LASmoons: Chloe Brown

Chloe Brown (recipient of three LASmoons)
Geosciences, School of Geography
University of Nottingham, UK

Background:
Malaysia’s North Selangor peat swamp forest is experiencing rapid and large scale conversion of peat swampland to oil palm agriculture, contrary to prevailing environmental guidelines. Given the global importance of tropical peat lands, and the uncertainties surrounding historical and future oil palm development, quantifying the spatial distribution of ecosystem service values, such as climate mitigation, is key to understanding the trade-offs associated with anthropogenic land use change.
The study explores the capabilities and methods of remote sensing and field-based data sets for extracting relevant metrics for the assessment of carbon stocks held in North Selangor peat swamp forest reserve, estimating both the current carbon stored in the above and below ground biomass, as well as the changes in carbon stock over time driven by anthropogenic land use change. Project findings will feed directly into peat land management practices and environmental accounting in Malaysia through the Tropical Catchments Research Initiative (TROCARI), and support the Integrated Management Plan of the Selangor State Forest Department (see here for a sample).

some clever caption

Goal:
LiDAR data is now seen as the practical option when assessing canopy height over large scales (Fassnacht et al., 2014), with Lucas et al., (2008) believing LiDAR data to produce more accurate tree height estimates than those derived from manual field based methods. At this stage of the project, the goal is to produce a high quality LiDAR-derived Canopy Height Model (CHM) following the “pit-free” algorithm of Khosravipour et.al., 2014 using the LAStools software.

Data:
+ LiDAR provided by the Natural Environment Research Council (NERC) Airborne Research and Survey Facility’s 2014 Malaysia Campaign.
+ covers 685 square kilometers (closed source)
+ collected with Leica ALS50-II LiDAR system
+ average pulse spacing < 1 meter, average pulse density 1.8 per square meter

LAStools processing:
1) Create 1000 meter tiles with 35 meter buffer to avoid edge artifacts [lastile]
2) Remove noise points (class 7) that are already classified [las2las]
3) Classify point clouds into ground (class 2) and non-ground (class 1) [lasground]
4) Generate normalized above-ground heights [lasheight]
5) Create DSM and DTM [las2dem]
6) Generate a pit-free Canopy Height Model (CHM) as described here [lasthin, las2dem, lasgrid]
7) Generate a spike-free Canopy Height Model (CHM) as described here for comparison [las2dem]

References:
Fassnacht, F.E., Hartig, F., Latifi, H., Berger, C., Hernández, J., Corvalán, and P., Koch, B. (2014). Importance of sample size, data type and prediction method for remote sensing-based estimations of above-ground forest biomass. Remote Sensing. Environment. 154, 102–114.
Khosravipour, A., Skidmore, A. K., Isenburg, M., Wang, T., and Hussin, Y. A. (2014). Generating pit-free canopy height models from airborne LiDAR. Photogrammetric Engineering & Remote Sensing, 80(9), 863-872.
Lucas, R. M., Lee, A. C., and Bunting, P. J., (2008). Retrieving forest biomass through integration of casi and lidar data. International Journal of Remote Sensing, 29 (5), 1553-1577.

LASmoons: Elia Palop-Navarro

Elia Palop-Navarro (recipient of three LASmoons)
Research Unit in Biodiversity (UO-PA-CSIC)
University of Oviedo, SPAIN.

Background:
Old-growth forests play an important role in biodiversity conservation. However, long history of human transformation of the landscape has led to the existence of few such forests nowadays. Its structure, characterized by multiple tree species and ages, old trees and abundant deadwood, is particularly sensible to management practices (Paillet et al. 2015) and requires long time to recover from disturbance (Burrascano et al. 2013). Within protected areas we would expect higher proportions of old-growth forests since these areas are in principle managed to ensure conservation of natural ecosystems and processes. Nevertheless, most protected areas in the EU sustained use and exploitation in the past, or even still do.

lasmoons_elia_palopnavarro_0

Part of the study area. Dotted area corresponds to forest surface under protection.

