Getting started

Welcome to Esmraldi!

Esmraldi is an open source Python 3 library used to analyze Mass Spectrometry Imaging (MSI) jointly with Magnetic Resonance Imaging (MRI) images. It focuses on precise and efficient methods for the fusion of these images. The code in this library is particularly aimed at :

  1. Efficient spectra processing of IMS images

  2. Precise registration between several modalities

  3. Easily interpretable statistical analysis

This library is designed to be as generic as possible and can be, in principle, used for the fusion of IMS images with any other imaging modality.

Setting up Esmraldi

To install Esmraldi, we strongly recommend using a scientific Python distribution. Esmraldi relies on packages such as NumPy, Matplotlib and SciPy.

Esmraldi requires Python 3. All packages dependencies are listed in requirements.txt.

You can set up Esmraldi with:

git clone https://github.com/fgrelard/Esmraldi.git
cd Esmraldi
cat requirements.txt | xargs -n 1 -L 1 pip install

Note that the dependencies listed in requirements.txt are associated to minimum required versions, tested on Ubuntu 18.04 LTS. We do not guarantee that older versions will function properly.

Checking the installation

To check whether everything has been installed properly, run:

python -m examples.check_install

The following output should appear after a few seconds, possibly along with some unimportant missing ms_peak_picker and ms_deisotope module warnings:

Esmraldi set-up successful!
All required dependencies installed

If it does, congratulations! You can now use Esmraldi.