Installation

Anaconda

pyCellAnalyst now requires Anaconda Python from Continuum Analytics. You can install either the full Anaconda package or Miniconda.

Note

You must install the 64 bit 2.x version not the 3.x version.

Installing from Anaconda Cloud

  1. Add additional channels to fetch packages from.

    conda config --add channels conda-forge
conda config --add channels salilab
conda config --add channels SimpleITK
conda config --add channels siboles

  2. Install

    To install to your root conda environment:

    conda install -c siboles pycellanalyst

    To install to a conda virtual environment for just pyCellAnalyst:

    conda create --name pyCell pycellanalyst

Optional

It is still possible to install pyCellAnalyst to a standard Python build. Although the dependencies must be resolved by the user. pyCellAnalyst depends on the following:

Available in PyPi

  • numpy
  • scipy
  • scikit-learn
  • matplotlib
  • wquantiles
  • xlrd
  • xlwt
  • trimesh
  • febio

Others:

Troubleshooting

  • If the Anaconda version of Python does not start when you type python in a command terminal you likely need to unset your PYTHONPATH and PYTHONHOME variables.

  • Other problems with Anaconda can be researched here

  • If the pycellanalyst does not work with conda install on Linux, the user can build the package themself. - Download the source code - Unzip and open a command terminal in the src directory containing build.sh. - Type the following:

    conda build .
conda install --use-local pycellanalyst