Pre-conference workshops, Monday 26 June 

These workshops are offered by researchers from around the world in the lead up to Pedometrics 2017. They cover topics ranging from those specifically aligned to Pedometrics to more general soil science, software, programming, decision making, scientific publishing and statistical topics. Workshops are open to all, also those not participating in the conference.

  • Full-day workshops (100 euro pp. including lunch)
  • Half-day workshops (60 euro pp. including lunch)
  • Two half-day workshops (100 euro pp. including lunch)

Please register for the workshop(s) you wish to attend. Morning tea and/or afternoon tea as well as lunch is included for all workshops. Please note that each workshop may have specific requirements listed (such as own laptop, pre-installed software, readings, etc) which we strongly encourage you to follow to get the most from your participation.   

Each workshop requires a minimum of 15 participants to be held. If a workshop does not proceed, participants will be offered the option to transfer to another workshop or receive a full refund. There is also a maximum number of places per workshop and a place can only be assured once payment has been made. We advise you to book early to avoid disappointment.  

 

register now

Note: when registering, you will be redirected to a Wageningen University & Research page in a new window to process your registration and payment. For PE&RC and WIMEK PhD candidates: to receive the PE&RC or WIMEK subsidy for workshop participation, please inform the PE & RC Office (office.pe@wur.nl ) or WIMEK office (WIMEK@wur.nl) about your participation in one or more workshops, so that we can arrange the subsidy with your group. You will still need to register and pay for the workshop/s using this system.

 

Full-day Workshops 9:00-17:00

Morning Workshops 9:00-12:30

Afternoon Workshops 13:30-17:00

USE R! PEDOMETRICS TUTORIALS

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The statistical programming environment R has been of continuous interest for development of applications and tools implementing state-of-the-art knowledge of pedometrics. Under R umbrella already many Special Interest Groups (SIGs) exist that cover e.g. spatial data, environmental problems and similar.

This workshop aims at bringing together experienced R package developers that have, over the years, produced some frequently used tools for importing, organizing and processing soil data. We will try to educate and inform Pedometrics conference participants on possibilities of analyzing and visualizing their data using Open Source software tools, especially for the purpose of making reproducible research and for data processing automation. The workshop will also be a chance for Pedometrics conference participants to meet the original package developers and get an insight into development trends and opportunities.

Specific tutorials will cover:

➢ Soil data classes in R and conversion and harmonization of data (GSIF package)
➢ Plotting soil-depth relationships (aqp package)
➢ Soil spectroscopy packages (prospectr, inspectr, asdreader, soil.spec packages) 
➢ Using Machine Learning Algorithms for predictive modelling and soil data analytics (caret, ranger, randomForestSRC, xgboost, h2o packages)
➢ Using R for 2D, 3D and 3D+T visualization of soil maps and soil processes
➢ Using R for the production of web maps and visualisations (mapview, shiny, leaflet packages)
➢ Exporting soil data to standard formats (OGC standards and similar)

Preliminary timetable

  •   9:00–10:30 Programme overview, software installation and first steps
  • 10:30–11:00 Coffee break
  • 11:00–13:00 R tutorials: importing and organizing soil data
  • 13:00–14:00 Lunch break 
  • 14:00–15:30 R tutorials: predictive modelling using Machine Learning algorithms
  • 15:30–16:00 Coffee break
  • 16:00–17:00 R tutorials: visualizing soil data and models (webinar by Dylan Beaudette from California)

REQUIREMENTS

  • Laptop computer (preferably with Linux OS and/or Windows 7+ OS) with at least 4GB RAM and wifi
  • Preinstalled software following the installation instructions
  • Bringing your own data sets is highly recommended but not required

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lecturers

T. (Tom) Hengl is a senior researcher at ISRIC — World Soil Information with core speciality in big data analytics and automated soil mapping. Tom has backgrounds in soil mapping and geo-information science. He is currently the project leader of the Global Soil Information Facilities — a suite of software tools, web-facilities and data sets (SoilGrids, soil profiles) for automated global soil mapping. ORCID ID: http://orcid.org/0000-0002-9921-5129

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P. (Pierre) Roudier is a soil scientists at Landcare Research National Institute in New Zealand. He has over 10 years of experience with developing tools and software solutions for soil sampling, soil spectroscopy and soil data analytics. Pierre is author of multiple R package including aqp, inspectr, clhs and plotKML

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D. (Dylan) Beaudette is a soil scientist working for the NRCS on soil survey in the Sierra Foothill Region of California. He was formerly a graduate student in the Soils and Biogeochemistry group at UC Davis. Dylan leads development of the R package aqp and soildb. He is also the leading author of the SoilWeb app and web interface for accessing soil data in USA.

Hands-on modelling of soil - and soilscape development

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As we are reaching the limits of human use of our lands, there is an increasing need to design climate-smart, sustainable land use and land management solutions. To provide this it is crucial to have a mechanistic understanding of interactions between soils and landscapes. This is the topic of the very active research field of soil-landscape modelling under the umbrella of the IUSS-working group on modelling of soil and landscape evolution. Following a recent review and the development of novel models, the working group now organizes a 1-day soil-landscape modelling crash course. Learning objectives include gaining a basic understanding of modelling approaches, and practical working experience with some of the available models.

The workshop will cover soilscape (3D), Catena (2D) and pedon (1D) models. Participants will receive a working model, sets of input files for a particular case, a user guide and some key papers on model concepts and applications. The workshop will take the format of a guided exercise by the model builder (or a very close colleague) and will allow for ample interaction.

PRELIMINARY TIMETABLE

  • 09:00 – 09:10 Scope of the day (Peter Finke)
  • 09:10 – 10:40 3D Soilscape modelling with LORICA (Arnaud Temme)
  • 10:40 – 10:55 Coffee break
  • 10:55 – 12:25 Be2D model (Benjamin Campforts)
  • 12:25 – 13:25 Lunch break
  • 13:25 – 14:55 1D Soil modelling with SoilGen (Peter Finke)
  • 14:55 – 15:10 Coffee break
  • 15:10 – 16:40 1D Soil modelling with VSoil (Saba Keyvanshokouhi)

REQUIREMENTS

All participants must bring their own laptops with pre-installed software (to be advised after registration). PDF copies of user manuals and case descriptions will be supplied. Case files will be supplied on the day. 

