Hi Lars,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">One more question with the OME-Metadata:<br>
I have not yet brought the channel coding to work correctly.<br>
As far as i see from the data structure, this is coded in the "DisplayOptions" block.<br>
Is there any trick?<br></blockquote></div><br>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.<br>
<br>-Curtis<br><br><div class="gmail_quote">On Thu, Apr 23, 2009 at 2:39 AM, Lars Lehmann <span dir="ltr"><<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de">Lars.Lehmann@bioquant.uni-heidelberg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Curtis,<br>
<br>
i am coding the software in c++ /c#. It is an integrated Image Acquisition Software and Image processing<br>
software for out high throughput microscopes. The data processing part is running in c++.<br>
<br>
To make this software more flexible i am now implementing the Bio-Formats support.<br>
<br>
One more question with the OME-Metadata:<br>
I have not yet brought the channel coding to work correctly.<br>
As far as i see from the data structure, this is coded in the "DisplayOptions" block.<br>
Is there any trick?<br>
<br>
Maybe you can provide me a small example for the color coding of the images...<br>
<br>
Thanks in advance<br>
Lars<br>
<br>
Curtis Rueden schrieb:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Lars,<br>
<br><div><div></div><div class="h5">
it works :-)<br>
after changing the filename to ".ome.tif" and setting the<br>
BigEndian correctly, everything<br>
is shown correctly in ImageJ. I'm currently using the loci tools<br>
4.0 (March 3rd).<br>
<br>
<br>
Glad to hear it.<br>
<br>
Now i can start integrating full OME-support in our image<br>
acquisition software.<br>
<br>
<br>
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.<br>
<br>
BTW: is it possible to put individual OME-meta information in<br>
stacked images?<br>
e.g. individual exposure times for different time points in z-stacks<br>
<br>
<br>
Yes, you can use the Plane and PlaneTiming elements, which lets you specify individual DeltaT and ExposureTime for each plane. Here is an example:<br>
<br>
<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"><br>
<Plane TheC="0" TheT="0" TheZ="0"><br>
<PlaneTiming DeltaT="0.0" ExposureTime="1.5"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="0.401"/><br>
</Plane><br>
<Plane TheC="1" TheT="0" TheZ="0"><br>
<PlaneTiming DeltaT="2.115" ExposureTime="1.2"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="0.401"/><br>
</Plane><br>
<Plane TheC="0" TheT="0" TheZ="1"><br>
<PlaneTiming DeltaT="3.954" ExposureTime="1.5"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="0.201"/><br>
</Plane><br>
<Plane TheC="1" TheT="0" TheZ="1"><br>
<PlaneTiming DeltaT="6.068" ExposureTime="1.2"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="0.201"/><br>
</Plane><br>
<Plane TheC="0" TheT="0" TheZ="2"><br>
<PlaneTiming DeltaT="7.908" ExposureTime="1.5"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="0.0030"/> </Plane><br>
<Plane TheC="1" TheT="0" TheZ="2"><br>
<PlaneTiming DeltaT="10.023" ExposureTime="1.2"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="0.0030"/> </Plane><br>
<Plane TheC="0" TheT="0" TheZ="3"><br>
<PlaneTiming DeltaT="11.863" ExposureTime="1.5"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="-0.198"/> </Plane><br>
<Plane TheC="1" TheT="0" TheZ="3"><br>
<PlaneTiming DeltaT="13.979" ExposureTime="1.2"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="-0.198"/> </Plane><br>
<Plane TheC="0" TheT="0" TheZ="4"><br>
<PlaneTiming DeltaT="15.819" ExposureTime="1.5"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="-0.396"/> </Plane><br>
<Plane TheC="1" TheT="0" TheZ="4"><br>
<PlaneTiming DeltaT="17.933" ExposureTime="1.2"/><br>
<StagePosition PositionX="909.51" PositionY="-3365.11" PositionZ="-0.396"/> </Plane><br>
</Pixels><br>
<br>
A bit verbose, but it does the trick.<br>
<br>
-Curtis<br>
<br></div></div><div><div></div><div class="h5">
On Wed, Apr 8, 2009 at 3:29 AM, Lars Lehmann <<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de" target="_blank">Lars.Lehmann@bioquant.uni-heidelberg.de</a> <mailto:<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de" target="_blank">Lars.Lehmann@bioquant.uni-heidelberg.de</a>>> wrote:<br>
<br>
Hi Melissa,<br>
Hi Curtis,<br>
<br>
it works :-)<br>
after changing the filename to ".ome.tif" and setting the<br>
