Our Objectives

Progress in the general area of soil science has been significant over recent years due to technological advances in X-ray scanners, improvements in the mathematical description of porous media, as well as the prediction of microbial processes. Nevertheless, many questions still remain unanswered. In particular, the computer vision tools that are currently available, and the techniques used to simulate biogeochemical processes in porous media need to be far more computationally efficient than they are at the moment. The objective of the proposed research is to cause a quantum leap forward in the geometric description and modeling of porous media, to enable researchers to simulate efficiently the various biogeochemical processes involved in groundwater recharge, aquifer decontamination, microbially-enhanced oil recovery and devise ways to speed computations significantly, to make it feasible to upscale modeling efforts from the microscale to spatial scales of practical interest in Qatar.

Microcosms setting up and images acquisition

This work package is decomposed into two tasks: (i) Setting up the microcosms, and CT scanning.

Voxel-based description of the pore space and modeling

This work package is decomposed into segmentation of images with available and new algorithms.

Shape-based description of the pore space

Final output of WP3 will consist of innovative algorithms to represent 3D complex shape from voxel-based representation.

Improvements of voxel-based modeling capability

This work package of the project as it ensures dynamic simulation at microscopic scale by implementing transformation processes

Experiments and comparison with modeling results

This WP of the project aims at conducting real microcosm experiments, then scanning them via X-ray CT and then dynamic simulation will performed.


In this is work package we will use the simulation software developed through the previous packages (and possibly extend it as needed) to address the upscaling issues.


Largest Annotated Dataset for Tomographic Images of Porous Media

In this study, a benchmark dataset (aka SIMUPOR) of 68 3D volumetric images of porous media with varying grain geometry and composition is composed .

3D volumetric images were obtained from the experiments conducted in [42] to study the effect of grain geometry on the morphology of non-aqueous phase liquids in porous media. The volumes correspond to samples from 34 different experiments, each corresponding to a specific constitution of porous medium. Among the 68 volumetric images used, 40 belong to the experiments that employ silica sand to model the porous media whereas the remaining 28 used quartz crystals. In addition to this variation in the shape of grains, there is also a variety in the size, with the median grain diameter ranging from 0.179 to 0.433 mm. This provides a comprehensive benchmark to check for robustness of any segmentation algorithms to changes in porous media composition.

A multi-phase ground truth segmentation for the volumetric images was obtained by applying a manual operator-guided process based on the indicator kriging approach [9]. For each phase, images obtained from the samples scanned at different energy levels were aligned and subtracted in order to emphasize that particular phase. Afterwards, segmentation for that phase was obtained by using the method of [9]. Furthermore, the accuracy of the segmented output was verified by comparing the porosity values for each phase. A visual example showing a slice of a test image along with its annotated ground truth is presented in Fig. 5. For more details about the image acquisition and annotation process, the reader is referred to [42].

The dataset that was used for experimentation can be downloaded from the following link. Decryption key can be obtained by contacting the first author at hafiz [dot] malik [at] qu [dot] edu [dot] qa. It consists of 38 folders, named “Column_xx”, each belonging to a different experiment.



Research Outputs

Following is a list of publications that have been made as part of the SIMUPOR project.

  • Malik J, Serkan Kiranyaz, Senior Member, R.I. Al-Raoush , Olivier Monga, Patricia Garnier, Sebti Foufou, Abdelaziz Bouras, Alexandros Iosifidis, Moncef Gabbouj, Philippe C. Baveye. 3D Quantum Cuts for Automatic Segmentation of Porous Media in Tomography Images. Under review at IEEE TPAMI, September 2018.
  • Baveye PC, Otten W, Kravchenko A, Balseiro-Romero M, Beckers É, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H and Vogel H-J (2018) Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain. Front. Microbiol. 9:1929. doi: 10.3389/fmicb.2018.01929
  • Baveye P., Valérie Pot, Patricia Garnier, Accounting for sub-resolution pores in models of water and solute transport in soils based on computed tomography images: Are we there yet?, In Journal of Hydrology, Volume 555, 2017, Pages 253-256, ISSN 0022-1694. /
  • Kemgue A.T. , O. Monga. From Voxels to Ellipsoids: Application to Pore Space Geometrical Modelling. Springer Nature Singapore Pte Ltd. 2018, K.J. Kim et al. (eds.), IT Convergence and Security 2017, Lecture Notes in Electrical Engineering 449, DOI 10.1007/978-981-10- 6451-7_23
  • Kemgue A.T, O. Monga, S. Moto and S. Foufou, Modeling complex volume shape using ellipsoid: application to pore space representation. Accepted for IEEE SITIS 2017.
  • Kemgue A.T, Olivier Monga, Serge Moto, Valérie Pot, Patricia Garnier, and Philippe C. Baveye. From spheres to ellipsoids: Speeding up considerably the morphological modeling of pore space and water retention in soils, under review for Computers & Geosciences, 2018
  • Kemgue A.T, Olivier Monga, Serge Moto, Valérie Pot, Patricia Garnier, and Philippe C. Baveye Geometrical modeling of pore space using ellipsoids: application to the simulation of water retention in soils, accepted for oral presentation at 21 World Congress of Soil Sciences (WCSS), Rio De Janeiro, August 2018


Collaborating Institutions