Source installation (Linux)

CellProfiler 4

CellProfiler 4 should be pip installable in python 3.8+ by simply using pip install cellprofiler, when a number of prerequisite packages are installed. Prerequisites are:

• The basic development packages installed, typically from a base package like build-essential, including make and gcc,
• A Java or OpenJDK JDK (8+) package installed, and the JAVA_HOME environment variable to point to it,
• A recent Python 3 with pip and numpy,
• A MySQL or MariaDB client development environment, and
• A GTK3+ development environment

More details can be found on the individual platform installation pages like https://github.com/CellProfiler/CellProfiler/wiki/Ubuntu-20.04.

Please check out the image.sc forum or our Github issues (and submit new issues as needed) if these instructions fail to work for you.

General Linux Installation Recommendations

To simplify CellProfiler installation on Linux, the generic, standardized installation instructions are based on Conda. While recent versions of CellProfiler should work well with the standard system packages, users may like to follow the Conda-Installation of CellProfiler because it achieves a uniform environment that is easy to maintain, keep up to date and debug in case of problems.

CellProfiler for Batch processing

Note that with CellProfiler 2 and newer, there is no need for a separate CPCluster module anymore. See the command line options for CellProfiler.py to invoke it in (headless) batch mode for cluster operation.