The thing is I am also new to ubuntu so I did not know if I installed properly Icy.
To answer you question:
- You installed Icy (version 22.214.171.124 I guess?) on Ubuntu (20.04?)
Yes, this is my icy version that I download directly from the website. I have obtained a folder “Icy_all_126.96.36.199” that I unzipped in my documents. Then, I made the Icy.jar file executable from the file properties to be able to launch it. My ubuntu version is 18.04
- You started Icy. Did you start Icy from its folder ? the download notes says the following: “ Icy now includes the VTK binaries (with java binding), be sure to start Icy from its folder so VTK library can load correctly.
Still you may experience incompatibilities depending your Linux distribution (we tested only for Ubuntu and Mint), in this case you may need to install (or compile) the dedicated VTK package (version 6.3 currently) with java wrapper for your distribution and move the library files (.so) into the lib/linux64/vtk folder of Icy. ”
I guess yes, because as I mentionned before, I unzipped the folder and made Icy.jar executable and launch from this
- You installed the ec-CLEM plugin. Did you install it from the search bar of the Icy software or by copying the .jar in the plugin folder?
I installed it from the search bar
- You managed to follow& reproduce the first videos from the plugin description page, I mean the introduction to Icy and the rigid registration.
Yes, I was able to place a few points a get an overlay with some imprecisions in the corners due to TEM deformation
- When trying the non-rigid registration, you observe the error code “java.lang.UnsatisfiedLinkError:…”.
Yes. From what I understand in the video, I let my images open and changed the transformation mode to “non ridid”, ticked the box to show grid deformation, run the plugin and click on “update transformation” and at this time the error message appears
- On top of this you have a second error message when opening Icy.
Yes, It is apparently an ImageJ windows that pop and say this message when opening icy
Here is the output console. Yes apparently it cannot run the VTK library
OpenJDK Runtime Environment 11.0.7+10-post-Ubuntu-2ubuntu218.04 (64 bit)
Running on Linux 4.15.0-1087-oem (amd64)
Number of processors : 64
System total memory : 97.6 GB
System available memory : 54.4 GB
Max java memory : 24.4 GB
Image cache initialized (reserved memory = 9531 MB, disk cache location = /tmp)
java.lang.UnsatisfiedLinkError: no vtkalglib in java.library.path: [/usr/local/IMOD/lib, ., /usr/java/packages/lib, /usr/lib/x86_64-linux-gnu/jni, /lib/x86_64-linux-gnu, /usr/lib/x86_64-linux-gnu, /usr/lib/jni, /lib, /usr/lib, /home/ameliebernard/lib/unix64, /tmp/lib, /lib64, /lib/x86_64, /usr/lib64, /usr/lib/x86_64]
Cannot load VTK library…
Icy Version 188.8.131.52 started !