Install CellProfiler dev on Windows

install_on_windows.txt

Install Microsoft SDK for Windows 7
Install JDK 8 64-bit
Install Python 2.7
Install Git for Windows (and choose the option that lets you run git from the Windows command-line)
Install CMake (https://cmake.org/download) (choose the option to aqdd CMake to the system PATH for current user)
pip install --upgrade pip
pip install virtualenv
#
# The wheels (.whl) from Christoph Gohlke's site can be installed like this:
# pip install c:/Users/<me>/Downloads/mywheel_amd64.whl
#
Install Numpy from http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
Install Scipy from http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy
Install MySQLdb from http://www.lfd.uci.edu/~gohlke/pythonlibs/#mysql-python
Install h5py from http://www.lfd.uci.edu/~gohlke/pythonlibs/#h5py
Install wx 3.0 from http://www.lfd.uci.edu/~gohlke/pythonlibs/#wxpython
Install wxpython-common from http://www.lfd.uci.edu/~gohlke/pythonlibs/#wxpython-common
Install cython from http://www.lfd.uci.edu/~gohlke/pythonlibs/#cython
Install lxml from http://www.lfd.uci.edu/~gohlke/pythonlibx/#lxml
pip install pandas

virtualenv --system-site-packages <venv-dir>
git clone https://github.com/CellProfiler/CellProfiler <cp-dir>
   Open the Windows SDK 7.1 command prompt (from the start menu)
   <venv-dir>\Scripts\activate
   set MSSdk=1
   set DISTUTILS_USE_SDK=1
   pip install --no-deps javabridge
   cd <cp-dir>
   pip install -r requirements.txt
   pip install --editable git+https://github.com/CellH5/cellh5.git#egg=cellh5
   python setup.py prokaryote
   python setup.py develop install
   
If you want Ilastik:
Install pqt4 from here: http://www.lfd.uci.edu/~gohlke/pythonlibs/#pyqt4
git clone https://github.com/LeeKamentsky/build-ilastik-on-windows
    Open the Windows SDK 7.1 command prompt
   <venv-dir>\Scripts\activate
   set MSSdk=1
   set DISTUTILS_USE_SDK=1
   cd to the build-ilastik-on-windows folder
   python setup.py build

You should be able to run CellProfiler within the virtual environment at the command-line.
   

Also had to pip install wheel before installing wheels.