[ome-users] Problems with OME-TIFF
Curtis Rueden
ctrueden at wisc.edu
Thu Apr 23 21:43:09 BST 2009
Hi Lars,
One more question with the OME-Metadata:
> I have not yet brought the channel coding to work correctly.
> As far as i see from the data structure, this is coded in the
> "DisplayOptions" block.
> Is there any trick?
>
By "channel coding" I assume you mean assigning a color table to each of
your physical color channels? If so, DisplayOptions was the way to go for
the original OME server, but I am not sure whether it is still the preferred
means for OMERO, or whether it is deprecated in favor of another way. I am
forwarding your question on to the OME users mailing list -- one of the
OMERO developers will know what to recommend.
-Curtis
On Thu, Apr 23, 2009 at 2:39 AM, Lars Lehmann <
Lars.Lehmann at bioquant.uni-heidelberg.de> wrote:
> Hi Curtis,
>
> i am coding the software in c++ /c#. It is an integrated Image Acquisition
> Software and Image processing
> software for out high throughput microscopes. The data processing part is
> running in c++.
>
> To make this software more flexible i am now implementing the Bio-Formats
> support.
>
> One more question with the OME-Metadata:
> I have not yet brought the channel coding to work correctly.
> As far as i see from the data structure, this is coded in the
> "DisplayOptions" block.
> Is there any trick?
>
> Maybe you can provide me a small example for the color coding of the
> images...
>
> Thanks in advance
> Lars
>
> Curtis Rueden schrieb:
>
>> Hi Lars,
>>
>> it works :-)
>> after changing the filename to ".ome.tif" and setting the
>> BigEndian correctly, everything
>> is shown correctly in ImageJ. I'm currently using the loci tools
>> 4.0 (March 3rd).
>>
>>
>> Glad to hear it.
>>
>> Now i can start integrating full OME-support in our image
>> acquisition software.
>>
>>
>> What language are you using to code your software? Bio-Formats can be used
>> to easily build up an OME-XML metadata block using its flat metadata API,
>> and we are have recently completed an initial implementation of C++ JNI
>> bindings for Bio-Formats. We have also successfully interfaced Bio-Formats
>> with C++ acquisition software using ZeroC's Ice. I am in the process of
>> updating the "Interfacing from non-Java code" section of the web site to
>> reflect these developments and provide some documentation.
>>
>> BTW: is it possible to put individual OME-meta information in
>> stacked images?
>> e.g. individual exposure times for different time points in z-stacks
>>
>>
>> Yes, you can use the Plane and PlaneTiming elements, which lets you
>> specify individual DeltaT and ExposureTime for each plane. Here is an
>> example:
>>
>> <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0"
>> PhysicalSizeX="0.01" PhysicalSizeY="0.01" PhysicalSizeZ="0.2"
>> PixelType="uint16" SizeC="2" SizeT="1" SizeX="768" SizeY="768" SizeZ="5">
>> <Plane TheC="0" TheT="0" TheZ="0">
>> <PlaneTiming DeltaT="0.0" ExposureTime="1.5"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="0.401"/>
>> </Plane>
>> <Plane TheC="1" TheT="0" TheZ="0">
>> <PlaneTiming DeltaT="2.115" ExposureTime="1.2"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="0.401"/>
>> </Plane>
>> <Plane TheC="0" TheT="0" TheZ="1">
>> <PlaneTiming DeltaT="3.954" ExposureTime="1.5"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="0.201"/>
>> </Plane>
>> <Plane TheC="1" TheT="0" TheZ="1">
>> <PlaneTiming DeltaT="6.068" ExposureTime="1.2"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="0.201"/>
>> </Plane>
>> <Plane TheC="0" TheT="0" TheZ="2">
>> <PlaneTiming DeltaT="7.908" ExposureTime="1.5"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="0.0030"/> </Plane>
>> <Plane TheC="1" TheT="0" TheZ="2">
>> <PlaneTiming DeltaT="10.023" ExposureTime="1.2"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="0.0030"/> </Plane>
>> <Plane TheC="0" TheT="0" TheZ="3">
>> <PlaneTiming DeltaT="11.863" ExposureTime="1.5"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="-0.198"/> </Plane>
>> <Plane TheC="1" TheT="0" TheZ="3">
>> <PlaneTiming DeltaT="13.979" ExposureTime="1.2"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="-0.198"/> </Plane>
>> <Plane TheC="0" TheT="0" TheZ="4">
>> <PlaneTiming DeltaT="15.819" ExposureTime="1.5"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="-0.396"/> </Plane>
>> <Plane TheC="1" TheT="0" TheZ="4">
>> <PlaneTiming DeltaT="17.933" ExposureTime="1.2"/>
>> <StagePosition PositionX="909.51" PositionY="-3365.11"
>> PositionZ="-0.396"/> </Plane>
>> </Pixels>
>>
>> A bit verbose, but it does the trick.