Goal:
Through the application of a model developed in the study area, using public LiDAR and forest inventory data (Palop-Navarro et al. 2016), we’d like to know how much of the forest in a network of mountain protected areas retains structural attributes compatible with old-growth forests. The LiDAR processing tasks which LAStools will be used for involve a total of 614,808 plots in which we have to derive height metrics, such as mean or median canopy height and its variability.

Vegetation profile colored by height in a LiDAR sample of the study area.

Vegetation profile colored by height in a LiDAR sample of the study area.

Data:
+ Public LiDAR data that can be downloaded here with mean pulse density 0.5 points per square meter. This data has up to 5 returns and is already classified into ground, low, mid or high vegetation, building, noise or overlapped.
+ The area covers forested areas within protected areas in Cantabrian Mountains, occupying 1,207 km2.

LAStools processing:
1) quality checking of the data as described in several videos and blog posts [lasinfo, lasvalidate, lasoverlap, lasgrid, las2dem]
2) use existing ground classification (if quality suffices) to normalize the elevations of to heights above ground using tile-based processing with on-the-fly buffers of 50 meters to avoid edge artifacts [lasheight]
3) compute height-based forestry metrics (e.g. ‘-avg’, ‘-std’, and ‘-p 50’) for each plot in the study area [lascanopy]

References:
Burrascano, S., Keeton, W.S., Sabatini, F.M., Blasi, C. 2013. Commonality and variability in the structural attributes of moist temperate old-growth forests: a global review. Forest Ecology and Management 291:458-479.
Paillet, Y., Pernot, C., Boulanger, V., Debaive, N., Fuhr, M., Gilg, O., Gosselin, F. 2015. Quantifying the recovery of old-growth attributes in forest reserves: A first reference for France. Forest Ecology and Management 346:51-64.
Palop-Navarro, E., Bañuelos, M.J., Quevedo, M. 2016. Combinando datos lidar e inventario forestal para identificar estados avanzados de desarrollo en bosques caducifolios. Ecosistemas 25(3):35-42.

LASmoons: Jesús García Sánchez

Jesús García Sánchez (recipient of three LASmoons)
Landscapes of Early Roman Colonization (LERC) project
Faculty of Archaeology, Leiden University, The Netherlands

Background:
Our project Landscapes of Early Roman Colonization (LERC) has been studying the hinterland of the Latin colony of Aesernia (Molise region, Italy) using several non-destructive techniques, chiefly artefactual survey, geophysics, and interpretation of aerial photographs. Nevertheless large areas of the territory are covered by the dense forests of the Matese mountains, a ridge belonging the Apennine chain, or covered by bushes due to the abandonment of the countryside. The project won’t be complete without integrating the marginal, remote and forested areas into our study of the Roman hinterland. Besides, it’s also relevant to discuss the feasibility of LiDAR data sets in the study of Mediterranean landscapes and its role within contemporary Landscape Archaeology.

some clever caption

LiDAR coverage in Molise region, Italy.

Goal:
+ to study in detail forested areas in the colonial hinterland of Aesernia.
+ to found the correct parameters of the classification algorithm to be able to locate possible archaeological structures or to document appropriately those we already known.
+ to document and create new visualization of hill-top fortified sites that belong to the indigenous population and are currently poorly studied due to inaccessibility and forest coverage (Monte San Paolo, Civitalla, Castelriporso, etc.)
+ to demonstrate the archaeological potential of LiDAR data in Italy and help other scholars to work with that kind of data, explaining basic information about data quality, where and how to acquire imagery and examples of application in archaeology. A paper entitled “Working with ALS – LiDAR data in Central South Italy. Tips and experiences”, will be presented in the International Mediterranean Survey Workshop by the end of February in Athens.

Civitella hillfort (Longano, IS) and its local context: ridges and forest belonging to the Materse mountains and the Appenines.

Data:
Recently the LERC project has acquired a large LiDAR dataset created by the Italian Geoportale Nazionale and the Minisstero dell’Ambiente e della Tutella del Territorio e del Mare. The data was produced originally to monitor land-slides and erosive risk.
The average point resolution is 1 meter.
+ The data sets were cropped originally in 1 sq km. tiles by the Geoportale Nazionale for distribution purposes.

