Open Microscopy Environment

Hi,

I don't know if my question will be relevant since i dont know if the functionnality i ll talk about
was meant to be in OMERO.insight-ij-4.4.10-ice35-b112.zip. The fact is that when i open a file (.czi) with
OMERO.insight-ij-4.4.10-ice35-b112.zip, work on it and save it via the bio-fomat exporter in .OME-TIFF, i lose all the metadata when i "re-import" it with omero importer. Is it normal? it would be nice to keep track of thèses metadata.

English is not my native language, so i don't know if i made myself clear but tell me if it s not and i ll try to rephrase this topic.

I d like to precise that it actually works the other way around. If i import a .czi file in imageJ thanks to the bio-format import command, work on it, export it thanks to bio-format export command and import it on omero, metadata are still there.
Another point: except what i would call "big image modification" like the reslice command, the work you 've done on imageJ is not kept when imported on omero (like ROI, threshold adjustement and stuff)

Cheers,

laluminy

Hi,
The metadata that are part of the OME-XML model are stored in the DB but the metadata are always available.
We do not modify or delete them.

laluminy wrote:Another point: except what i would call "big image modification" like the reslice command, the work you 've done on imageJ is not kept when imported on omero (like ROI, threshold adjustement and stuff)

This is a current limitation of the plug-in. This is something we are planning to address e.g. ROI in a near future

Cheers

Jmarie

If I understand you correctly, you're asking about the loss of metadata when you export a czi from OMERO as an OME-TIFF and re-import it.

Unfortunately we don't export ALL OMERO metadata in OME-TIFFs, because of the technical issues with harvesting all this data from the database on export.
However, most of the key metadata should be preserved.

Please let us know what metadata you find missing, and if you could upload a sample file to http://qa.openmicroscopy.org.uk/qa/upload/ that would help us to replicate what you're seeing.

Regards,

Will.

Hi,

Thanks for your answer.
Only the metadata on the channel are kept. For the sample request, from wich point of the process do you want a sample? my original image in .czi format or the one in OME.TIFF exported with imageJ?

Best,

laluminy

Hi,

I found a CZI image in our sample set, so I think I can replicate what you're seeing.

When I export a CZI image from OMERO as OME-TIFF and then see what metadata I have using the LOCI command line tools (see below), I see various metadata missing compared with the original czi.

Mostly this is the Instrument, including Objectives and Filters (although filters weren't linked to the Image). Also Channels are missing some attributes.

I'm afraid that this is unlikely to improve any time soon, given the amount of work this involves.

Is there a particular workflow that you need this for? There may be other ways we can help you?

Regards,

Will.

Code: Select all

./bftools/showinf /Users/will/Documents/biology-data/exported.ome.tiff -nopix -omexml-only

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2012-06 http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd">
   <Image ID="Image:0" Name="test.czi">
      <AcquisitionDate>2011-11-23T09:56:36</AcquisitionDate>
      <ImagingEnvironment/>
      <Pixels DimensionOrder="XYZCT" ID="Pixels:0" PhysicalSizeX="0.10238095238095238" PhysicalSizeY="0.10238095238095238" SizeC="3" SizeT="1" SizeX="1388" SizeY="1040" SizeZ="1" Type="uint16">
         <Channel Color="65535" EmissionWavelength="465" ExcitationWavelength="353" ID="Channel:0:0" Name="" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel Color="16711935" EmissionWavelength="509" ExcitationWavelength="488" ID="Channel:0:1" Name="" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel Color="-16776961" EmissionWavelength="598" ExcitationWavelength="578" ID="Channel:0:2" Name="" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
            <UUID FileName="__omero_export__4933379458512353272.ome.tiff">urn:uuid:a7a18081-522c-47a7-be5a-a6666c9e7607</UUID>
         </TiffData>
         <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
            <UUID FileName="__omero_export__4933379458512353272.ome.tiff">urn:uuid:a7a18081-522c-47a7-be5a-a6666c9e7607</UUID>
         </TiffData>
         <TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1">
            <UUID FileName="__omero_export__4933379458512353272.ome.tiff">urn:uuid:a7a18081-522c-47a7-be5a-a6666c9e7607</UUID>
         </TiffData>
         <Plane DeltaT="1.0" PositionX="11551.7" PositionY="323.1" PositionZ="8575.625" TheC="0" TheT="0" TheZ="0"/>
         <Plane DeltaT="3.0" PositionX="11551.7" PositionY="323.1" PositionZ="8575.625" TheC="1" TheT="0" TheZ="0"/>
         <Plane DeltaT="5.0" PositionX="11551.7" PositionY="323.1" PositionZ="8575.625" TheC="2" TheT="0" TheZ="0"/>
      </Pixels>
   </Image>
   <StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2012-06"/>
</OME>


Hi,

Thanks again for your quick answer.
It doesn't really concern any particular workflow.
I m currently doing my master 2 internship in a biology institute and i m supposed to find an
answer to the question: how to retrieve efficiently images set in gigabytes of data so we thought of omero
and its easy way to annotate sets and read images metadata. Knowing, researchers work a lot with imageJ, i was concerned to see if the metadata were still available cause it appears they like to use some specific parameters from the metadata for their queries. I guess we can avoid this problem by making our own ontology for imageJ processed data.

Best,

laluminy

OK, let us know if you need any more help.

Are you aware of the OMERO ImageJ plugin - You have the Insight UI as an ImageJ plugin, so you can browse and annotate images, and when you open images you get the ImageJ viewer and tools (although the work you do in the ImageJ viewer is not saved back to OMERO - this is on our TODO list).

Regards,

Will