 

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lecturers

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Peter Finke is associate professor in pedology at Ghent University, Belgium. He obtained a “drs” degree in Physical Geography at the University of Amsterdam (1988), and a PhD in Agricultural and Environmental Sciences at Wageningen University (1992). Before coming to Ghent, he worked at several Wageningen research institutes as research manager. At this moment, his main research interest is the mechanistic modelling of soil formation at multimillennium temporal extents. He is the developer of the SoilGen model, a 1-D process model whichsimulates the co-evolution of a large number of soil properties over time and depth. He currently leads the IUSS working group on modelling of soil and landscape evolution.

Benjamin Campforts is Post-Doctoral student at the university of Leuven. During his PhD he developed numerical landscape evolution models with a main focus on numerical accuracy. His current research is oriented towards an active integration of analytical measurement techniques and numerical models. One of his current projects is the application of a two dimensional soil model (Be2D) to investigate how vertical (1D) soil processes such as chemical leaching and clay migration interact with lateral soil fluxes (2D) on hillslopes. To constrain the models, analytical tracers such as meteoric and in-situ 10Be are actively simulated.

@BenjaminCa

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Arnaud Temme is associate professor of soil geography and geomorphology at Kansas State University in the United States. His interests range from natural hazards and soils in high mountain landscapes, to the complexity of joint soil and landscape development. He gets inspiration and base data for his studies from fieldwork in places ranging from South Africa to Spitsbergen and from the European Alps to the Great Plains.  To complement and test field-derived understanding, dr. Temme has used and developed several computer models over the last decade. His most recent model, LORICA, was developed together with dr. Tom Vanwalleghem of the University of Cordoba, Spain, and allows for the simultaneous simulation of vertical soil forming processes and lateral landscape forming processes. Both sets of processes affect the same material: soil in various texture classes. The main advantage that comes with this, is that LORICA and comparable models can be parametrized with a very wide range of observations, both from standard soil mapping and from more modern techniques such as luminescence dating.

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Saba Keyvanshokouhi is a PhD student jointly in Aix-Marseille University and Ghent University. She obtained a M.Sc in Environmental physics and her B.Sc is in Physics. The focus of her thesis is on Soil Genesis modelling and projecting the evolution of soil due to global change. She has been working with mechanistic models (specifically SoilGen –a soil formation model) and also has experience in working with soil modelling platforms. Her work comprises implementing complicated, multi process models inside a soil modelling platform (Vsoil) with a goal of facilitating model modifications in a modular environment. This will allow to improve the model in different directions from process coverage and definition to coupling with other complicated models such as climate or plant models. The purpose of this study is to provide a suitable model to project the evolution of soil under climate change, land use and agricultural practices change in the horizon of 2100 and subsequently contribute to the soil management strategies for the coming century. Other than modelling she is interested in ethnopedology and the way soil is symbolized and perceived among indigenous and modern societies. 

Soil profile image analysis: estimating soil properties from digital photography

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The workshop will bring together researchers with practical experience of soil profile characterisation, and researchers with image analysis experience. The goals of the workshop are (1) to identify what is possible in terms of using automated image analysis to characterise soil profiles, and (2) to demonstrate the potential of this research area in a practical setting. Image analysis approaches will be described and then tested on images of soil profiles, and the practicalities of field-based soil profile image analysis discussed. Future work will also be discussed and linkages formed.

A worked example session will be used to demonstrate image analysis approaches applied to sample soil profile images. Software for analysing the sample images will be developed by Matt Aitkenhead prior to the workshop, and will include a range of image analysis methods/metrics that can be applied in real-time. The worked examples will be informed by discussion during the earlier session, in which the sample images are discussed and visible features identified and described. This will allow us to demonstrate the detection/measurement of profile features from automated image analysis.

PRELIMINARY TIMETABLE

  • Introductory presentation (Matt Aitkenhead)
  • Image analysis metrics
  • What can the eye do – and how could we use this?
  • Session on naked-eye observation of soil profile images (led by Alfred Hartemink)
  • Practicalities and protocols
  • Worked example session, with sample images analysed in real-time (led by Matt Aitkenhead)
  • Potential linkages to soil survey datasets
  • Closing discussion session (Matt Aitkenhead & Alfred Hartemink)

Each presentation will be 20 minutes, with 10 minutes for questions/discussion. The ‘naked eye observation’ and ‘worked examples’ sessions will last for ~2 hours each. 

REQUIREMENTS

There are no special requirements for this workshop. Participants may bring their own laptops. 

 

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Lecturers

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Alfred Hartemink is Chair and Professor of Soil Science at the University of Wisconsin – Madison. He teaches Pedology and Introduction Soil Science. His research focusses on digital soil morphometrics, soil mapping, and soil C.

 

 

Dr Matthew Aitkenhead is a soil scientist who currently works for the James Hutton Institute. Much of his work has involved linking remote sensing and field-based information with existing maps, to produce models of soil character in a rapid and cost-effective manner. Recent work has involved linking these models to mobile phone technology, to produce apps that enable researchers and land managers to monitor the environment.  The growth of national and international legislation requiring large-scale and repeatable environmental monitoring is driving the development of rapid assessment tools for soils, and he is working heavily in this area. He is currently an Associate Editor for three journals: Remote Sensing Letters, Advances in Artificial Neural Systems and Soil Use and Management. He also leads the Scottish Regional Group of the British Society of Soil Science.

