Installing HyperSpy

The easiest way to install HyperSpy in Microsoft Windows is installing the HyperSpy Bundle.

For quick instructions on how to install HyperSpy in Linux, MacOs or Windows using the Anaconda Python distribution see Quick instructions to install HyperSpy using Anaconda (Linux, MacOs, Windows).

Those experienced with Python may like to Install using Python installers or Install from source.


Since version 0.8.4 HyperSpy only supports Python 3. If you need to install HyperSpy in Python 2.7 install HyperSpy 0.8.3.

HyperSpy Bundle for Microsoft Windows

New in version 0.6.

The easiest way to install HyperSpy in Windows is installing the HyperSpy Bundle. This is a customised WinPython distribution that includes HyperSpy, all its dependencies and many other scientific Python packages. HyperSpy Bundle does not interact with any other Python installation in your system, so it can be safely installed alongside other Python distributions. Moreover it is portable, so it can be installed in an USB key. When intalling it with administator rights for all users it adds context menu entries to start the Jupyter Notebook and Juypter QtConsole. See start_jupyter_cm for details.

Quick instructions to install HyperSpy using Anaconda (Linux, MacOs, Windows)

  1. Download and install Anaconda. Anaconda is recommended for the best performance (it is compiled using Intel MKL libraries) and the easiest intallation (all the required libraries are included). The academic license is free.

    $ conda install -c conda-forge traits traitsui
    $ pip install hyperspy


Since version 0.8.4 HyperSpy only supports Python 3. If you need to install HyperSpy in Python 2.7 install version 0.8.3:

$ pip install --upgrade hyperspy==0.8.3-1

For convenience you may also consider installing start_jupyter_cm.

For more options and details read the rest of the documentation.

Install using Python installers

HyperSpy is listed in the Python Package Index. Therefore, it can be automatically downloaded and installed pip. You may need to install pip for the following commands to run.

Install using pip:

$ pip install hyperspy


The command above downloads and installs HyperSpy and all its dependencies. However, HyperSpy depends on several external libraries which are not written in pure Python. We recommend to those not familiar with the installation of Python libraries that may require compilation to install HyperSpy using Anaconda instead.


Since version 0.8.4 HyperSpy only supports Python 3. If you need to install HyperSpy in Python 2.7 install version 0.8.3:

$ pip install --upgrade hyperspy==0.8.3-1

pip installs automatically the stricly required libraries. However, for full functionality you may need to install some other dependencies, see Installing the required libraries.

Creating Conda environment for HyperSpy

Anaconda Python distribution can be easily set up using environment files. The two required steps are:

  1. Download HyperSpy environment file.
  2. Create and activate HyperSpy environment according to instructions here. For Unix, the following should work:
$ conda env create -f anaconda_hyperspy_environment.yml
$ source activate hyperspy

Install from a binary

We provide binary distributions for Windows (see the Downloads section of the website). To install easily in other platforms see Install using Python installers

Install from source

Released version

To install from source grab a tar.gz release and in Linux/Mac (requires to Installing the required libraries manually):

$ tar -xzf hyperspy.tar.gz
$ cd hyperspy
$ python install

You can also use a Python installer, e.g.

$ pip install hyperspy.tar.gz

Development version

To get the development version from our git repository you need to install git. Then just do:

$ git clone

To install HyperSpy you could proceed like in Released version. However, if you are installing from the development version most likely you will prefer to install HyperSpy using pip development mode:

$ cd hyperspy
$ pip install -e ./

All required dependencies are automatically installed by pip. However, for extra functonality you may need to install some extra dependencies, see Installing the required libraries. Note the pip installer requires root to install, so for Ubuntu:

$ cd hyperspy
$ sudo pip install -e ./

If using Arch Linux, the latest checkout of the master development branch can be installed through the AUR by installing the hyperspy-git package

Creating Debian/Ubuntu binaries

You can create binaries for Debian/Ubuntu from the source by running the release_debian script

$ ./release_debian


For this to work, the following packages must be installed in your system python-stdeb, debhelper, dpkg-dev and python-argparser are required.

Installing the required libraries

When installing HyperSpy using Python installers or from source the Python programming language and the following libraries must be installed in the system: numpy, scipy, matplotlib (>= 1.2), ipython, natsort, traits and traitsui. For full functionality it is recommended to also install h5py, scikit-learn and ipywidgets. In addition, since version 0.7.2 the lowess filter requires statsmodels. In Windows HyperSpy uses the Ipython’s QtConsole and therefore Qt and PyQt or PySide are also required.

In Debian/Ubuntu you can install the libraries as follows:

$ sudo apt-get install python-numpy python-matplotlib ipython
ipython-notebook python-traits python-traitsui python-h5py
python-scikits-learn python-nose python-statsmodels

In Arch Linux, the following command should install the required packages to get a fully functional installation:

$ sudo pacman -Sy python2 python2-numpy     python2-matplotlib      python2-pip
python2-traits python2-traitsui python2-h5py python2-scikit-learn python2-nose
python2-statsmodels python2-pillow python2-pyqt4 python2-pyqt5 python2-scipy
python2-pandas python2-setuptools ipython2  python2-jinja python2-pyzmq
python2-pyqt4 python2-tornado python2-sip python2-pygments

# Or, just run this command from the root hyperspy directory to import the
# list of packages and install automatically:
$ xargs sudo pacman -Sy --noconfirm < doc/package_lists/arch_linux_package_list.txt

# Once these are installed, go to the HyperSpy directory and run:
$ sudo pip2 install -e ./

# If desired, the python2-seaborn library can also be installed from AUR for prettier plotting

Known issues


  • If HyperSpy fails to start in Windows try installing the Microsoft Visual C++ 2008 redistributable packages ( 64 bit or 32 bit) before reporting a bug.

  • In some Windows machines an error is printed at the end of the installation and the entries in the context menu and the Start Menu are not installed properly. In most cases the problem can be solved by restarting the computer and reinstalling HyperSpy.

  • Due to a Python bug sometimes uninstalling HyperSpy does not uninstall the “HyperSpy Here” entries in the context menu. Please run the following code in a Windows Terminal with administrator rights to remove the entries manually:

    $ uninstall_hyperspy_here
  • If HyperSpy raise a MemoryError exceptions:

    • Install the 64bit if you’re using the 32bit one and you are running HyperSpy in a 64bit system.
    • Increase the available RAM but closing other applications or physically adding more RAM to your computer.