CellProfiler 3 installation issues (...for newbie)


Hi everyone,

I am sorry if I come back with such a common problem. I have seen many posts on the topic but can’t find an easy way to fix it. I am quite a newbie with Mac (I usually use CellProfiler on a PC with Windows) and don’t want to create a mess on the computer running a bunch of commands I don’t quite control.

I have a MacBook Pro with macOS High Sierra Version 10.13.4

I have Java 8 installed. Although when I try to see it on the Terminal here is what I get:

mac-l9:~ user$ java -version
java version “1.6.0_65”
Java™ SE Runtime Environment (build 1.6.0_65-b14-468)
Java HotSpot™ 64-Bit Server VM (build 20.65-b04-468, mixed mode)


mac-l9:~ user$ /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java -version
java version “1.8.0_171”
Java™ SE Runtime Environment (build 1.8.0_171-b11)
Java HotSpot™ 64-Bit Server VM (build 25.171-b11, mixed mode)

Sorry if it is trivial.

Thanks in advance for your help,



Sorry, I didn’t specify the actual problem. I have the same as a lot of other people.

I installed CellProfiler 3.0.0 on Desktop. Now, when I launch it, I can see it on the Dock. Then it disappears and nothing happens.



it doesn’t look like your main java is 1.8, but instead 1.6. Can you try downloading the recommend JDK from here and seeing if that fixes your problem?


Thanks!! Now it works perfectly. I can see my Java 8 version on the terminal with only “java - version” command. I had a problem with pipeline loading at the start of CellProfiler but at least it finally started. I have my pipeline so it should be fine.

…except that it has been built on an old version of CellProfiler but this is a different story.

Thanks again,