Spatial sampling for mapping

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Sound sampling design is essential for the collection of data to support reliable scientific inference and decision making for management and policy.  What counts as a sound design depends on the problem of interest, and the nature of the inference that is required.  Many statistical analyses of spatial data, particularly for the prediction of local values as in mapping, are done in a model-based context in which data are treated as realizations of an underlying random process.  In this setting it is not necessary to select sampling locations by probability sampling, and there is scope to optimize sampling patterns computationally.
In this course I shall introduce some of the concepts that underlay the optimization of spatial sampling.  These include methods to ensure good spatial coverage by a sample, experimental designs adapted for spatial surveys, model-based optimization of the grid-spacing and model-based optimization of the coordinates of sampling locations for ordinary kriging and kriging with an external drift. 

TIMETABLE

  • 9.00 - 9.30 Introduction sampling for mapping
  • 9.30 - 10.15 Spatial coverage sampling
  • 10.15 - 10.45 Break
  • 10.45 - 11.30  Fuzzy k-means sampling
  • 11.30 - 12.30  Response surface sampling and latin hypercube sampling
  • 12.30 - 13.30 Lunch
  • 13.30 - 14.30  Model-based optimization of grid-spacing
  • 14.30 - 15.00 Break
  • 15.00 - 16.00 Model-based optimization of coordinates of sampling locations
  • 16.00 - 17.00 Sampling for validation

requirements

Participants in the course will be provided with scripts for the free R platform which will allow them to use the  methods that are described to solve sampling optimization problems. Basic knowledge of R is required. 

Participants are encouraged to bring their own laptops with pre-installed R and if preferred, a GUI for R such as R Studio or Tinn-R.

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Lecturer

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Dr Dick J. Brus is senior scientist at Wageningen University and Research in the Netherlands and adjunct Professor at the School of Geography of Nanjing Normal University. He has rich experience in geostatistics and statistical sampling in space and time. He applies these statistical methodsin mapping and monitoring of natural resources such as soil, water and vegetation. He published numerous papers in international journals and is second co-author of the book Sampling for Natural Resource Monitoring (J.J. de Gruijter, D.J. Brus et al., 2006, Springer Verlag). In 2014 he was awarded the Visiting Professorship for Senior International Scientists by the Chinese Academy of Science.

Using R for infrared spectroscopy research

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Collecting and analysing large number of samples may often be expensive, although necessary for several studies. Infrared spectroscopy is a high-throughput, non-destructive, and cheap sensing method that has a large range of applications in agricultural, plant and environmental sciences.  The inherent complexity of Infrared data makes necessary the use of advanced statistical tools to extract relevant information from a sample of a given material (e.g. soil).

This half-day workshop intends to present a tutorial on multivariate analysis using the R statistical Software, with focus on chemometric methods for:

  • Pre-processing and outlier detection
  • Measuring the similarity/dissimilarity between spectra
  • Calibration sampling (what and how many samples to choose to build accurate multivariate models)
  • Multivariate calibration (global models, local models for large and complex datasets)
  • Transferring NIR data across different instruments

During the course, we will show how to efficiently integrate different R tools for advanced soil spectroscopy research. We will provide the attendees with several R code examples as well as soil datasets. Important links:

prospectr: https://cran.r-project.org/web/packages/prospectr/vignettes/prospectr-intro.pdf

resemble: http://l-ramirez-lopez.github.io/resemble/

 

PRELIMINARY TIMETABLE

  • 09:15– 09:30 Introduction 
  • 09:30–10:45 Pre-processing and sampling spectral information (with computer practical)
  • 10:45–11:00 Coffee break
  • 11:00–12:30 Multivariate calibration (with computer practical)
  • 12:30–13:30 Lunch

requirements

All participants must bring their own laptops with R > 3.3.1 and R Studio Desktop > 0.99.903 installed. The computer practicals are done in the R language. Prior experience with R is not a prerequisite but at least some experience is recommended. 

 

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lecturers

Leonardo Ramirez-Lopez – NIR Data Analytics, BUCHI Labortechnik. Switzerland.

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Leonardo holds a PhD in Soil Science and 10 years of experience on infrared spectroscopy. He has worked at several research groups, in Brazil (University of São Paulo), Germany (University of Tübingen), Belgium (Université catholique de Louvain) and Switzerland (ETH Zurich). He currently works as NIR Data Analytics Manager at BUCHI Labortechnik AG.  He has developed two (publicly available) R packages for the analysis of soil infrared spectral data: prospectr and resemble. The first one includes functions for spectral pre-processing and calibration sampling, while the second one includes functions for modeling complex spectral data.

 

Alexandre Wadoux – Soil Geography and Landscape group, Wageningen University, Netherlands

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Alexandre is PhD candidate at Wageningen University. He completed a M.Sc. in Physical Geography at the University of Tübingen (Germany) where he conducted research on soil spectroscopy and soil-landscape analysis. His work focuses on statistical analysis of environmental variables and sampling design optimization mostly using the R software. He is part since 2015 of the EU funded FP7 Marie Curie Initial Training Network (ITN) ‘Quantifying Uncertainty in Integrated Catchment Studies (QUICS)’.

Introduction to Digital Soil Mapping

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The aim of this workshop is to introduce the main approaches and challenges in Digital Soil Mapping to people unfamiliar with the topic.

PRELIMINARY TIMETABLE

09:00 -  9:30   Overview of main concepts and applications in  DSM 

09:30 - 11:30  Application of GIS and spatial statistics to soil mapping including uncertainty (with hands-on exercises and short demonstrations of the capabilities using open sources tools):

  • Mapping soil properties from scorpan kriging
  • Mapping soil classes by disaggregation techniques

11:30 -  12:30   Discussion: Opportunities and limitations of operational DSM in various locations across the globe (1 hour). This will be introduced by a few short examples (<5min without slides ) for “newcomers” to DSM. 

 

Requirements

Participants are encouraged to bring their own laptops with pre-installed R and if preferred, a GUI for R such as R Studio or Tinn-R.

