New CellProfiler Release! Plus Developer Resources!


An updated version of CellProfiler has been released!
It has some new features, and many bugfixes. Download it here

We are also introducing new resources for CellProfiler/CellProfiler Analyst developers here, including mailing lists, access to our SVN repositories, information on the next stage of CellProfiler development (namely, porting our entire code base from Matlab to Python) and more.


Hi. I’m getting

Network Error (tcp_error)

A communication error occurred: "Connection refused"
The Web Server may be down, too busy, or experiencing other problems preventing it from responding to requests. You may wish to try again at a later time.

For assistance, contact your network support team. [/code]

Not sure if it’s our proxy server or if there’s a problem with


Had the wrong links. It’s been corrected. Thanks!


This is great – I’m really excited to see the project moving in this direction! Thanks all of you for the work you’re putting in to make this happen.



Hello David, I’m new here, I try to find how to integrate Cellprofiler to Java, I’m using netbeans IDE. Is there any tutorial for this? Thanks


Hi jeanlucboeuf,

Sorry, we lost track of your question. We do have a python package called “javabridge” which…

Do you want to call CellProfiler the other way, i.e. from Java? I don’t know of anyone who has done this but note that we do have a developer’s wiki:
and one can run CellProfiler from the command line: … mmand_line
presumably from Java as well.

Hope that helps,