pIMZ: an integrative framework for imaging mass spectrometry analysis

Description

pIMZ is a framework for Imaging Mass Spectrometry (IMS) data analysis. The python implementation is available from github.com/mjoppich/pIMZ. For installation follow the instructions given here.

pIMZ focuses on a differential setting, where masses, specific to certain areas are first determined, and then serve as input for a cell-type detection framework and/or a differential expression setting.

pIMZ's documentation is available here: .

Installation

The easiest way to install most Python packages is via pip.

If not already done, you must first install the following dependencies manually. This is because at the time of writing this document, dabest requires pandas~=0.25, which is incompatible with probably the rest of the world nowadays. So first dabest is installed, then numpy and pandas are upgraded again ::

sudo pip3 install dabest
sudo pip3 install numpy pandas --upgrade

Only then we should install pIMZ :: sudo pip3 install pIMZ

pIMZ is now ready to go!

Usage

References to examples and example notebooks can be found in the examples folder, or in the documentation.

All available classes and their functions are explained in the modules/API documentation.