Summer School on 'Pore scale imaging and analysis for environmental science applications'


The pore structure of natural porous media, such as soils or rocks, impacts a whole range of macroscopic processes of interest in the field of environmental science. Pore scale analysis could provide a better understanding of phenomenon involved for example in contaminant transport, carbon storage, root growth, or microbiological species distribution. Pore structure is also an important field of research for non-natural media, such as in civil and processes engineering. Over the last decades observing porous media at the pore scale has been pushed forward by emerging techniques, such as X-ray or synchrotron computed tomography, and progress in computing performances. A wide range of scale from sub-micrometer to decimeter resolutions could be investigated in order to provide a new insight on porous media heterogeneity. These studies require integrated protocols including dedicated experimental set up, image acquisition and image analysis. 

This 3 days summer school aims at presenting up to date practices and methodologies used for 3D or 3+1D (3 spaces and 1 temporal dimensions) observations of porous media. It addresses the problem of setting up an experiment, defining adequate acquisition protocols and image reconstruction. The main focus is put on image analysis through courses and practical sessions concerning image treatment (filtering, segmentation) and computation of morphological parameters (porosity, tortuosity, connectivity, surfaces and others). Finally, various applications in the field of geosciences will be presented as short seminars.

This summer school is organised, within the frame of the H2020 European project PROTINUS, by LTHE, University of Grenoble Alpes. It aims at gathering local and international students (master and PhD students) and young researchers for information exchange and knowledge sharing on.


Steffen Schlüter (Center for Environmental Research, UFZ, Germany) will give a keynote lecture.

Lectures will be given by scientists and professors from Padova University (Italy), National University of Mexico (Mexico), University of Lorraine and Grenoble (France), University of Auckland (New Zealand) and Kumamoto University (Japan).

Organising committee:

Céline Duwig, Institut de Recherche pour le Développement IRD, France.

Anne Julie Tinet, University of Lorraine, France.

Laurent Oxarango, University of Grenoble-Alpes, France.

Scientific committee:

Céline Duwig, Institut de Recherche pour le Développement IRD, France.

Anne Julie Tinet, University of Lorraine, France.

Laurent Oxarango, University of Grenoble-Alpes, France.

Jean Martins, CNRS, University of Grenoble-Alpes, France.

Karin Müller, Plant and Food Research institute, New Zealand.

Alfonso Gastelum Strozzi, Universidad Nacional Autonoma de Mexico, Mexico.

Patrice Delmas, University of Auckland, New Zealand.


The course will start on Monday morning, and will end on Wednesday afternoon. Before the start of the course, participants will be asked to submit a short summary of the “pore-scale imaging and analysis” aspect of their studies, and of the datasets they have available.

Mornings will be focussed on lectures; afternoons will be focussed on supervised work by the participants, applying what they learned in the morning on their own case studies. This is a time-tested set-up that ensures students come away from the course with hands-on experience and

first results towards answering their research questions.

  • 18 July 2016: Imaging techniques
    – Introduction of the summer school: keynote speaker
    – Lectures on imaging techniques (Computer Tomography, Synchrotron, microscopy and others)
    – Oral / Poster session from the students explaining their research projects
  • 19 July 2016:  Image processing and analysis
    – Lectures on Image processing
    – Lectures on Pore morphology
    – Practical’s: 
    The students will be able to train themselves on image processing and pore morphology extraction from given CT images. The registered students will be sent beforehand the necessary software for image processing and analysis.
  • 20 July 2016 : Applications
    – Lectures on application cases (from experiments to processed images) in geoscience
    – Practical’s (2nd round)


Based on the CV, a maximum of 25 students will be admitted.

Target Group The course is aimed at PhD candidates and other academics
Group Size Min. 10, max. 25 participants
Course duration 3 days 25 hours
Language of instruction English
Number of credits To come (for updates visit the PROTINUS website)
Lecturers See above
Prior knowledge Basic knowledge of porous media physics/image analysis
Location OSUG-A, 414, rue de la Piscine, 38400 Saint Martin d’Hères, France. (see map)
Fees Cover course materials, coffee break and lunch: EUR 80.


Celine Duwig
Chargée de Recherche IRD
Laboratoire d'étude des Transferts en Hydrologie et Environnement (LTHE)

Source, further information and updates: PROTINUS