Source installation (Windows)

bethac07 edited this page Jul 23, 2018 · 15 revisions

Running CellProfiler from Source on Windows (as of v3.1.5)

Note: an alternative Windows installation is available using miniconda.

  • To obtain the source code from our GitHub repository, you will need to install Git: instructions
  • For those adverse to command lines, we recommend using GitHub for Windows (GFW) or GitKraken
  • After installing GFW, to clone the CellProfiler GitHub repo, do the following:
    • Sign in to your GitHub account on GFW and on the website
    • Browse to the CellProfiler GitHub page
    • On the webpage, click Clone or download -> Open in Desktop
    • It should prompt for the location of the cloned repo. By default, it will place the repository under C:\Users\<username>\Documents\GitHub (in Windows 7/Vista). If you want to place it elsewhere, you can move the cloned folder to a location of your choosing. If you select "Open this repo" in GFW (click on the small right arrow), it will ask for the new location which you can specify with "Find It".

Downloading CellProfiler's libraries and dependencies

  • Download and install packages for Python 2.7 on your machine (find the latest version less than 3.0, as 3.0+ is not yet supported).
    • If using Windows do NOT use Python XY, as it only installs as 32 bit.
    • When installing, it's a good idea to enable the "Add python to path" option
  • Download the Microsoft Visual C++ 2008 Redistributable Package and its 64-bit SP1
  • Install Microsoft .NET Framework 3.5 SP1
  • Install the Microsoft Visual C++ Compiler for Python 2.7
  • Install the Java Development Kit
  • Most packages can be install online via pip. However, some cannot (yet), and one must currently be installed from source. For each of the packages listed below, pip install them offline by:
    • Download the packages from this site
    • Open the Visual C++ 2008 64-bit Command Prompt (under Start Menu > Microsoft Visual C++ Compiler Package for Python 2.7)
    • cd to where you've downloaded the .whl package
    • Type pip install <package-name>.whl
  • The packages that need to be installed offline are
    1. NumPy: A Python extension which provides convenient and fast N-dimensional array manipulation. Important note: You will need to download the NumPy MKL version of the package for compatibility with Scipy.
    2. SciPy
    3. wxPython: Provides bindings to the wxWidgets cross-platform toolkit. You will need to install both wxPython and wxPython-common
    4. mysqlclient
  • Clone Javabridge ala the instructions for cloning CellProfiler.
    • cd into the javabridge directory and run pip install -e .
    • If you run into an error that cython can't be fetched, run pip install cython and then try pip install -e . again.
    • If you run into an error about numpy not being located:
      • run git fetch origin pull/138/head:numpy
      • run git checkout numpy
      • retry the pip install -e . command
  • After installing the above, cd into the directory where you cloned CellProfiler and run pip install -e .

Starting CellProfiler

  • At this point, CellProfiler is installed! You may now run CellProfiler by typing cellprofiler from the command line
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