Fiji on macOs catalina

Fiji doesnt start in Mac Os Catalina (isnt Fiji a 64 bit program)

2 Likes

Hi @VIROCON_2016,

Welcome to the forum, and sorry it took awhile for someone to reply.

Sorry to hear that and thanks for reporting this. Is there an error message? If so, could you post it here?

First thing that comes to mind is it may have to do with what java version you have installed.
Would you mind opening a terminal, running java -version, and posting the results?

Yes, it is.

I’m not sure what’s going on, but if you’re able to post answers to the questions above, hopefully it will help someone figure it out.

Thanks for reporting this problem!
John

1 Like

Sir, Initially Fiji didnt work, it had a white X on the tile,

when I reinstalled Fiji it works in Mac Catalina.

when I unzipped the file and saved to a location I could also update.

the java -version returns this

openjdk version “1.8.0_121”

OpenJDK Runtime Environment (Zulu 8.20.0.5-macosx) (build 1.8.0_121-b15)

OpenJDK 64-Bit Server VM (Zulu 8.20.0.5-macosx) (build 25.121-b15, mixed mode)

thanks Samuel

1 Like

@VIROCON_2016 Could you try the DMG installer here and see if that works any better?

Unfortunately, macOS makes it hard to use applications that come directly out of ZIP files. You need to:

  • Unzip it to Desktop
  • Move it from Desktop to Applications
  • Right-click the icon in Applications and choose “Open”, then confirm you want to open the application even though it is from an “unidentified developer”

Several people have reported problems running it from Desktop (due to a feature called Path Randomization)—although once you run it once using the right-click method, it may work from Desktop.

All of the above is true even before Catalina. Maybe Catalina brings new troubles; I’m not sure.

2 Likes

Dear all,

It seems that the issue somewhat came back: I just update my mac os to Catalina (10.15.2), and I can’t use any of the Life-Line versions of Fiji (application crashes seconds after being executed). Re-installing Java 6* did not help.
*using the official legacy version and this trick).
Am I missing something?

Many thanks in advance for any help and happy 2020,
Eli

@Eli Sorry for the delay in reply.

Did you try launching ImageJ from the console? What is the error message?

Are you seeing a popup dialog about a legacy Java 6 runtime being required?

Regardless—in my experience, Apple Java 6 simply does not function correctly on macOS 10.14+. At least: I have been unable to make Fiji (older Java-6-based Life-Line versions) run correctly on my Mojave system. It will start up, but the keyboard doesn’t work, there are stack traces, and other weirdness.

As such, I would recommend to always use Java 8 on Catalina—even with the older Life-Line versions of Fiji.

Dear @ctrueden,
Many thanks for your answer. Depending on the different Fiji versions, I get different error messages (given by the the terminal):

Warning: Could not access Java VM
Exception in thread "main" java.lang.NoClassDefFoundError: fiji/Main
Caused by: java.lang.ClassNotFoundException: fiji.Main
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find fiji/Main

or

Warning: could not find Java bundle
Warning: could not find Java bundle
No known JRE; cannot link to Java library
Warning: falling back to System JVM
MacEli:~ eli$ -Djava.ext.dirs=/Applications/Fiji-old/Fiji-lifeline/Fiji-lifeline.app/java/macosx-java3/Home/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext is not supported.  Use -classpath instead.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

I unfortunately cannot use Java 8, as I need BoneJ, which requires Java 6 (I know there is an experimental version of BoneJ that runs with Java 8, but from my current experience it is not quite ready yet).

Many thanks again for your help.

All the best,
Eli

Thanks for the additional details, @Eli. Unfortunately, I do not know how to make Java 6 work on Mojave or Catalina. (@mdoube have you had success with that?) I suggest you use a different operating system. Perhaps you could use Boot Camp to dual boot into Windows. Or you could try using BoneJ2.

Thanks again @ctrueden.

No Apple devices to test with here, I work with Ubuntu (mostly) and Windows (sometimes, for functional testing). In general @Eli it is better now to move to BoneJ2 unless you have a specific reason to stay with BoneJ1. If you have to stick with BoneJ1 please tell us why so that if appropriate we can ensure functionality is ported to BoneJ2.

1 Like

5 posts were split to a new topic: BoneJ2 usage questions

Hi!
I just downloaded fiji for macOS. When I try to open the application, I get the message: ‘Fiji cannot be opened because the developer cannot be verified’.
I tried downloading the latest java update, but this didn’t help.
How should i proceed?
Thanks!

@Viktorkopp After dragging Fiji to your Applications folder, right click the Fiji icon, select Open from the context menu, and then confirm to open the application from an “unidentified developer.” After doing that once, your system will green-light the app, and you will be able to double-click it as normal.

Alternately, you can “Allow apps downloaded from Anywhere” in the Security & Privacy settings, although this is a global setting for all future double-click launches.

I downloaded from https://fiji.sc
I was able to install it on Catalina. But it gives a warning like this:
[WARNING] Your ImageJ installation cannot be updated because it is read-only

And I cannot install plugins.

@Govind_Sharm Maybe these instructions help?

1 Like

Hi all,

I just bought a macbook air with Catalina OS and dl FIJi. No problem with the installation but when I start FIJI I got this warning

“Java SE 6 is required to open FIJI”

Can I switch back from the new FIJI I installed to this version? How can I resolved this situation.

Thank a lot !