[ome-users] CZI channel description

[forrest.collman at gmail.com]

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
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