 

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LECTURERS

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Laura Poggio is a spatial modeller (The James Hutton Institute, Aberdeen, Scotland, UK) since 2008. Her main research focus is Integration of information on soil-climate interactions with land use and ecosystem processes in a spatial context. In particular she is interested in mapping spatio-temporal relationships between ground data and remote sensing-derived information for digital soil mapping with quantification and propagation of uncertainty. The background is in forestry and environmental sciences from University of Turin (I) with a PhD focusing on the development of a simplified land-use modelling method for the assessment of the risk of heavy metal polluted soil towards human health.

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Philippe Lagacherie trained as an Agronomist and completed his PhD in soil science in 1992.  He obtained his senior scientist degree from Montpellier 2 University in 2002 for his researches on digital soil mapping methods. He is currently senior researcher at INRA Montpellier (France). Dr Philippe Lagacherie has been involved in research dealing with Digital Soil Mapping, remote sensing and spatial modelling of cultivated landscapes. He developed spatial approaches that associated field knowledge, GIS, remote sensing, geostatistics, and fuzzy logic. He organized the first Global Workshop on Digital Soil mapping in Montpellier in 2004 and has been involved in the GlobalSoilMap initiative since  2007

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Brendan Malone is a scientific researcher working in the field of soil informatics and geospatial soil science at the University of Sydney. His research focus is in using quantitative methods to precisely understand how soils function and change- spatially, and through time. Interests include researching methods for comprehensive digital soil mapping aiming to characterize soil both in the lateral and vertical dimensions. Researching methods for quantifying (and validating) measures of uncertainty for these comprehensive soil information systems. Additionally, Brendan investigates innovative systems for soil measurement, which includes that associated with remote and proximal soil sensing instrumentation. He has a particular interest in infrared and x-ray spectroscopy. The importance of these research interests have been recognized by successful funding grants from both the Australian Research Council and Australian Government Department of Agriculture. Brendan has attained Bachelor (2009) and Doctoral (2012) degrees from the University of Sydney.

 

Lubos Boruvka (Czech University of Life Sciences)

Lubos Boruvka (Czech University of Life Sciences)

The '4 per 1000 Initiative – Soils for Food Security and Climate' for pedometricians 

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In this workshop we provide the attendees with an overview of the '4 per 1000 Initiative – Soils for Food Security and  Climate'. This initiative aims to ensure that agriculture plays its part in combating climate change. It  promotes a  4/1000 annual growth rate of the soil carbon  stock  to  improve  soil  fertility  and agricultural  production  and  to  contribute  to achieving the long-term objective of limiting  the temperature increase to +1.5/2°C.  This initiative consists of a voluntary action plan under the Lima-Paris Action Agenda (LPAA), backed up by an ambitious research programme.  Pedometrics has the potential to contribute and benefit from this research programme. Therefore, we deem it important to inform and engage the participants of Pedometrics 2017 in the ‘4 per 1000 Initiative’. 

The workshop entails different lectures  given by experts from both inside and outside the field of Pedometrics  and  outlines  relevant issues for soil carbon mappers and modellers. The first part of this workshop introduces the ‘4 per 1000 Initiative’ and welcomes invited speakers from the Scientific Committee of the ‘4 per  1000  Initiative’. The second part of this  workshop  focuses  on  the  feasibility  of  the  initiative,  the  theory of  soil  carbon sequestration  and  the  different  dimensions  of  soil-landscape  modelling  and  soil  carbon modelling. After the lectures, we will have an elaborate discussion with the invited speakers on how the pedometrics community can engage and contribute to the ‘4 per 1000 Initiative’.

 

PRELIMINARY TIMETABLE

  • Dominique Arrouays: Overview of the ‘4 per 1000 Initiative’ (30 min.)
  • Invited speaker I Scientific Committee ‘4 per 1000 Initiative’ (30 min.)
  • Invited speaker II Scientific Committee ‘4 per 1000 Initiative’ (30 min.)
  • Budiman Minasny: Feasibility of the ‘4 per 1000 Initiative’ (30 min.)
  • Uta Stockmann: Explaining carbon sequestration (30 min.)
  • Titia Mulder: Soil-landscape modelling and soil carbon modelling (30 min.)
  • Discussion between pedometricians and invited speakers from the Scientific Committee

Requirements

At this time there are no special requirements.

 

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LECTURERS

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Titia Mulder is an assistant professor at the Soil Geography and Landscape group, Wageningen University, The Netherlands. She has a background in remote sensing and soil sciences. Her PhD involved the use of spectroscopy for supporting digital soil mapping, and she contributed to research projects e-SOTER, GlobalSoilMap and SAT-EX. Her main research interest involves spatial, temporal and soil-landscape modelling for understanding large-extent soil and ecosystem dynamics. In her current work she focusses on soil carbon dynamics and climate change adaptation. 

 

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Dominique Arrouays is a senior researcher at INRA Infosol, Orleans, France. He is the scientific coordinator for the GlobalSoilMap project and member of the Intergovernmental Technical Panel on Soils (ITPS) for the Global Soil Partnership (GSP), among other national and international projects. Currently, he is also involved in the ‘4 per 1000 Initiative’ Soils for Food Security and Climate' and aims to promote this initiative widespread and engage different scientific and social communities.

 

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Budiman Minasny is Professor at the Centre for Carbon, Water and Food, The University of Sydney.  He is interested to find out how soil change in space and time. He created novel methodologies that try to explain the dynamic of soil in the landscape. These include mechanistic models that quantify soil formation processes, and empirical models based on modern mathematical and statistical techniques that explain the complexity of soil variation in space and time. These techniques are being used e.g. in the GlobalSoilMap project, which will supply the global demand for soil data for food security assessment. 

 

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Uta Stockmann is a Research Fellow at the Soil Security Laboratory at The University of Sydney, Australia. Uta has a genuine interest in the functioning of agro-ecosystems. Her research expertise is in quantitative pedology, proximal soil sensing, and digital soil mapping. In addition, Uta has led, and together with researchers from world soil agencies worked on large global projects on SOC research, evaluating mechanisms and management practices of SOC sequestration and performing a global assessment of the change in SOC stocks in space and time.

