CellProfiler Catalina

Cellprofiler is not starting up on Mac OS Catalina.
It was fine before I updated last year.
Is there a solution?

Hi @rhk1,
Welcome to the forum!

What version of CellProfiler are you using?

Hi,

I tried 3.0.0 as well as the new 3.1.9.
I have Java 8 update 211 and JDK jdk-13.0.2_osx-x64_bin.dmg.

3.1.9 open an icon in the side bar and says “Application not responding” when I right click it.

3.0.0 just shows in icon and then disappears again.

Best wishes Rainer

Hi Rainer,
I’m sorry that you’re having this issue.
CP has been tested on Mac OS up to version 10.14! It seems that it hasn’t been tested on Catalina, which is version 10.15.
I’ll report this to the developers team and we’ll defiantly test the new version of CP on Catalina.

Hi,

I am not in front of my mac, so I can’t test this myself, but it is worth mentioning:
Have you verified that you allow apps from anywhere (under Security and Privacy)?
After trying to run cellprofiler, open Security and Privacy and check if you have to allow the app to run.

More info here.

Best regards,
Mario

Hi,

This function does not exist anymore under OS Catalna.

Choices are: App store

		App Store and identified developers

Best wishes

Rainer

Hi Rainer.

Maybe the “anyone” option is not there anymore, but after executing cellprofiler (unsuccessfully) you should have a message in the security and privacy panel saying:

“cellprofiler” was blocked from use because it is not from an identified developer.

And right next to it you should be able to click “open anyway”.

Best regards,
Mario

Hi,

Thanks for your suggestion.

I found a way to disable all security settings and allow all apps from anywhere.

sudo spctl --master-disabl

The old button “anywhere” appears in security &Privacy

CellProfiler still did not start even after I reinstalled it.

I might have a problem with JAVA.

rhk:~ rkohler$ java version

Error: Could not find or load main class version

Caused by: java.lang.ClassNotFoundException: version

I will try to find the cause for the error.

Thanks

rainer

try: java -version
(java “space” "dash"version)

Thanks

That worked to show the java -version.

RHK:~ rkohler$ java -version

java version “13.0.2” 2020-01-14

Java™ SE Runtime Environment (build 13.0.2+8)

Java HotSpot™ 64-Bit Server VM (build 13.0.2+8, mixed mode, sharing)

When I search for Java in finder I find a lot of versions.

Java 1.7.51.13
Java 1.8.65.17
Java 1.8.73.02
Java 1.8.91.14
Java 1.8.91.14 1
Java 1.8.101.13
Java 1.8.111.14
Java 1.8.111.14 1
Java 1.8.131.11 1
Java 1.8.131.11 2
Java 1.8.201.09

Best wishes

Rainer

Hi Rainer,

I am finally back at my laptop and can confirm your issue. Cellprofiler does not start under OSX catalina.
My Java version is “1.8.0_172”.

Best regards,
Mario

Curious… CellProfiler-3.1.9 does start for me under Catalina (10.15.2) on my slightly-aging MacBook Pro (13-inch, Mid 2014) after right-clicking to get the required ‘Open’ option.

The CellProfiler.app file contains OpenJDK 11.0.2. I also have other Java versions installed, but presume they aren’t interfering.

Hi,

Please help

I still have not found a way to start CellProfiler 3.0 or 3.19 or any other version on Mac OS Catalina 10.15.3.

However, a lab mate runs version 3.0 on Catalina. It works fine for her.

Something must interfere with the program start up on my computer.

Best wishes

Rainer