CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.

Binary installation

Compiled releases for CentOS 6, OS X, and Windows are available from cellprofiler.org/releases.

Source installation

CellProfiler requires Python 2 and NumPy, the fundamental package for scientific computing with Python. More information about installation from source can be found in the wiki, i.e. for Linux, OS X and Windows PC.

Install from the Python Package Index (PyPI)

$ pip install --editable [email protected]:CellProfiler/CellProfiler.git#egg=cellprofiler

Install manually

$ pip install numpy
$ git clone https://github.com/CellProfiler/CellProfiler.git
$ cd CellProfiler
$ pip install --editable .