Open Microscopy Environment

Hi ,
I'm trying to add some of the meta data information to the existing software written by VC++.And I'm new to the OME Data Structure. I wants to add exicitation information such as multiple wavelength and their attenuations. I tried to add under the Channel tag-> LightSourceSettings. Under the Channel tag, the detector tag is already implemented before. So, I followed the way how the detector tag is added. I cannot see any info about the LightSourceSettings under the Channel.

Can I use LightSourceSettings for Multiple channel wavelength (eg.455nm,588nm,...)?

Thanks
Su

Dear Su,

Would it be possible to fully describe the set of light sources, detectors, channels and wavelengths for each which you wish to represent. I'll try to create a suitable example, along with any constraints in what's possible to model.


Thanks,
Roger

Hi rleigh,

Sorry for reply late because I'm stuck at the other things.
Below metadata is what I want to be appear in my meta data, Light source setting ,ID, Attenuation,wavelength. I use more than one light source sometime so that light source will be 1-8.Although I tried to add code in the way like detector Settings and Light Path, it does't appear in my meta data when I open with Image J.
I'm using vc++2010.

<Pixels DimensionOrder="XYCZT" ID="Pixels:0:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:0:1">
<LightSourceSettings ID="LightSource:0" Attenuation="0.8" Wavelength="510"/>
<DetectorSettings ID="Detector:0" Binning="2x2" Gain="1.2" Offset="0.7" ReadOutRate="3200" Voltage="120"/>
<LightPath>

Thanks
Su

Hi rleigh,
When I open the .ome.tiff with Image J version1.48b, I can see the LightSourcrsettings tag like in the following:
<Channel ContrastMethod="Brightfield" ID="Channel:0:0" Name="CH0" PinholeSize="64.0" SamplesPerPixel="1">
<LightSourceSettings Attenuation="0.32" ID="LightSource:0" Wavelength="488"/>
<DetectorSettings Binning="1x1" ID="urn:lsid:loci.visitech:Detector:VTI:01" ReadOutRate="0.0"/>

However, I drag and drop the tiff to the FIJI version ImageJ 1.51h, LightSourceSettings tag is not there, only the Channel and detectorSettings tag was there.

Do I miss something to install in the new ImageJ version?

Thanks Su

This should be independent of the ImageJ version, though it might well depend upon the version of the Bio-Formats plugin you are using, and also the model version of the OME-TIFF you are creating. So long as the features you are using are supported by the model version in use by Bio-Formats, it should work. The current model version is 2016-06 http://www.openmicroscopy.org/site/support/ome-model/, but all recent model versions (back to at least 2012-06) support all the features you were using in your examples.

You can define multiple lightsources, but the limitations in the current model are:

• LightSourceSettings only allows a single wavelength
• only one LightSourceSettings is allowed per Channel

This is certainly an area of the model which we could look at extending to remove these limitations for a future model release, once we have a better understanding of your needs.

To get a better idea of exactly what you want to represent in the model, it would be useful to know exactly what the instrument setup is, and the acquisition parameters. While you showed some sample OME-XML, this is clearly not able to represent exactly what you want to store. A simple text description would be greatly helpful here.

When looking at extending the LightSource and Detector settings, is moving from a single wavelength to multiple discrete wavelengths sufficient, or is multiple wavelengths with cutin/out tolerances a better representation (or multiple wavelength ranges)?


Kind regards,
Roger

Hi rleigh,

I want to send some of my ome.tiff. How can i send them to u? The size is too big to attach here.

Thanks
Su

You can use http://qa.openmicroscopy.org.uk/qa/upload/ to upload files to us, and I'll be happy to take a look.

This will work for files up to 2GB. If it's larger, there are other options.


Regards,
Roger

Hi rleigh,

I uploaded my tiff file(new13 1.ome.tiff) and print screen(ome.jpg) which i try to add light source settings to ome data. I captureed a printscreen which shows the same tiff file open with different Image J version. The top one is opened by the later version and the bottom one is opened by the old version.

Could u pls help me take a look at them.

Thanks alot
Su

The reason why they are disappearing is that they are being ignored on read (deliberately).

LightSourceSettings references a LightSource.

Your LightSource has ID="urn:lsid:loci.visitech:LightSource:VTI:1".
The LightSourceSettings is using ID="LightSource:0"

And they don't match up. There is no "LightSource:0". Contrast this with Dectector and DetectorSettings where they do match up, and are not removed.


Hope that helps,
Roger

hi rleigh,

It solved the problem.It appears in the meta data now. Thanks a lot.

regards
Su