Publication of scientific papers, reviewing and statistics in soil science

Our aim is to help authors and reviewers through the many stages that lead to the successful publication of papers. Many papers are rejected at the first stage of assessment without going for peer review, for reasons that authors could have prevented. 

Source: http://xkcd.com/

Source: http://xkcd.com/

Our workshop will guide new authors and those with less experience of publishing in international scientific journals on the preparation and submission of papers to ensure greater success in getting their research published. This is not a workshop about writing per se, but on how best to approach the development of a paper, target the most appropriate Journal and ensure the best possible chance of it being accepted for publication. 

Editors not only make a decision on your paper, but can also provide access to expert advice during its preparation, or if reviewers identify areas that require revision. The guidelines we present include the handling of comments from reviewers and responding to the copy editor’s questions at the proofs stage. 

Many papers contain statistical analyses that are poorly described and often done incorrectly. The workshop will address some of the commonest statistical problems in papers submitted to soil science journals. These include the failure to report analyses of variance correctly, the use of analyses which do not reflect the randomization of the original experiment or survey, misuse of methods for multiple comparisons and confusions about spatial dependence. These problems will be explored, and examples will be given of how to avoid them, including analyses of example data sets on the R platform.
 
Reviewers are essential to the peer review process and to ensure that the scientific content provides new, relevant, up-to-date and accurate knowledge. Part of becoming a successful author is being involved in peer review. Every author needs to act as a reviewer to maintain high scientific standards. 

 

PRELIMINARY TIMETABLE

  1. Publication of scientific papers  (60 min)
  2. Statistics in soil science  (90 min)
  3. Reviewing of scientific papers (45 min)
  4. Discussion (15 min)

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LECTURERS

Professor Margaret A. Oliver, University of Reading, Reading

Professor Margaret A. Oliver, University of Reading, Reading

Margaret Oliver did her first degree in Geography and Geology at the University of Bristol, followed by a PhD in soil science at the University of Birmingham. Her early research focused on the multivariate and geostatistical analysis of soil data from the Wyre Forest, The Midlands, England. Since then her research interests have included the application of a wide range of numerical and geostatistical methods to soil and other data including pollen counts, forestry, radon emission, remotely sensed imagery, precision agriculture and the incidence of childhood cancer. Specific interests are in sample design for spatial analysis and eventual mapping, risk analysis associated with prescribed thresholds in relation to soil pollutants or deficiencies of crop nutrients, and the relations between different scales of spatial variation. Most recent research has been in the field of precision agriculture.

Margaret retired at the end of September 2004 from her post as Reader in Spatial Analysis at the University of Reading. She has retained a link and a base at the University as a Visiting Professor since January 2005. Since her retirement she was been Deputy Editor of the European Journal of Soil Science for four years and then took over as Editor-in-Chief in 2015. She was also Co-Editor-in-Chief of Precision Agriculture with John Stafford for six years until the end of 2010, and she still remains on the Editorial Board

 

Professor R. Murray Lark, British Geological Survey, Keyworth

Professor R. Murray Lark, British Geological Survey, Keyworth

Murray Lark obtained his D.Phil. in the Soil Science Laboratory at Oxford University under the supervision of Dr Philip Beckett.  His topic was spatial and multivariate analysis of remote sensor data.  After holding a University of Wales Fellowship for two years, when he studied methodological problems in remote sensing, he started work at the Silsoe Research Institute in Bedfordshire, focussing initially on precision agriculture.  He established the Environmetrics Research Group at Silsoe, which worked on pedometrical problems in land management, soil monitoring and biophysical modelling.  The group was eventually transferred to Rothamsted Research, where he was deputy head of Biomathematics.  In 2011 he transferred to the British Geological Survey where he is environmental statistician, working on his own programme of research in statistical methodology, and contributing to the survey’s research portfolio from volcanology to soil geochemistry.  From 2006–2010 he was Chair of the IUSS Pedometrics Commission and from 2013–2016 he was Chair of the EGU’s Soil System Science’s subdivision on Statistics in Soil Science.  He chairs the European Journal of Soil Science Statistical Advisory Panel.

Infrared spectroscopy as a fast and reliable method of soil testing in practice - morning session

The Scanner. SoilCares.

The Scanner. SoilCares.

SoilCares is a Wageningen based company who offer two soil testing products using spectroscopy; the Lab-in-a-box and the Scanner.

The Lab-in-a-box is a compact laboratory that can be set up in any office or building and uses mid-infrared (MIR) and X-ray fluorecence (XRF) to analyse soil samples. The Scanner is a handheld near-infrared (NIR) sensor that can be used to scan soil samples in a lab or in the field.

The Lab-in-a-box is more accurate and can predict more soil properties and elements. The Scanner, on the other hand, is cheaper, faster and more mobile. The true power behind both sensor products is a vast spectral library with calibration samples collected from all over the world and analysed according to strict standardised protocols at SoilCares’ Golden Standard Laboratory.

The workshop will demonstrate the Lab-in-a-box and the participants will be able to test a number of prepared soil samples using the Scanner themselves.

Lab-in-a-box. SoilCares.

Lab-in-a-box. SoilCares.

PRELIMINARY TIMETABLE

09:00 Introduction and SoilCares concept
09:15 Theoretical background & development
09:45 Tour at SoilCares and the Golden Standard Laboratory
10:15 Demonstration Lab-in-a-box
11:15 Practical with the Scanner
12:15 Wrap-up

Requirements

The workshop takes place on SoilCares premises at the Nieuwe Kanaal 7c in Wageningen. SoilCares will provide facilities. It is not necessary for participants to bring a notebook.

Line bus 88 takes you from the campus (bus stop Droevendaalsesteeg) to SoilCares (bus stop Ooststeeg) in about 10 minutes.

 

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lecturers

Herman Vedder Senior Researcher Spectroscopy and Sensor Technology Changing traditional soil analysis from ‘sending your sample to a central lab’ to ‘having it analysed on your doorstep’ is one the challenges. My experience in developing and maintaining NIRS applications is valuable for this work. I am also involved in selecting suitable sensors. I enjoy working on innovative concepts like this.

