Open Microscopy Environment

Hi
I wonder if you can help me.
On opening an ome-tiff from Fiji using Plugins->Bio-Formats->Bio-Formats Importer I get the following: "Warning: Could not get charToByteConverterClass" on my first attempt to open the file. Is this something that I need to address?

Best Wishes

Ian

Hi Ian,

These are likely relevant:

http://bugs.java.com/bugdatabase/view_b ... id=6254234
https://github.com/openspim/micromanager/issues/5

which suggests that the warning is an unresolved but non-fatal bug in some JDK and/or Xalan versions, and not something in Bio-Formats. Could you please note the Java version that you're using so that we can reproduce the warning? We can then see if a newer Xalan version would fix it, or if it's just safe to ignore.

-Melissa

Thanks Melissa

java -version gives me:

java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)

I'm assuming that's the one Fiji uses?
At some point I've inadvertently upgraded to El Cap 10.11.4 in case that's relevant.

Best Wishes

Ian

Same issue here and it also happens with other file formats

ImageJ 2.0.0-rc-43/1.51d

openjdk version "1.8.0_92"
OpenJDK Runtime Environment (build 1.8.0_92-b14)
OpenJDK 64-Bit Server VM (build 25.92-b14, mixed mode)

Gregor

Just to follow up based on ongoing testing this afternoon:
- We have been unable to reproduce the issue with clean ImageJ installs, using either the standard install or the Java bundled install from https://imagej.nih.gov/ij/download.html
- The latest Fiji download also does not show the issue when installed clean
- Changing Java versions from Java 6 to Java 8 does not show any difference
- The warning has so far only been reproduced with an existing Fiji install with changes to plugins

We are still investigating and comparing various plugin configurations to attempt to locate the root cause of the issue.

With Thanks,
David Gault

Hi Gregor,

We have managed to narrow down the cause of this warning to be due to the OMERO.insight-ij plugin.

It is just a warning message so can be ignored, or if your are not using the plugin then removing the plugin will also see the warning removed.

With Thanks,
David Gault

I have opened the following bug report to track this issue - https://trac.openmicroscopy.org/ome/ticket/13259#ticket

David