How to get started¶

Installation of emzed as part of Spyder (recommended)¶

The easiest way to get started is to install emzed as part of the integrated development environment (IDE) Spyder. For that purpose, we provide emzed-spyder, which consists of a modified version of Spyder that automatically installs emzed and emzed-gui during the first startup.

Installation on Windows¶

For Windows, we offer an installer for the latest version here.

Note, that the Windows installer has to be unblocked first in the Properties window of the setup .exe file before it can be run:

Installation on any operating system using pip¶

For all operating systems (Linux, Mac, Windows), emzed-spyder can also be installed using pip:

pip install emzed-spyder

After successful installation you can start emzed-spyder either using the shortcut in the start menu (only available using the Windows installer) or by running emzed.spyder from the command line.

Notes when using pip:

We recommend using a virtual environment when installing emzed or emzed-spyder using pip.
Requirements: Python 3.10 up to 3.12

Installation of emzed and emzed-gui using pip¶

If you do not need the Spyder IDE (e.g. for notebooks, servers, etc.), you can also install emzed and emzed-gui (not required for head-less environments) using pip:

pip install emzed emzed-gui

Tutorials and example workflow¶

You want to see how you can use emzed and what functionalities it offers? Have a look at our tutorials.

We also provide a complex example workflow as a notebook on Binder, showcasing how emzed can be used to solve case-specific problems such as retention time drifts in targeted analysis:

About the emzed components¶

emzed consists of three base components:

The core library, also called emzed which offers all functionalities which do not require a graphical user interface and as such can be used on head-less computing environments like stand-alone servers or high performance computing environments. The documentation is hosted at https://emzed.ethz.ch/3/emzed.
The interactive inspection tools to visualize samples or peak lists are available within emzed-gui which serves as an add-on to the core library. Documentation can be found at https://emzed.ethz.ch/3/emzed_gui.
The integrated development environment emzed-spyder offers a development environment tailored to emzed. Documentation is hosted at https://emzed.ethz.ch/3/emzed_spyder.

As we wanted to avoid cluttering emzed with machine or application specific functionalities, emzed offers an extension mechanism which is also intended to support community contributions.

At the moment we offer an extension to wrap some selected algorithms from MZmine2. The extension can be installed using: emzed_install_ext('mzmine2')