Herman Vedder
Senior Researcher Spectroscopy and Sensor Technology
Changing traditional soil analysis from ‘sending your sample to a central lab’ to ‘having it analysed on your doorstep’ is one the challenges. My experience in developing and maintaining NIRS applications is valuable for this work. I am also involved in selecting suitable sensors. I enjoy working on innovative concepts like this.

Angelique van Helvoort Head of Marketing & Communication It’s great to work for SoilCares, where ‘being good’ is part of the DNA, by contributing to solving the huge problem of feeding the world. Now it’s time to tell the world about our revolutionary soil testing!

Angelique van Helvoort
Head of Marketing & Communication
It’s great to work for SoilCares, where ‘being good’ is part of the DNA, by contributing to solving the huge problem of feeding the world. Now it’s time to tell the world about our revolutionary soil testing!

Thomas Urselmans-Terhoeven Senior Researcher Soil Spectroscopy and Data Mining A researcher at heart, I’m strongly motivated by the fact that knowledge generated in our team is useful for farmers and helps to improve living conditions on our planet. We are a living embodiment of this at SoilCares.

Thomas Urselmans-Terhoeven
Senior Researcher Soil Spectroscopy and Data Mining
A researcher at heart, I’m strongly motivated by the fact that knowledge generated in our team is useful for farmers and helps to improve living conditions on our planet. We are a living embodiment of this at SoilCares.

Leonne de Bruijn Golden Standard Lab Manager My background is very diverse. I started as an analyst in hospital, division clinical chemistry. After that I left for Surinam and helped to get a laboratory to be accredited. I also worked in the food-, pharmacy- and environmental industry. As the lab manager I have to make sure that all the samples (soil and feed) will be analyzed in time. The idea that in the future we can provide farmers all over the world with good fertilization advice, is a very sublime goal.

Leonne de Bruijn
Golden Standard Lab Manager
My background is very diverse. I started as an analyst in hospital, division clinical chemistry. After that I left for Surinam and helped to get a laboratory to be accredited. I also worked in the food-, pharmacy- and environmental industry. As the lab manager I have to make sure that all the samples (soil and feed) will be analyzed in time. The idea that in the future we can provide farmers all over the world with good fertilization advice, is a very sublime goal.

David Marcelis GIS and Remote Sensing Researcher At SoilCares I am in the ideal position where I can combine geo-informatics, mapping and remote sensing for real-life applications that matter. It’s great to work in the dynamic environment of SoilCares where developments go fast yet without losing their scientific foundation.

David Marcelis
GIS and Remote Sensing Researcher
At SoilCares I am in the ideal position where I can combine geo-informatics, mapping and remote sensing for real-life applications that matter. It’s great to work in the dynamic environment of SoilCares where developments go fast yet without losing their scientific foundation.

Eric Wijnen International Coordinator Sample Collection

Eric Wijnen
International Coordinator Sample Collection

Geostatistical Toolbox for the Earth Sciences

The British Geological Survey has produced a freely available Geostatistical Toolbox for the Earth Sciences (GaTES). GaTES includes classical and model-based (i.e. REML) geostatistical methods for estimating, validating and predicting from linear mixed models, linear models of coregionalization and space-time models. The toolbox is written in Matlab but it can be accessed from a graphical user interface with no need for a Matlab license. In this half-day workshop I will introduce GaTES and demonstrate its capabilities. Participants will be able to use GaTES for themselves and make suggestions for features to be included in future updates of the toolbox. 

 

PRELIMINARY TIMETABLE

  • 14:00 Introduction to GaTES, installation and data requirements.
  • 14:30 Estimating geostatistical models by REML, validation and spatial prediction (i.e. kriging) using GaTES
  • 15:20 Break
  • 15:40 Linear models of coregionalization (i.e. co-kriging)
  • 16:10 Space-time models
  • 16:30 Exercises using provided datasets or participants can test GaTES on their own datasets
  • 17:15 Feedback and suggestions for future updates to GaTES.

 

requirements

Participants may either use their own laptops with software pre-installed or use one of the computers which will be made available.

 

REGISTER NOW


LECTURERS

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Ben Marchant, British Geological Survey

Ben Marchant is an Environmental Statistician at the British Geological Survey. His research is primarily concerned with the development and application of geostatistical algorithms particularly in circumstances when standard models are insufficiently flexible to adequately represent the complex variation of environmental properties.  

Interpretation of Mid Infrared (MIR) Spectra of Soils 

Image illustrating a soil profile, FTIR spectrometer and FTIR spectrum of the top horizon of the soil in the MIR range

Image illustrating a soil profile, FTIR spectrometer and FTIR spectrum of the top horizon of the soil in the MIR range

he infrared region of the spectrum  is widely  used  for soil sensing and monitoring.  To date, the  near  infrared  (NIR)  region  has  been  far more  extensively  used  than  the  mid infrared  (MIR) region. However, MIR  spectra  can  provide  more information, particularly in  relation  to mineralogy,  than  NIR  spectra.    Hence MIR  spectra  give  more  complete chemical  profiles or “fingerprints” of soil  and,  in addition,  are more readily interpreted. An  MIR spectrum  is  generated  by plotting  absorption  against  frequency, which  to  the untrained  eye  can  appear meaningless.  Though much of the  information  concealed  in these  absorption  bands  can ultimately  be  extracted  via  chemometrics  and statistical modelling, the ability to  interpret the MIR spectra  is  fundamental  to obtain preliminary information that will help us understand the nature of the soil sample(s).  In  a  typical  MIR  spectrum,  different  absorption bands  are  observable  along  the frequency  range  (4000-400 cm-1) and  are  related  to  the  type  of  chemical  bonds  and functional groups present in the substrate. These bands occur at specific frequencies for particular  chemical  components,  thus  making  it possible  to  infer  the  organic  and inorganic  constituents  of  a  sample.  The  MIR spectra  can  therefore  be  invaluable  in providing a rapid insight into,  and a means of visualising,  the differences between soils. Although interpreting  MIR  spectra  of  soil  can  be  difficult  and complex,  with  some training  in  spectral  interpretation,  aspects  of  the  soil  such  as the  nature  and  relative proportions  of  organic  matter, minerals  and  clay  minerals  can  all  be  readily  assessed. Training  in  MIR  spectral interpretation  of  soil  is  not  readily  available,  and  so this workshop aims to try and address this by providing  the attendees with  an overview and basic  guidance  on  the  fundamental  steps  required for  an  accurate  diagnostic assessment of soil MIR spectra. 

