Transform 22



pyGIMLi is an open-source library for modeling and inversion in geophysics. This tutorial is particularly suited for new users but adds up to last-years tutorial on Transform 2021 with the following subjects:

  • Create a subsurface geometry and explore the pyGIMLi meshtools
  • Simulate the stationary 2D heat equation
  • Simulate synthetic crosshole traveltime measurements
  • Invert seismic traveltime and field ERT data
  • Show how to build inversions with own forward operators (e.g., from other packages)

This years tutorial will demonstrate some basic pyGIMLi classes (DataContainer, Mesh, different kinds of supported matrices) but also some topics that might be of interest for the experienced users:

  • geostatistical regularization vs. classical smoothness types
  • region-specific behaviour
  • different kinds of joint inversion
  • incorporation of prior knowledge
  • overview of other packages in the pyGIMLi ecosystem (BERT, COMET, custEM)
  • induced polarization modelling and spectrally constrained inversion


  1. RWTH Aachen University, Applied Geophysics and Geothermal Energy, Aachen, Germany
  2. Berlin University of Technology, Department of Applied Geophysics, Berlin, Germany
  3. Leibniz Institute for Applied Geophysics, Hannover, Germany



Tuesday, April 26 • 17:00 - 19:00 UTC (starts at 08.00 a.m. CET)

Slack (Q&A)

Software Underground channel #t22-tue-pygimli

Live Stream ☝️

pyGIMLi documentation


Make sure you've done these things before the tutorial on Monday:

  1. Sign up for the Software Underground Slack
  2. Join the channel #t21-mon-pygimli channel. This is where all communication will happen and where we will answer any question about installation and the tutorial
  3. Install the pyGIMLi conda environment as described below.

Setup instructions

To start the tutorial setup, please follow the next steps:

Step 1: Prerequisites

There are a few things you'll need to follow the tutorial:

  1. A working Python installation (Anaconda or Miniconda). For details on how to install Anaconda, we refer to:
  2. A modern web browser that works with JupyterLab or Jupyter Notebook (Internet explorer will not work)
  3. Intermediate experience in Python programming (Python, numpy, matplotlib, jupyter)
  4. Background on geophysical modeling and inversion

Step 2: Download material for the tutorial

  • Windows: Download the course material and unzip it a folder of your choice.
  • Mac/Linux: You can do the same as above, or alternatively open a terminal, navigate to a folder of your choice, and execute git clone

Step 3: Install the tutorial environment

  1. Open a terminal (Linux & Mac) or the Anaconda Powershell Prompt (Windows). Navigate to the folder from step 2 (using the cd command) and type:
conda env create
  1. Activate the environment in the terminal by typing:
conda activate pg-transform2022
  1. To test if everything works correctly you can do the following:
python -c "import pygimli; pygimli.test(show=False, onlydoctests=True)"

If none of these commands gives an error, then your installation is working fine. If you get any errors, please let us know on Slack at #t21-mon-pygimli.

Step 4: Start JupyterLab

  1. Windows users: Make sure you set a default browser that is not Internet Explorer.
  2. Activate the conda environment: conda activate pg-transform
  3. Start JupyterLab: jupyter lab
  4. Jupyter should open in your default web browser. We'll start from here in the tutorial and create a new notebook together.