LAStools processing:
1) data is provided in *.txt files thus the first step is to create appropriate LAS files to work with [txt2las]
2) combine areas of circa 16 sq km (still fewer than 20 million points to be processed in one piece with LAStools) in the surroundings of the colony of Aesernia and in the Matese mountains [lasmerge]
3) assign the correct projection to the data [lasmerge or las2las]
4) extract the care-earth with the best-fitting parameters [lasground or lasground_new]
5) create bare-earth terrain rasters as a first step to visualize and analyze the area [lasdem]

LASmoons: Rachel Opitz

Rachel Opitz (recipient of three LASmoons)
Center for Virtualization and Applied Spatial Technologies
Department of Anthropology, University of South Florida, USA

Background:
In Spring 2017 Rachel Opitz will be teaching a course on Remote Sensing for Human Ecology and Archaeology at the University of South Florida. The aim of the course is to provide students with the practical skills and knowledge needed to work with contemporary remote sensing data. The course focuses on airborne laser scanning and hyper-spectral data and their application in Human Ecology and Archaeology. Through the course students will be introduced to a number of software packages commonly used to process and interpret these data, with an emphasis on free and/or open source tools.

Classification parameters and the resolution at which the DTM is interpolated both have a significant impact on our ability to recognize anthropogenic features in the landscape. Here we see a small quarry. More aggressive filtering and a coarser DTM resolution (left) makes it difficult to recognize that this is a quarry. Less aggressive filtering and a higher resolution (right) leaves some vegetation behind, but makes the edges of the quarry and some in-situ blocks clearly visible.

Goal:
The students will develop practical skills in applied remote sensing through hands-on exercises. Learning to assess, manage and process large data sets is essential. In particular, the students in the course will learn to:
+ Identify the set of techniques needed to solve a problem in applied remote sensing
+ Find public imagery and specify acquisitions
+ Assess data quality
+ Process airborne LiDAR data
+ Combine complementary remote sensing data sources
+ Create effective data visualizations
+ Analyze digital topographic and spectral data to answer questions in human ecology and archaeology

Data:
The course will include case studies that draw on a variety of publicly available data sets that will all be used in the exercises:
+ the PNOA data from Spain
+ data held by NOAA
+ data collected using NASA’s GLiHT platform

LAStools processing:
LAStools will be used throughout the course, as students learn to assess the quality of LiDAR data, classify raw LiDAR point clouds, create raster terrain and canopy models, and produce visualizations. The online tutorials and videos available via the company website and the over 50 hours of video on YouTube as well as the LAStools user forum will be used as resources during the course.

LASmoons: Alen Berta

Alen Berta (recipient of three LASmoons)
Department of Terrestrial Ecosystems and Landscape, Faculty of Forestry
University of Zagreb and Oikon Ltd Institute for Applied Ecology, CROATIA

Background:
After becoming the EU member state, Croatia is obliged to fulfill the obligation risen from the Kyoto protocol: National Inventory Report (NIR) of the Green House Gasses according to UNFCCC. One of the most important things during the creation of the NIR is to know how many forested areas there are and their wood stock and increment. This is needed to calculate the size of the existing carbon pool and its potential for sequestration. Since in Croatia, according to legislative, it is not mandatory to calculate the wood stock and yield of the degraded forest areas (shrubbery and thickets) during the creation of the usual forest management plans, this data is missing. So far, only a rough approximation of the wood stock and increment is used during the creation of NIR. However, these areas are expanding every year due to depopulation of the rural areas and the cessation of traditional farming.

very diverse stand structure of degraded forest areas (shrubbery and thickets)

Goal:
This study will focus on two things: (1) Developing regression models for biomass volume estimation in continental shrubberies and thickets based on airborne LiDAR data. To correlate LiDAR data with biomass volume, over 70 field plots with a radius of 12 meters have been established in more than 550 ha of the hilly and lowland shrubberies in Central Croatia and all trees and shrubberies above 1 cm Diameter at Breast Height (DBH) were recorded with information about tree species, DBH and height. Precise locations of the field plots are measured with survey GNNS and biomass is calculated with parameters from literature. For regression modeling, various statistics from the point clouds matching the field plots will be used (i.e. height percentiles, standard deviation, skewness, kurtosis, …). 2) Testing the developed models for different laser pulse densities to find out if there is a significant deviation from results if the LiDAR point cloud is thinner. This will be helpful for planning of the later scanning for the change detection (increment or degradation).