PRELIMINARY TIMETABLE

  1. Introduction to MIR spectra of soil (presentation/lecture) – 30 min
  2. Spectral features of organic soils (presentation/lecture) - 30 min + practical exercise -15 min
  3. Spectral features of mineral soils - (presentation/lecture) - 30 min + practical exercise -15 min
  4. Practical exercise – interpretation of soil spectra – 1 hour
  5. Summary/ discussion – 30 min
     

REQUIREMENTS

Participants may either use their own laptops with software pre-installed or use one of the computers which will be made available. Spectral files and other materials will be made available during the workshop.

 

REGISTER NOW


lecturers

Jean Robertson
Jean has been head of the IR section at The James Hutton Institute for over 10 years, working with both Fourier Transform Infrared spectroscopy (FTIR) and Near Infrared (NIR) spectroscopy. She trained as a chemist, and her expertise in FTIR spectroscopy was first developed through her PhD, awarded in 1990, in which she studied structures of organometallic compounds. Through her work at the Institute she now applies this expertise in IR spectroscopy to a wide range of naturally occurring samples. She has developed the specialist knowledge necessary for interpreting the complex FTIR spectra of minerals, soils, sediments, fungal species and vegetation. In addition, from the samples generated for the National Soil Inventory of Scotland, she has been responsible for the creation of high quality FTIR and NIR national spectral datasets for Scotland. Much of her research relates to analysis of relationships between this spectral data and the other data held for the soils. She is also responsible for providing commercial FTIR analysis for a wide range of industrial clients.


Jean.robertson@hutton.ac.uk
The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland (UK)

 

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Estefanía Pérez-Fernández
Estefanía is a biologist by training and gained her PhD with the University of Seville (Spain), in collaboration with The James Hutton Institute (Scotland), where she specialized in the use of near infrared spectroscopy for the study of animal ecology (herbivores). She has ample expertise in the application of chemometrics to develop predictive calibrations that allow estimation of a range of chemical properties of different types of natural samples, mainly soil, vegetation and animal faeces. Currently undertaking post doc research within the IR Section at The James Hutton Institute, Estefanía is in charge of developing new applications for crop, plant and soil research using both FTIR (Fourier Transform Infrared) spectroscopy and NIR (Near Infrared) spectroscopy analytical techniques. In addition to this, she also collaborates with the commercial analysis of samples from the oil, gas, engineering and food industries. 


estefania.perez-fernandez@hutton.ac.uk
The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland (UK)

 

Functional Land Management- Understanding the supply of soil functions in a landscape context

Understanding the supply and demand of soil functions at a landscape scale is essential if we are to enhance sustainable production systems in the future. We will be considering five key soil functions for agricultural productivity; 1) primary productivity, nutrient cycling of external nutrients, 3) carbon cycling and sequestration, 4) water regulation and 5) habitat for functional  biodiversity.

This workshop is designed to make you think about the practicalities of supply and demand of soil functions to and/or delivered by society. In this workshop we will create 5-6 map based scenarios, with example areas from around the world in which participants will be asked to play the role of part of society that places a demand on the soils from the area. You will be supplied with the basic information to make decisions on what the local demands are on soils to supply specific soil functions and how this can be delivered across a local (10 x 10 km2)  landscape. Multiple demands will be placed upon the soils of the area and you will be asked to play the part of the farmers, local forester, policy maker, river catchment manager, local supermarket manager etc to ensure that you can deliver the range of functions through the most appropriate landscape planning and management. What policies are needed, how do we manage the soils, what are the societal benefits? This workshop is designed to challenge you and make you think outside of the box a little. The end-point of this workshop will be to assess the differences across a range of pedo-climatic zones in the world. The map based exercises will be carried out for a range of regions encompassing; Europe, Africa, N. America, S. America, Australia, Asia (x2). 

PRELIMINARY TIMETABLE

To be advised.

 

Requirements

There are no special requirements however please note this is an interactive workshop, where A1 or A0 maps and overlays will be supplied. Workshop members will write on the map products and design a multi-functional landscape.  

 

REGISTER NOW


LECTURERS

Rachel Creamer is Chair of the Soil Biology and Biological Soil Quality group in Wageningen University and Research. The Soil Biology and Biological Soil Quality Group is one of the two parts of the sub-department of Soil Quality within Environmental Sciences. Rachel Creamer has worked as a soil pedologist for the last 21 years, specialising in soil quality, soil biological indicator assessment and soil classification. She has coordinated various national and European research projects and published over 40 papers. She is an Associate Editor of the Journal: Soil Use and Management and recently appointed onto the Editorial Board of Environmental Research Letters.

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Prof Rogier Schulte worked at Teagasc as leader in Translational Research on Sustainable Food Production, which meant that he worked closely with policy makers in Ireland and the EU, to ‘translate’ research outcomes on sustainable farming into policy advice, and vice versa. He developed the concept of Functional Land Management jointly with Prof Rachel Creamer, and is currently extending and applying this framework in projects across five continents. Recently, Rogier has moved to Wageningen University and Research in the Netherlands, to take up the position of Chair of the Farming Systems Ecology group from the 1st February 2017.

