AfSIS Newsletter: Issue II, 2012

Using the latest technology to screen soil health

Significant progress is being made in analyzing soil and plant samples collected from the AfSIS sentinel sites, with over 17,000 samples being received since the project began. Of this, 70% of the samples have been characterized with infrared spectroscopy and reference methods. After harmonization and quality checks, the data is stored in a meta-file database. This database also includes data from non-AfSIS sentinel sites that have been analyzed using the same methodology, as they provide additional information — such as high values of soil carbon, strongly acid or alkaline soils — to expand the range in the spectral calibrations.

Scanning a soil sample with a portable mid-infrared spectrometer

AfSIS utilizes the innovative practice of infrared spectroscopy (IR) to analyze soil samples gathered at the sentinel sites. IR is a proven technology for rapid, non-destructive characterization of the composition of materials based on the interaction of electromagnetic energy with matter. It is now routinely used for analyses of a wide range of materials in laboratory and process control applications in agriculture, food and feed technology, geology, biomedicine, and space exploration, and has been a key technology in enabling the development of soil health surveillance systems by providing a rapid and reliable tool for soil health screening (Shepherd & Walsh, 2007).

The graphs on the next page show the actual values determined by conventional laboratory methods plotted against values predicted from mid infrared spectral measurements samples for soil organic carbon and soil pH. The graphs on the left show the calibration values and those on the right show validation values. The validation values are ‘out-of-bag’ validation samples, which provide an indication of the prediction performance one can expect if a new sample belonging to the same population of soils was scanned.

Figure 1 part 1: results obtained from diagnostic screening tests of sentinel site data

The infrared spectral measurements provide capability for rapid and low cost prediction of a suite of soil properties in one pass. Only 5% of the AfSIS soil samples need to be analyzed using conventional laboratory measurements and the remaining 95% are predicted using the spectral method. The technology enables characterization of important soil properties in landscapes and at the scale at which AfSIS operates. This not only allows population-based sampling of Africa’s soils, providing unbiased estimates of different soil health constraints, but also provides a basis for wall-to-wall mapping of soil properties at Africa scale through calibration of the georeferenced soil observations to remote sensing imagery.

Figure 1 part 2: results obtained from diagnostic screening tests of sentinel site data

AfSIS is also building the capacity of laboratories in Africa to conduct their own spectral analysis. The central ICRAF facility located in Nairobi, supports Near Infrared Spectroscopy (NIR) labs: in Mali at the Institut d’Economie Rural (IER) in Bamako, in Tanzania at the Agricultural Research Institute (ARI) in Mlingano, near Arusha, in Malawi at theDepartment of Agricultural Research and Services in Chitedze, near Lilongwe, and atthe Agricultural Research Institute of Mozambique (IIAM) in Maputo, Mozambique. Mid infrared spectroscopy labs have been established with national institutions in Cote D’Ivoire, Cameroon, Kenya, Nigeria, and Ethiopia (in progress). With this capacity, these labs can support national soil information systems and soil health baselines and impact assessment in land management projects. These laboratories will be able to benefit from the Africa-wide infrared spectral calibrations that AfSIS is building and also contribute to the continuous improvement of the calibration libraries by inclusion of new samples.

AfSIS is also working with private sector soil testing companies to develop spectral-based soil testing services that are accessible and affordable by smallholder farmers. For example AfSIS is working with BLGG Netherlands to pilot a soil testing service for smallholders in Kenya. In addition, assistance has been provided to the US National Soil Survey Center Laboratory in Lincoln, Nebraska to set up a high throughput mid-infrared scanning system, similar to the robotic system already operational at ICRAF.

It is anticipated that analysis of 40 sentinel sites will have been completed by the end of 2012.

Using Mobile Data Collection Tools for Field Data Collection

AfSIS is assisting national agencies in Africa with developing end-to-end soil information systems, which can be continuously updated with both ground-based and remote sensing observations and measurements. One important emerging system includes the use of mobile and sensor technologies for field data collection. This works leverages tools such as formhub, a web-based mobile data management and visualization platform, and ODK Collect, an open-source survey tool for Android.

Mobile data collection is much more efficient than traditional methods of data collection. Rather than paper-based forms that must be later typed into a computer, researchers and enumerators enter information directly onto an Android device through a form tailored for the specific data collection exercise. The data can then be uploaded to a central database. There are numerous benefits to collecting data this way, including

  1.  Surveyors arrive at site
  2. They use Samsung tablets and their GPS functionality to find the specific sample plot
  3. Surveyors sample soil and collect information about the surrounding area, taking pictures and recording observations with the tablets
  4. Surveyors ship soil samples for analysis using tablets to record what samples have been sent
  • Need for less staff
  • Use of one piece of equipment in place of several (GPS unit, camera, paper forms) 
  • Ease of data collection
  • No need to wait for data entry
  • Ability to check data quality daily during collection

Leveraging XLSForms, a standard for authoring surveys in Excel, the AfSIS teams have developed data instruments for conducting and storing data from field surveys (e.g. LDSF, carbon inventory, and socioeconomic surveys) to AfSIS standards. Data gathering is managed by formhub, a mobile data collection service developed by the Modi Research Group at Columbia University, that leverages Open Data Kit (ODK) Collect on the phone. ODK Collect, developed by the University of Washington, is an open source survey tool that can run on nearly any Android phone or tablet, giving organizations the flexibility to choose from a broad range of devices based on availability, budget, hardware specifica- tions, and more. The tool is packaged with compre- hensive supporting materials culled from our experiences piloting the tools and the observations of many others who have implemented mobile past surveys over the past years.

