTitle().
>> 
>> ———————————————————————————————————
>> 
>> 
>> 
>>> On 21 Nov 2016, at 15:00, Sebastien Besson (Staff) <s.besson at dundee.ac.uk <mailto:s.besson at dundee.ac.uk>> wrote:
>>> 
>>> 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 <https://github.com/openmicroscopy/bioformats/blob/develop/CONTRIBUTING.md>
>>> [2] https://www.openmicroscopy.org/site/support/contributing/ <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 <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 <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 <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 <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-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>
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> 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 <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>>>>>> 
>>>>>>> 
>>>>>>> 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 <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
>>>>>> 
>>>>>> 
>>>>>> 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 <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 <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 <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>> 
>>> 
>>> 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 <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
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

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