Lilian O’Sullivan is currently completing an Environmental Protection Agency Research Fellowship to coordinate the delivery of a book entitled “The Soils of Ireland”.  This will be the Irish contribution to the World Soils Book Series.  She is based at Teagasc, Environment Research Centre in Co. Wexford as a researcher in soil quality. Stakeholder engagement and shared learning represent important aspects of her work, and she has already co-hosted and facilitated 11 Functional Land Management workshops to a broad range of stakeholders including: farmers, policy makers, researchers and industry.  Following the current research fellowship, she will commence work as a research officer with Teagasc on the LANDMARK project, a European Research Project on the sustainable management of land and soil in Europe. Her research interests and work include soils and sustainability, agricultural development, food security and food policy.

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Iolanda Simó (PhD) is an independent research associate at Smart Soil & Land (ES). She has an expertise in Soil Science, Environmental Science, Agronomy and GIS. Her main research topics are soil quality and soil mapping, such as mapping carbon stock in soils, desertification and soil cartography, soil classification and drainage mapping. She is interested in mapping spatio-temporal relationships between ground data -derived information for digital soil mapping, as well as, soil sustainability and agricultural development. The background is in Agronomy from University of Lleida (ES) with a PhD focusing on the study of soil quality indicators for the assessment of the multifunctional land health qualities and pedogenesis.

Infrared spectroscopy as a fast and reliable method of soil testing in practice - afternoon session

The Scanner. SoilCares.

The Scanner. SoilCares.

SoilCares is a Wageningen based company who offer two soil testing products using spectroscopy; the Lab-in-a-box and the Scanner.

The Lab-in-a-box is a compact laboratory that can be set up in any office or building and uses mid-infrared (MIR) and X-ray fluorecence (XRF) to analyse soil samples. The Scanner is a handheld near-infrared (NIR) sensor that can be used to scan soil samples in a lab or in the field.

The Lab-in-a-box is more accurate and can predict more soil properties and elements. The Scanner, on the other hand, is cheaper, faster and more mobile. The true power behind both sensor products is a vast spectral library with calibration samples collected from all over the world and analysed according to strict standardised protocols at SoilCares’ Golden Standard Laboratory.

The workshop will demonstrate the Lab-in-a-box and the participants will be able to test a number of prepared soil samples using the Scanner themselves.

Lab-in-a-box. SoilCares.

Lab-in-a-box. SoilCares.

PRELIMINARY TIMETABLE

13:30 Introduction and SoilCares concept
13:45 Theoretical background & development
14:15 Tour at SoilCares and the Golden Standard Laboratory
14:45 Demonstration Lab-in-a-box
15:45 Practical with the Scanner
16:45 Wrap-up

Requirements

The workshop takes place on SoilCares premises at the Nieuwe Kanaal 7c in Wageningen. SoilCares will provide facilities. It is not necessary for participants to bring a notebook.

Line bus 88 takes you from the campus (bus stop Droevendaalsesteeg) to SoilCares (bus stop Ooststeeg) in about 10 minutes.

 

REGISTER NOW


lecturers

Herman Vedder Senior Researcher Sensor Technology Changing traditional soil analysis from ‘sending your sample to a central lab’ to ‘having it analysed on your doorstep’ is one the challenges. My experience in developing and maintaining NIRS applications is valuable for this work. I am also involved in selecting suitable sensors. I enjoy working on innovative concepts like this.

Herman Vedder
Senior Researcher Sensor Technology
Changing traditional soil analysis from ‘sending your sample to a central lab’ to ‘having it analysed on your doorstep’ is one the challenges. My experience in developing and maintaining NIRS applications is valuable for this work. I am also involved in selecting suitable sensors. I enjoy working on innovative concepts like this.

Angelique van Helvoort Head of Marketing & Communication It’s great to work for SoilCares, where ‘being good’ is part of the DNA, by contributing to solving the huge problem of feeding the world. Now it’s time to tell the world about our revolutionary soil testing!

Angelique van Helvoort
Head of Marketing & Communication
It’s great to work for SoilCares, where ‘being good’ is part of the DNA, by contributing to solving the huge problem of feeding the world. Now it’s time to tell the world about our revolutionary soil testing!

Thomas Urselmans-Terhoeven Senior Researcher Sensor Technology A researcher at heart, I’m strongly motivated by the fact that knowledge generated in our team is useful for farmers and helps to improve living conditions on our planet. We are a living embodiment of this at SoilCares.

Thomas Urselmans-Terhoeven
Senior Researcher Sensor Technology
A researcher at heart, I’m strongly motivated by the fact that knowledge generated in our team is useful for farmers and helps to improve living conditions on our planet. We are a living embodiment of this at SoilCares.

Leonne de Bruijn Golden Standard Lab Manager My background is very diverse. I started as an analyst in hospital, division clinical chemistry. After that I left for Surinam and helped to get a laboratory to be accredited. I also worked in the food-, pharmacy- and environmental industry. As the lab manager I have to make sure that all the samples (soil and feed) will be analyzed in time. The idea that in the future we can provide farmers all over the world with good fertilization advice, is a very sublime goal.

Leonne de Bruijn
Golden Standard Lab Manager
My background is very diverse. I started as an analyst in hospital, division clinical chemistry. After that I left for Surinam and helped to get a laboratory to be accredited. I also worked in the food-, pharmacy- and environmental industry. As the lab manager I have to make sure that all the samples (soil and feed) will be analyzed in time. The idea that in the future we can provide farmers all over the world with good fertilization advice, is a very sublime goal.

David Marcelis GIS and Remote Sensing Researcher At SoilCares I am in the ideal position where I can combine geo-informatics, mapping and remote sensing for real-life applications that matter. It’s great to work in the dynamic environment of SoilCares where developments go fast yet without losing their scientific foundation.

David Marcelis
GIS and Remote Sensing Researcher
At SoilCares I am in the ideal position where I can combine geo-informatics, mapping and remote sensing for real-life applications that matter. It’s great to work in the dynamic environment of SoilCares where developments go fast yet without losing their scientific foundation.

Eric Wijnen International Coordinator

Eric Wijnen
International Coordinator