Data:
+
641 square km of discrete returns LiDAR data around the City of Zagreb, the capitol of Croatia (but since it is highly populated area, only the outskirts of the area will be used)
+ raw geo-referenced LAS files with up to 3 returns and an average last return point density of 1 pts/m².

LAStools processing:
1)
extract area of interest [lasclip or las2las]
2) create differently dense versions (for goal no. 2) [lasthin]
3) remove isolated noise points [lasnoise]
4) classify point clouds into ground and non-ground [lasground]
5) create a Digital Terrain Model (DTM) [las2dem]
6) compute height of points above the ground [lasheight]
7) classify point clouds into vegetation and other [lasclassify]
8) normalize height of the vegetation points [lasheight]
9) extract the areas of the field plots [lasclip]
10) compute various metrics for each plot [lascanopy]
11) convert LAZ to TXT for regression modeling in R [las2txt]

LASmoons: Stéphane Henriod

Stéphane Henriod (recipient of three LASmoons)
National Statistical Committee of the Kyrgyz Republic
Bishkek, Kyrgyzstan

This pilot study is part of the International Climate Initiative project called “Ecosystem based Adaptation to Climate change in the high mountainous regions of Central Asia” that is funded by the Federal Ministry for the Environment, Nature Conservation, Building and Nuclear Safety (BMU) of Germany and implemented by the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH in Kyrgyzstan, Tajikistan and Kazakhstan.

lasmoons_Stephane_Henriod_1

Background:
The ecosystems in high mountainous regions of Central Asia are characterized by a unique diversity of flora and fauna. In addition, they are the foundation of the livelihoods of the local population. Specific benefits include clean water, pasture, forest products, protection against floods and landslides, maintenance of soil fertility, and ecotourism. However, the consequences of climate change such as melting glaciers, changing river runoff regimes, and weather anomalies including sharp temperature fluctuations and non-typical precipitation result in negative impacts on these ecosystems. Coupled with unwise land use, these events damage fragile mountain ecosystems and reduce their regeneration ability undermining the local population’s livelihoods. Therefore, people living in rural areas and directly depending on natural resources must adapt to adverse impacts of climate change. This can be done through a set of measures, known in the world practice as ecosystem-based adaptation (EbA) approach. It promotes the sustainable use of natural resources to sustain and enhance the livelihood of the population depending on those resources.

lasmoons_Stephane_Henriod_2 Goal:
In two selected pilot regions of Kyrgyzstan and Tajikistan, planned measures will concentrate on climate-informed management of ecosystems in order to maintain their services for the rural population. EbA always starts with identifying the vulnerability of the local population. Besides analyzing the socio-economic situation of the local population, this includes (1) assessing the ecological conditions of the ecosystems in the watershed and the related ecosystem services people benefit from, (2) identifying potential disaster risks, and (3) analyzing glacier dynamics with its response to water runoff. As a baseline to achieve this and to get spatially explicit, remote sensing based techniques and mapping activities need to be utilized.

A first UAV (unmanned aerial vehicle) mission has taken place in the Darjomj watershed of the Bartang valley in July 2016. RGB-NIR images as well as a high-resolution Digital Surface Model have been produced that now need to be segmented and analysed in order to produce comprehensive information. The main processing that will take advantage of LAStools is the generation of a DTM from the DSM that will then be used for identifying risk areas (flood zones, landslides and avalanches, etc.). The results of this approach will ultimately be compared with lower-cost satellite images (RapidEye, Planet, Sentinel).

