[ome-users] CZI channel description

[Emil Rozbicki]

Hi Forrest,

I have looked into the file you have sent us and it appears that everything is correct.
As given by the ZEN software, the Channel names are: DAPI, Alexa Fluor 488, Alexa Fluor 594 and Alexa Fluor 647.
The values you mentioned are indeed called Channel Description: DAPI1, YFP, ASIC1, Syntaxin1A, and as such are not included in the current OME-XML model.

We have fixed the code (https://github.com/openmicroscopy/bioformats/pull/1213) and values for all the channels will appear in the OriginalMetadata, so instead of:

"Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description: Syntaxin1"

you should get now:

Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #1: DAPI1
Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #2: YFP
Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #3: ASIC1
Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #4: Syntaxin1A

I hope that helps you proceed with your analysis workflow.

Regards,
Emil



On 9 Jul 2014, at 16:15, "forrest.collman at gmail.com" <forrest.collman at gmail.com> wrote:

> Hi,
> 
> I am trying to automate some image processing acquired from ZEN through
> FIJI.
> 
> In ZEN there is an option to have the user write down the name of the each
> channel.
> 
> This information is saved within the .czi file, and i'd like to access it
> in order to name each channel according to this user specified name (as
> opposed to the cryptic Channel 1, Channel 2, etc) so the users don't have
> refer back to ZEN and reenter information.
> 
> This data appears to be available to metadata reader, but is not properly
> implemented.
> 
> I can find an original metadata key,value pair from the ImporterMetadata
> class which is
> key
> "Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description"
> value
> "Syntaxin1" (which in this case is the name of one of the channel names
> written into ZEN).
> 
> However, that is the only one available and there are 2 other channels.
> Nor does this tag appear to specify which channel this name goes with.
> Syntaxin1 is the last channel of the 3 channels in this example file, so
> one explanation might be that the code has each channel overwrite the same
> key/value pair, rather than having the keys be distinct such as...
> 
> Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description#1
> Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description#2
> etc...
> 
> This data is also apparently not pushed into the OME-XML tree.. and it
> seems it should be pushed into the Channel/Name field of the OME-XML model,
> but instead it puts the filter set name there ("Alexa Fluor 488") for
> example.  This should be stored somewhere else .. probably in the FilterSet
> portion of the XML.
> 
> I am currently uploading (its about half way done right now) an example
> file called
> 
> LAL2_070814_ses1big_ASIC1_Syntax1A.czi
> 
> to the OMERO.qa server, which should have 3 channels names (DAPI, ASIC1,
> and Syntaxin1) with taken across many positions.
> 
> This is the first time I have attempted to use bioformats to
> programmatically access metadata, so perhaps I am doing something
> incorrectly, or could access the channel specific tags if i used some other
> lower level classes.. so any help would be appreciated.
> 
> Best,
> Forrest
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140711/c066ced9/attachment.html>