>>
>> -Curtis
>>
>> On Wed, Apr 8, 2009 at 3:29 AM, Lars Lehmann <
>> Lars.Lehmann at bioquant.uni-heidelberg.de <mailto:
>> Lars.Lehmann at bioquant.uni-heidelberg.de>> wrote:
>>
>> Hi Melissa,
>> Hi Curtis,
>>
>> it works :-)
>> after changing the filename to ".ome.tif" and setting the
>> BigEndian correctly, everything
>> is shown correctly in ImageJ. I'm currently using the loci tools
>> 4.0 (March 3rd).
>>
>> Now i can start integrating full OME-support in our image
>> acquisition software.
>> BTW: is it possible to put individual OME-meta information in
>> stacked images?
>> e.g. individual exposure times for different time points in z-stacks
>>
>> Thanks,
>> Lars
>>
>> Curtis Rueden schrieb:
>>
>> Hi Lars,
>>
>> I cannot duplicate your problem with the latest Bio-Formats
>> trunk build. However, with older versions of Bio-Formats, the
>> extension ".ome.tif" was required to indicate an OME-TIFF
>> file. Which version of Bio-Formats are you using, and have you
>> tried upgrading?
>>
>> Regarding your OME-TIFF file, I see you are using the old
>> 2003-FC version of the schema. This is probably my fault,
>> because I have still not updated most of the OME-TIFF sample
>> datasets on the website to the new schema. Nonetheless, I
>> highly encourage you to adopt the latest 2008-09 version,
>> available at:
>> http://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd
>>
>> You can find documentation on the OME-XML site at:
>> http://www.ome-xml.org/
>>
>> Also, the sample biological datasets (tubhiswt) use 2008-02
>> (very similar to 2008-09):
>> http://www.loci.wisc.edu/ome/ome-tiff-data.html
>>
>> Please let us know if you have any further questions or problems.
>>
>> -Curtis
>>
>> On Tue, Apr 7, 2009 at 9:44 AM, Lars Lehmann
>> <Lars.Lehmann at bioquant.uni-heidelberg.de
>> <mailto:Lars.Lehmann at bioquant.uni-heidelberg.de>
>> <mailto:Lars.Lehmann at bioquant.uni-heidelberg.de
>> <mailto:Lars.Lehmann at bioquant.uni-heidelberg.de>>> wrote:
>>
>> Hi,
>>
>> i'm having problems with implementing a correct TIFF-XML
>> structure.
>> First checked the attached file with the OME-XML validator:
>> http://validator.openmicroscopy.org.uk
>> and it shows me that the XML-structure is valid.
>>
>> But importing this file in ImageJ gives me a different result.
>> After opening the file via ImageJ->Plugins->LOCI->Bio-Formats
>> Importer,
>> activating the option "Metadata viewing"->"Display OME-XML
>> metadata"
>> shows me that my header information are discarded and tagged as
>> "description".
>> Is there something wrong in my header (checked by
>> validator) or is
>> this a problem
>> with the import function in ImageJ?
>>
>> Best regards,
>> Lars
>>
>> -- Lars Lehmann
>>
>> lars.lehmann at bioquant.uni-heidelberg.de
>> <mailto:lars.lehmann at bioquant.uni-heidelberg.de>
>> <mailto:lars.lehmann at bioquant.uni-heidelberg.de
>> <mailto:lars.lehmann at bioquant.uni-heidelberg.de>>
>>
>> VIROQUANT Optik
>> BIOQUANT INF 267, R022 69120 HD Tel.: (+49) 6221/54-51219
>>
>> http://www.bioquant.uni-heidelberg.de/
>>
>>
>>
>>
>> -- Lars Lehmann
>>
>> lars.lehmann at bioquant.uni-heidelberg.de
>> <mailto:lars.lehmann at bioquant.uni-heidelberg.de>
>> VIROQUANT Optik
>> BIOQUANT INF 267, R022 69120 HD Tel.: (+49) 6221/54-51219
>>
>> http://www.bioquant.uni-heidelberg.de/
>>
>>
>>
>
> --
> Lars Lehmann
>
> lars.lehmann at bioquant.uni-heidelberg.de
> VIROQUANT Optik
> BIOQUANT INF 267, R022 69120 HD Tel.: (+49) 6221/54-51219
>
> http://www.bioquant.uni-heidelberg.de/
>
>
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