[WARN] Unknown IlluminationType value 'Fluorescence' will be stored as "Others"

Dear Forum,

I am currently analyzing viability stainings with a Zeiss Apotome and Fiji (ImageJ 150g). Until updating Fiji this morning (Java 1.6.0_24 64-bit), everything was fine and I could easily open .czi files. Now however and when opening the same files I opened last week, the console opens and gives out the following warning:

ZeissCZIReader initializing… (directory of .czi file)
[WARN] Unknown IlluminationType value ‘Fluorescence’ will be stored as “Other”
[WARN] Unknown IlluminationType value ‘Fluorescence’ will be stored as “Other”

Although there are no further problems with the pictures later on (at least until now), this warning worries me and I would be glad if someone would know how to turn it off / prevent it triggering.

I someone having a similar problem with bfconvert (http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-July/003875.html) but the issue remained unresolved.

Thank you very much for your help!

That warning is harmless, and can be ignored.

Short version: Unfortunately, it is something that must be fixed on the Bio-Formats side.

Long version: With older versions of ImageJ, that sort of output was simply silently discarded. However, there was a problem in that some error messages were never seen by users. We were receiving error reports of the form “I ran plugin XYZ and nothing happens.” Rather than continuing to tell everyone to please relaunch ImageJ in debug mode so that these silently discarded errors would become visible, I decided to add that console window to ImageJ so that everyone would always see the details when something exceptional occurs.

The downside is that any existing plugins which are fond of dumping stuff to the standard error stream now cause the Console window to pop up. Bio-Formats is one of those plugins. While we could add a way to disable the console window, doing so would defeat the purpose of adding it, since people would disable it, forget they disabled it, and then report bugs where “nothing happens” again.

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Thank you very much for your detailed answer! I totally understand the need for the console window and since there seem to be no further problems with the image analysis, I’ll just ignore the warning.

Hi Tino,

Firstly let me introduce myself, I am a developer with the OME team responsible for the Bio-Formats plugin.

Although the warning for an Unknown IlluminationType can be ignored I have created a bug ticket on our tracking system to investigate this further - http://trac.openmicroscopy.org/ome/ticket/13203#ticket

With regards to the warning messages being displayed in the console, we are aware that many users would like more flexibility with the logging reported by the Bio-Formats plugin. As such we have an ongoing ticket for this work also which you can keep track of - https://trac.openmicroscopy.org/ome/ticket/13151

With Thanks,
David Gault

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