Data:
+ High-resolution RGB and NIR image (10 cm) from a SenseFly Ebee
+ High-resolution DSM (10 cm) from a SenseFly Ebee

LAStools processing:
1)
classify DSM points obtained via dense-matching photogrammetry into a SenseFly Ebee imagery into ground and non-ground points via processing pipelines as described here and here [lastile, lassort, lasnoise, lasground]
2) create a DTM [las2dem, lasgrid, blast2dem]
3) produce 3D visualisations to facilitate the communication around adaptation to climate change [lasview]
lasmoons_Stephane_Henriod_0

LASmoons: Jane Meiforth

Jane Meiforth (recipient of three LASmoons)
Environmental Remote Sensing and Geoinformatics
University of Trier, GERMANY

Background:
The New Zealand Kauri trees (or Agathis australis) are under threat by the so called Kauri dieback disease. This disease is caused by a fungi like spore, which blocks the transport for nutrition and water in the trunk and finally kills the trees. Symptoms of the disease in the canopy like dropping of leaves and bare branches offer an opportunity for analysing the state of the disease by remote sensing. The study site covers three areas in the Waitakere Ranges, west of Auckland with Kauri trees in different growth and health classes.

Goal:

The main objective of this study is to identify Kauri trees and canopy symptoms of the disease by remote sensing, in order to support the monitoring of the disease. In the first step LAStools will be used to extract the tree crowns and describe their characteristics based on height metrics, shapes and intensity values from airborne LiDAR data. In the second step, the spectral characteristics of the tree crowns will be analyzed based on very high resolution satellite data (WV02 and WV03). Finally the best describing spatial and spectral parameters will be combined in an object based classification, in order to identify the Kauri trees and different states of the disease..

Data:
+
 high resolution airborne LiDAR data (15-35p/sqm, ground classified) taken in January 2016
+ 15cm RGB aerial images taken on the same flight as the LIDAR data
+ ground truth field data from 2100 canopy trees in the study areas, recorded January – March 2016
+ helicopter images taken in January – April 2016 from selected Kauri trees by Auckland Council
+ vector layers with infrastructure data like roads and hiking trackslasmoons_CHM_Jane_Meiforth_0

 

LAStools processing:
1)
create square tiles with edge length of 1000 m and a 25 m buffer to avoid edge artifacts [lastile]
2) generate DTMs and DSMs [las2dem]
3).produce height normalized tiles [lasheight]
4) generate a pit-free Canopy Height Model (CHM) using the method of Khosravipour et al. (2014) with the workflow described here [lasthin, las2dem, lasgrid]
5) extract crown polygons based on the pit-free CHM [inverse watershed method in GIS, las2iso]
6) normalize the points of each crown with constant ground elevation to avoid slope effects [lasclip, las2las with external source for the ground elevation]
7) derive height metrics for each crown on base of the normalized crown points [lascanopy]
8) derive intensity statistics for the crown points [lascanopy with ‘-int_avg’, ‘-int_std’ etc. on first returns]
9) derive metrics correlated with the dropping of leaves like canopy density, canopy cover and gap fraction for the crown points [lascanopy with ‘–cov’, ‘–dns’, ‘–gap’, ‘–fraction’]

Reference:
Hu B, Li J, Jing L, Judah A. Improving the efficiency and accuracy of individual tree crown delineation from high-density LiDAR data. International Journal of Applied Earth Observation and Geoinformation. 2014; 26: 145-55.
Khosravipour, A., Skidmore, A.K., Isenburg, M., Wang, T.J., Hussin, Y.A., 2014. Generating pit-free Canopy Height Models from Airborne LiDAR. PE&RS = Photogrammetric Engineering and Remote Sensing 80, 863-872.
Li J, Hu B, Noland TL. Classification of tree species based on structural features derived from high density LiDAR data. Agricultural and Forest Meteorology. 2013; 171-172: 104-14.
MPI New Zealand http://www.kauridieback.co.nz – website with information on the kauri dieback disease
Vauhkonen, J., Ene, L., Gupta, S., Heinzel, J., Holmgren, J., Pitkänen, J., Solberg, S., Wang, Y., Weinacker, H., Hauglin, K. M., Lien, V., Packalén, P., Gobakken, T., Koch, B., Næsset, E., Tokola, T. and Maltamo, M. (2012) Comparative testing of single-tree detection algorithms under different types of forest. Forestry, 85, 27-40.