Installation

Contents

• Installation
  • Introduction
  • Prerequisites
  • SIMA installation
    • Linux
    • Windows
    • Mac OS X

Introduction

We recommended that you perform a binary installation. You should not attempt to build SIMA if you are not familiar with compiling software from sources.

On Windows, we recommend using a scientific python distribution for installing the various prerequisites. Recommended distributions are:

• Python(x,y) (http://code.google.com/p/pythonxy/)
• WinPython (http://code.google.com/p/winpython/)
• Anaconda (https://store.continuum.io/cshop/anaconda)
• EPD (http://www.enthought.com/products/epd.php)

For Mac OS X, we recommend installing the prerequisites, especially OpenCV, using a package manager, such as MacPorts (http://www.macports.org).

Prerequisites

SIMA depends on various freely available, open source software that must be installed prior to using SIMA:

• Python 2.7 (http://python.org)
• numpy >= 1.6.2 (http://www.scipy.org)
• scipy >= 0.13.0 (http://www.scipy.org)
• matplotlib >= 1.2.1 (http://matplotlib.org)
• scikit-image >= 0.9.3 (http://scikit-image.org)
• shapely >= 1.2.14 (https://pypi.python.org/pypi/Shapely)

Depending on the features and data formats you wish to use, you may also need to install the following packages:

• OpenCV 2.4 (http://opencv.org), required for segmentation, registration of ROIs across multiple datasets, and the ROI Buddy GUI
• scikit-learn >= 0.11 (http://scikit-learn.org), required for stICA segmentation
• h5py >= 2.3.1 (http://http://www.h5py.org), required for HDF5 file format
• pylibtiff (https://code.google.com/p/pylibtiff/), required for more efficient handling of large TIFF files
• mdp (http://mdp-toolkit.sourceforge.net), required for ICA demixing of channels

If you build the package from source, you may also need:

• Cython (http://cython.org)

SIMA installation

Linux

The SIMA package can be installed from the python package index:

$ sudo pip install sima

The easy_install tool can also be used:

$ sudo easy_install sima

Source code can be downloaded from https://pypi.python.org/pypi/sima. If you download the source, you can install the package with setuptools:

$ cython sima/*.pyx
$ python setup.py build
$ sudo python setup.py install

Windows

On Windows, you can simply execute the Windows installer that can be downloaded from https://pypi.python.org/pypi/sima. If you run Windows Vista or Windows 7, you may need to right-click on the installer and select “Run as Administrator”.

If building SIMA from source or using pip or easy_install on Windows, you may also need to follow these instructions for compiling the Cython extensions.

Mac OS X

For installing the dependencies, we recommend using MacPorts. If you do not already have XCode installed, downloading XCode from the App Store, and then run the following commands in the Terminal to complete the XCode installation and license agreement:

$ xcode-select --install
$ gcc -v

Next, download and install MacPorts. Then run the following command in terminal to install SIMA and its dependencies:

$ sudo port install python27 py27-numpy py27-scipy py27-matplotlib py27-shapely py27-pip py27-h5py opencv +python27
$ sudo port select --set python python27
$ sudo port select --set pip pip27
$ sudo pip install sima