[ome-users] CZI channel description

[Emil Rozbicki]

Forwarded response from Forrest Collman:

Hi Emil, 

thank you so much for taking a look at this issue, and making this available via the original metadata to me. I think i can use this to make my workflow work correctly. 

However, I respectively disagree about the channel names in Zen.  It seems to me that the schema should be able to specify what the meaning of the channel that is acquired is, and that this information is critical to understanding what the image contains.  So with respect to Alexa 594 vs ASIC1... Alexa 594 corresponds to a fluorophore that Zen has preprogramed.. which corresponds to a choice of filter cube optimized to observe that fluorophore.  The user cannot enter ASIC1 as the channel name in ZEN, as ASIC1 is biological molecule, and ZEN doesn't know apriori what filter cube to use with it.  Alexa 594 is the fluorophore is attached to ASIC1 molecule of interest.  This is the meaning of the biological image.  To not have a way to include this in the OME-XML model seems fundamentally flawed.  

Put another way, our microscope only has 4 filter wheels.  Every image it takes will have those channel names in ZEN, but we take images using hundreds of different antibodies which are tagged with different fluorophores. If the OME-XML schema doesn't let me write down what antibodies i was using when i snapped a picture, how it a useful tool to keep track of my data. 

In ZEN, its only this description field that the user can use to input a "meaningful" name to display, that keeps track of what the true biological meaning of the image is.  That seems to me, to fit the description of the schema, much better than the name of the dye/filterset that was used in the image. Perhaps you still disagree, but there should be somewhere else that it exists within the data?  

In any case, again, thank you so much for fixing this, I'll attempt to get the code pulled and compiled today.  I have been able to access the original metadata, so by pulling out these Keys I can get access to these channel names, so I'm happy, but I thought I'd lobby for the change to the OME-XML as well.

Best,
Forrest


On 9 Jul 2014, at 16:15, 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/20140712/d5d3db83/attachment.html>