<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div apple-content-edited="true"><div>Hi Forrest,<br><br>I have looked into the file you have sent us and it appears that everything is correct.<br>As given by the ZEN software, the Channel names are: DAPI, Alexa Fluor 488, Alexa Fluor 594 and Alexa Fluor 647.<br>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.<br><br>We have fixed the code (<a href="https://github.com/openmicroscopy/bioformats/pull/1213">https://github.com/openmicroscopy/bioformats/pull/1213</a>) and values for all the channels will appear in the OriginalMetadata, so instead of:<br><br>"Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description: Syntaxin1"<br><br>you should get now:<br><br>Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #1: DAPI1<br>Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #2: YFP<br>Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #3: ASIC1<br>Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #4: Syntaxin1A<br><br>I hope that helps you proceed with your analysis workflow.<br><br>Regards,<br>Emil</div><div><br></div><br class="Apple-interchange-newline">
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<br><div><div>On 9 Jul 2014, at 16:15, "<a href="mailto:forrest.collman@gmail.com">forrest.collman@gmail.com</a>" <<a href="mailto:forrest.collman@gmail.com">forrest.collman@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>I am trying to automate some image processing acquired from ZEN through<br>FIJI.<br><br>In ZEN there is an option to have the user write down the name of the each<br>channel.<br><br>This information is saved within the .czi file, and i'd like to access it<br>in order to name each channel according to this user specified name (as<br>opposed to the cryptic Channel 1, Channel 2, etc) so the users don't have<br>refer back to ZEN and reenter information.<br><br>This data appears to be available to metadata reader, but is not properly<br>implemented.<br><br>I can find an original metadata key,value pair from the ImporterMetadata<br>class which is<br>key<br>"Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description"<br>value<br>"Syntaxin1" (which in this case is the name of one of the channel names<br>written into ZEN).<br><br>However, that is the only one available and there are 2 other channels.<br>Nor does this tag appear to specify which channel this name goes with.<br>Syntaxin1 is the last channel of the 3 channels in this example file, so<br>one explanation might be that the code has each channel overwrite the same<br>key/value pair, rather than having the keys be distinct such as...<br><br>Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description#1<br>Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description#2<br>etc...<br><br>This data is also apparently not pushed into the OME-XML tree.. and it<br>seems it should be pushed into the Channel/Name field of the OME-XML model,<br>but instead it puts the filter set name there ("Alexa Fluor 488") for<br>example. This should be stored somewhere else .. probably in the FilterSet<br>portion of the XML.<br><br>I am currently uploading (its about half way done right now) an example<br>file called<br><br>LAL2_070814_ses1big_ASIC1_Syntax1A.czi<br><br>to the OMERO.qa server, which should have 3 channels names (DAPI, ASIC1,<br>and Syntaxin1) with taken across many positions.<br><br>This is the first time I have attempted to use bioformats to<br>programmatically access metadata, so perhaps I am doing something<br>incorrectly, or could access the channel specific tags if i used some other<br>lower level classes.. so any help would be appreciated.<br><br>Best,<br>Forrest<br>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br></body></html>