Failed to install ": java.nio.charset.UnsupportedCharsetException: cp0

[RSeddonGB]

Hello

Received the following error while trying to run MiNA Analyze Morphology via Fiji on a new Windows 10 AIO Desktop:

console: Failed to install ": java.nio.charset.UnsupportedCharsetException: cp0 3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily

Latest version of Fij/ImageJ being used. All plugins and updates installed as detailed in the MiNa Wiki: https://imagej.net/MiNA_-_Mitochondrial_Network_Analysis

MiNa and related plugins work fine on my two other computers (both with dedicated nvidia GPUs). New desktop is running a i7-9700 with Intel integrated graphics (Intel Uhd 630 graphics driver).

Do you have any information or fixes concerning these two error messages?

Many Thanks,

Richard

[RodoVJ]

Hello Richard,

Does MiNA run fine despite the message? This has been a problem with ImageJ when running scripts written in Jython (MiNA is written in Jython) and it also seems to appear more frequently in systems running Windows. This has to do with Jython having trouble finding the encoding of the console. Usually this does not affect the functionality of the program but there are ways to get rid of the message by explicitly stating the encoding. You can do this by by modifying/creating the file jvm.cfg in the same directory as the Fiji launcher and adding the following: -Dpython.console.encoding=UTF-8 or to the command line in headless mode. https://imagej.net/Java_Options https://github.com/imagej/imagej-launcher/issues/56

Concerning the 3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily message, it is simply a message displayed after the Image3DUniverse library is imported. https://github.com/StuartLab/MiNA/blob/dc02fc7c25738c323755bcc6461bf4faeec2af93/src/MiNA_Analyze_Morphology.py#L37

Please let me know if you have any further questions,

Rodrigo

[RSeddonGB]

Hello Rodrigo,

Thanks so much for your reply. MiNa was starting and asking for input but not going onto give results.

I created the jvm.cfg file in the Fiji directory as you said and that did get rid of the error message however MiNa is still not running as normal.

I thought it would be best to capture my screen to show you what is happening as the behaviour is interesting. Plugin shown as permanently running in the source code viewer:

https://www.youtube.com/watch?v=2MI_GPMbLS4

Good point on Windows, I installed a Linux Virtual Machine to rule out hardware issues with the pc and the tool ran perfectly within that.

If you have the time to have a look at this I would really appreciate it!

Thanks Again, Richard

[RodoVJ]

Hi Richard,

Thanks for the video. Seems like MiNA may be having speed performance issues analyzing big 3D images. Does this lack of response only occur with large 3D images or does it also occur in 2D and small 3D images? If the large 3D images are the problem, I would recommend you take a look at MitoGraph, a tool to calculate and analyze three-dimensional morphology of mitochondria. https://github.com/vianamp/MitoGraph

Unfortunately it only runs on mac at the moment, but ScienceToolKit has a forked branch of MitoGraph that can run on Linux, so that you may use it on a Linux VM. https://github.com/ScienceToolkit/MitoGraph/tree/linux-build

[RSeddonGB]

Hi Rodrigo,

Thanks very much for your recommendation of MicroGraph, have installed it on a Linux VM and it is just what I was looking for!

Yes the issue was with the 3D files however I have another computer with a dedicated GPU which runs MiNa well so now have both programs working.

It's interesting that, on the same PC, MiNa ran on well Linux Virtual Machine but not on Windows. Do you know what would cause that as in this case the hardware is equal?

Thanks again for the help and recommendation,

Richard

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