Open Microscopy Environment

Hi

I am having an issue with LUTs being assigned to some datasets in the image viewer in both Insight and the webclient.

I am uploading an example to the ftp server ('IP-Stitching-01_s1_140716.ome.tiff'). This image was exported to ome.tiff in Zen (I am still having trouble with czi - reported in a separate post). This consists of 3 channels and in the viewer two of them have a black LUT and a white LUT (but green in the webclient). I can change the channel with the black LUT in both Insight and the webclient. However, I cannot change the white in Insight but I can in the webclient. Additionally although I can successfully save changes in Insight, I cannot in the webclient.

Cheers,

Dan.

Dear Dan,

Firstly, the channel colours. I'm afraid these are what is present in the OME-XML exported from Zen:

Code: Select all

         <Channel AcquisitionMode="WideField" Color="255" ContrastMethod="Fluorescence" EmissionWavelength="465" ExcitationWavelength="353" Fluor="DAPI" ID="Channel:0:0" IlluminationType="Epifluorescence" Name="DAPI" SamplesPerPixel="1">
            <DetectorSettings Binning="1x1" ID="Detector:1"/>
            <FilterSetRef ID="FilterSet:1"/>
            <LightPath/>
         </Channel>
         <Channel AcquisitionMode="WideField" Color="16711680" ContrastMethod="Fluorescence" EmissionWavelength="603" ExcitationWavelength="577" Fluor="Alexa Fluor 568" ID="Channel:0:1" IlluminationType="Epifluorescence" Name="Alexa Fluor 568" SamplesPerPixel="1">
            <DetectorSettings Binning="1x1" ID="Detector:1"/>
            <FilterSetRef ID="FilterSet:2"/>
            <LightPath/>
         </Channel>
         <Channel AcquisitionMode="WideField" Color="16711935" ContrastMethod="Fluorescence" EmissionWavelength="668" ExcitationWavelength="653" Fluor="Alexa Fluor 647" ID="Channel:0:2" IlluminationType="Epifluorescence" Name="Alexa Fluor 647" SamplesPerPixel="1">
            <DetectorSettings Binning="1x1" ID="Detector:1"/>
            <FilterSetRef ID="FilterSet:3"/>
            <LightPath/>
         </Channel>

The colours values are 255, 16711680 and 16711935. These are black (opaque), green (transparent) and green (opaque) respectively. Not a particularly useful combination, but that's what's in the exported OME-TIFF, and this is retained as the channel colour after import into Insight. If this is not what was set in Zen, then this is likely an issue with the OME-TIFF export functionality in Zen, and I would suggest contacting Zeiss about it.

Secondly, for setting the channel colours in the webclient, this should certainly work. Click on the "edit" link, choose the channel colours, and then press "save" (not "apply"), and the changes should be preserved on the server, and the image thumbnail should update to reflect the changes.


Regards,
Roger Leigh

Hi Roger,

Many thanks for taking a look. I will report the issue to Zeiss.

As for setting colours in the webclient - I did exactly what you describe. I pressed 'save' but the colours did not get saved.

Cheers,

Dan.

Hi Dan,

The only failure I see when saving channel colour changes in the web image viewer is if I hit "Apply" then "Save". This doesn't save (bug is fixed in the upcoming 5.0.3 release).

But if you hit "Save" without hitting "Apply" then it works fine for me.

I'll attach a couple of screenshots of what I'm seeing, just to be sure we're talking about the same functionality.
Notice the thumbnail in the main webclient window behind (top left).
After hitting "Save", the colours are updated and the thumbnail is refreshed (first screenshot).
Second screenshot is before hitting Save.

You can also confirm whether the save has worked by simply refreshing the browser full-viewer window.

Hope that helps,

Will.

Hi Will,

That is exactly what I did - 'apply' then 'save'. I was just reporting that this seemed to be a bug. Great to know it has already been addressed - thank you!

Cheers,

Dan.