BigEndian correctly, everything<br>
is shown correctly in ImageJ. I'm currently using the loci tools<br>
4.0 (March 3rd).<br>
<br>
Now i can start integrating full OME-support in our image<br>
acquisition software.<br>
BTW: is it possible to put individual OME-meta information in<br>
stacked images?<br>
e.g. individual exposure times for different time points in z-stacks<br>
<br>
Thanks,<br>
Lars<br>
<br>
Curtis Rueden schrieb:<br>
<br>
Hi Lars,<br>
<br>
I cannot duplicate your problem with the latest Bio-Formats<br>
trunk build. However, with older versions of Bio-Formats, the<br>
extension ".ome.tif" was required to indicate an OME-TIFF<br>
file. Which version of Bio-Formats are you using, and have you<br>
tried upgrading?<br>
<br>
Regarding your OME-TIFF file, I see you are using the old<br>
2003-FC version of the schema. This is probably my fault,<br>
because I have still not updated most of the OME-TIFF sample<br>
datasets on the website to the new schema. Nonetheless, I<br>
highly encourage you to adopt the latest 2008-09 version,<br>
available at:<br>
<a href="http://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd" target="_blank">http://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd</a><br>
<br>
You can find documentation on the OME-XML site at:<br>
<a href="http://www.ome-xml.org/" target="_blank">http://www.ome-xml.org/</a><br>
<br>
Also, the sample biological datasets (tubhiswt) use 2008-02<br>
(very similar to 2008-09):<br>
<a href="http://www.loci.wisc.edu/ome/ome-tiff-data.html" target="_blank">http://www.loci.wisc.edu/ome/ome-tiff-data.html</a><br>
<br>
Please let us know if you have any further questions or problems.<br>
<br>
-Curtis<br>
<br>
On Tue, Apr 7, 2009 at 9:44 AM, Lars Lehmann<br>
<<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de" target="_blank">Lars.Lehmann@bioquant.uni-heidelberg.de</a><br>
<mailto:<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de" target="_blank">Lars.Lehmann@bioquant.uni-heidelberg.de</a>><br>
<mailto:<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de" target="_blank">Lars.Lehmann@bioquant.uni-heidelberg.de</a><br>
<mailto:<a href="mailto:Lars.Lehmann@bioquant.uni-heidelberg.de" target="_blank">Lars.Lehmann@bioquant.uni-heidelberg.de</a>>>> wrote:<br>
<br>
Hi,<br>
<br>
i'm having problems with implementing a correct TIFF-XML<br>
structure.<br>
First checked the attached file with the OME-XML validator:<br>
<a href="http://validator.openmicroscopy.org.uk" target="_blank">http://validator.openmicroscopy.org.uk</a><br>
and it shows me that the XML-structure is valid.<br>
<br>
But importing this file in ImageJ gives me a different result.<br>
After opening the file via ImageJ->Plugins->LOCI->Bio-Formats<br>
Importer,<br>
activating the option "Metadata viewing"->"Display OME-XML<br>
metadata"<br>
shows me that my header information are discarded and tagged as<br>
"description".<br>
Is there something wrong in my header (checked by<br>
validator) or is<br>
this a problem<br>
with the import function in ImageJ?<br>
<br>
Best regards,<br>
Lars<br>
<br>
-- Lars Lehmann<br>
<br>
<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a><br>
<mailto:<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a>><br>
<mailto:<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a><br>
<mailto:<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a>>><br>
<br>
VIROQUANT Optik<br>
BIOQUANT INF 267, R022 69120 HD Tel.: (+49) 6221/54-51219<br>
<br>
<a href="http://www.bioquant.uni-heidelberg.de/" target="_blank">http://www.bioquant.uni-heidelberg.de/</a><br>
<br>
<br>
<br>
<br>
-- Lars Lehmann<br>
<br>
<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a><br>
<mailto:<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a>><br>
VIROQUANT Optik<br>
BIOQUANT INF 267, R022 69120 HD Tel.: (+49) 6221/54-51219<br>
<br>
<a href="http://www.bioquant.uni-heidelberg.de/" target="_blank">http://www.bioquant.uni-heidelberg.de/</a><br>
<br>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
<br>
-- <br>
Lars Lehmann<br>
<br>
<a href="mailto:lars.lehmann@bioquant.uni-heidelberg.de" target="_blank">lars.lehmann@bioquant.uni-heidelberg.de</a><br>
VIROQUANT Optik<br>
BIOQUANT INF 267, R022 69120 HD Tel.: (+49) 6221/54-51219<br>
<br>
<a href="http://www.bioquant.uni-heidelberg.de/" target="_blank">http://www.bioquant.uni-heidelberg.de/</a><br>
<br>
</div></div></blockquote></div><br>