Land Degradation Surveillance Framework (LDSF) field surveys are underway in Ethiopia using mobile toolkits for field data collection as part of the joint AfSIS/Ethiopia Agricultural Transformation Agency (ATA) and Ethiopia Ministry of Agriculture (MoA)project called EthioSIS. This marks the first time that soil research has been conducted this way. Ethiopia field teams were trained in LDSF procedures and the use of mobile devices to collect data, navigate to sampling points and track soil sample processing. A range of supplementary forms were developed to facilitate logistical support for field data collection. According to Venance Kengwa, a field assistant on the AfSIS project who recently spent some time in Ethiopia helping train a crew on mobile data collection methods for the EthioSIS project, the mobile data collection was much quicker than paper-based collection because data can be sent directly to a central location after data collection is done, which has great benefits to a project because data is submitted in a timely way when the team is still doing field work. Already, teams have used the tablets to collect information from more than 2,600 sample plots and gathered approximately 14,000 soil samples.

The project is also developing a mobile-based tracking system for soil samples from field to lab. A tracking system for soil samples from field to lab to storage facility will be developed with ATA in close coordination with the Modi Research Group at the Earth Institute. Each sample receives a unique identifier contained in a mobile readable code that links to soil sample metadata.

Continued Collaboration in Ethiopia to Build a National Soil System

AfSIS partners in Ethiopia, the Agriculture Transformation Agency and the Ministry of Agriculture, have made great progress in the past few months. The Ethiopian Soil Information Service (EthioSIS) operations team, supported by AfSIS staff, has nearly completed the roll out of the soil surveying teams. They are now heavily focused in supporting Ethiopia’s soil laboratories and turning their attention more and more to the work of concerting raw data into digital soil maps.

The EthioSIS team proposed a "catchment area" model as part of our phasing plan. The model assigns CPs to each processing center based on geographic distribution.

Figure 1. Catchment area model for AfSIS field sampling and laboratory processing. Slide taken from weekly EthioSIS updates to ATA.

To date, EthioSIS has trained 38 soil survey- ors to use AfSIS survey methods, and the surveyors have visited 22 sample sites around the country. The teams have collected more than 4000 soil samples, and the samples are now being processed at six processing centers. To offer insight and experience, AfSIS sent two of its senior soil surveyors to Ethiopia in May. The surveyors were embedded with EthioSIS teams for two weeks and concluded their trip with a presentation to the EthioSIS team.

“With the launch of the project, Ethiopia is jumping to the front of the queue in using satellite technology and spectral analysis to create one of the world’s most comprehensive digital soil maps. This is truly an innovative and pioneering endeavor. EthioSIS will help Ethiopians to make informed land use decisions and to better manage our soil resources,” explained Sam Gameda, Director, Soil Health and Fertility, Agricultural Transformation Agency.

In June, a high level delegation from Ethiopia visited with AfSIS staff in Nairobi and Arusha. The delegation included Professor Tekalign Mamo, EthioSIS Project Leader and Advisor to the Minister with the rank of State Minister, Dr. Take Bekele, ATA Senior Technical Advisor for the Soil Program, Dr. Tilahun Geleto, Director of Soil and Water Research, Oromia Agricultural Institute, and Eric Couper, then AfSIS ICT and Agriculture Coordinator. The very fruitful visit included extensive discussions around the lab procedures at the ICRAF laboratory in Nairobi and around sampling methods in Arusha. Most importantly, they visit laid the groundwork for formal MOUs between AfSIS and those

EthioSIS has trained soil surveyors to use AfSIS survey methods, and the surveyors have visited sample sites around the country.
Photo credit: Agriculture Transformation Agency, Ethiopia

managing EthioSIS. ‘’It was an invaluable trip as we have discussed and agreed on a range of technical issues as well as on key collaborative initiatives that we plan to implement soon,” stated Professor Tekalign Mamo, Advisor to the Minister of Agriculture with the rank of State Minister and EthioSIS Program Leader.

In the coming months, EthioSIS will begin wet chemistry analysis, receive their spectral equipment, and begin the spectral analysis. AfSIS staff will support the efforts with remote consultations and visits to Ethiopia for collaborative training. Additionally, Joseph Muhlhausen, a staff member from the Center for International Earth Science Information Network (CIESIN) recently completed two and a half months in Ethiopia where he trained and supported the staff who will develop EthioSIS’s soil maps.

False color composite images of mid-, near-infrared, and red spectral bands (MODIS bands 7, 2, and 1) showing vegetation and thermal properties. These and additional MODIS bands are used to generate numerous global datasets, including land ecosystem variables (vegetation indices, leaf area index, vegetation net primary production), as well as atmospheric and ocean variables.

Many of these land ecosystem variables are strongly correlated with soil properties and conditions and can therefore be used as powerful predictors of those properties, particularly when ground observations and physical soil samples for a given location are not available, as is the case with much of the African continent.

Africa Soil Information Service: False Color Surface Reflectance Composite, Long Term Averages. This image was derived from NASA MODIS dataset MOD13Q1, Bands 1, 2 and 7 using the International Research Institute's Climate Data Library. Palisades, NY: Center for International Earth Science Information Network (CIESIN), Columbia University. Available at ftp://africagrids.net/ and ftp://africagrids.org/.

Modis map

AfSIS Collaborating Institutions and Partners

The project is led by the International Center for Tropical Agriculture (CIAT), with subgrants to the Tropical Agriculture and Rural Environment Program and the Center for International Earth Science Information Network (CIESIN), both at the Earth Institute, Columbia University; the World Agro-Forestry Centre (ICRAF); and ISRIC - World Soil Information.

AfSIS has many other partners throughout Africa. It also has a number of partners through the Global Soil Consortium in other regions around the world, including government research and academic institutions in East Asia, Europe, the Middle East, North America, Oceania, and South America.

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