Hyperspectral scan of simulated mangrove forest

Leaves were randomly selected and collected from healthy Ceriops australis mangrove trees in the Jack Barnes Bicentennial Mangrove Boardwalk site in Cairns (16° 52.976′S, 145° 45.663′E) (n = 96). We inspected the samples to avoid any obvious damage by insects, sunburn or disease and then placed them into coolers with ice on sealed plastic bags and taken to the remote sensing laboratory at James Cook University - Cairns. We selected this species because it is widespread throughout Australia and the size of their leaves (5.5–10 cm x 2.0–3.4 cm) was suitable for this experiment (Duke et al., 2006; Wightman et al., 2006). The leaves were divided into three groups of 32 leaves, where each group represented a different tidal height scenario. Each group of leaves was then divided into stacks of one, three, five and seven leaves and attached to a wooden platform as shown in Fig. 1. Stacks were arranged perpendicularly to each other to reduce the effects of the position of the sun, shadows or other factors when scanning. Furthermore, to reduce the effects of leaf dehydration and solar angle changes, all scenarios (i.e. 5, 15 and 30 cm of water) were scanned at the same time. Because our aim was to determine if water depth affects our ability to estimate FVC from remotely sensed data, we simulated low, transition and high tide by filling the containers with 5, 15 and 30 cm of water respectively. We decided to use 5, 15 and 30 cm of water for our experiment for several reasons: i) we were able to replicate realistic scenarios where mangrove mud is exposed and fully covered with water; ii) if 15 or 30 cm of water have an effect on the spectral reflectance of mangrove leaves, a more thorough experiment should be proposed; however, if there is no effect at these depths, no effect could be expected from other tidal heights; and iii) the containers used limited our ability to simulate the entire tidal range of the Cairns region (i.e. 3.6 m). We also collected mud from the study site and used it to create a 5 cm coating for the bottom of the containers. We did this for two main reasons: i) to better simulate the mangrove environment in our study site (turbid water) and ii) to prevent the bottom of the container from contributing to the spectral readings from the leaves. With the mud in place, water was poured into the container and left for 24 h to ensure any solids would settle, though water remained turbid throughout the experiment, as it is often the case in our study area. Lastly, our design allowed us to isolate the effects of tidal height on FVC estimation from the interference of stems, branches and dead leaves commonly found in mangrove ecosystems.

Hyperspectral imagery acquisition and pre-processing: We obtained hyperspectral imagery over the leaf arrangement using a Headwall NANO Hyperspectral Scanner (Headwall Photonics Inc.), with a spectral resolution of 270 bands between 400–1000 nm (spectral bandwidth of 1.4–2 nm) and a Field of View equal to 15.3 degrees. The spectral range of this pushbroom scanner incorporates the visible (400–650 nm), red edge (650–750 nm) and NIR regions (750–1000 nm), which are often used to discriminate plant species. The scanner was turned on and left to warm up for 3 min before the first scan. Dark signal measurements were taken before and after the scans by completely covering the sensor and recording the signal in each spectral band. The samples were illuminated by direct sunlight and the scanner was positioned two meters above the samples, centered above the leaf arrangement. A 75% white Spectralon® panel was scanned alongside all images, thereby ensuring that any corrections due to changing illumination could be made during the image pre-processing stages. This set-up allowed us to i) reduce to the minimum any bidirectional reflectance distribution effects, ii) attain imagery of the mangrove leaves such that each pixel represented approximately 1 x 1 mm, and iii) isolate the effects of tidal height on mangrove leaves to assess FVC.

    Data Record Details
    Data record related to this publication Hyperspectral scan of simulated mangrove forest
    Data Publication title Hyperspectral scan of simulated mangrove forest
  • Description

    Leaves were randomly selected and collected from healthy Ceriops australis mangrove trees in the Jack Barnes Bicentennial Mangrove Boardwalk site in Cairns (16° 52.976′S, 145° 45.663′E) (n = 96). We inspected the samples to avoid any obvious damage by insects, sunburn or disease and then placed them into coolers with ice on sealed plastic bags and taken to the remote sensing laboratory at James Cook University - Cairns. We selected this species because it is widespread throughout Australia and the size of their leaves (5.5–10 cm x 2.0–3.4 cm) was suitable for this experiment (Duke et al., 2006; Wightman et al., 2006). The leaves were divided into three groups of 32 leaves, where each group represented a different tidal height scenario. Each group of leaves was then divided into stacks of one, three, five and seven leaves and attached to a wooden platform as shown in Fig. 1. Stacks were arranged perpendicularly to each other to reduce the effects of the position of the sun, shadows or other factors when scanning. Furthermore, to reduce the effects of leaf dehydration and solar angle changes, all scenarios (i.e. 5, 15 and 30 cm of water) were scanned at the same time. Because our aim was to determine if water depth affects our ability to estimate FVC from remotely sensed data, we simulated low, transition and high tide by filling the containers with 5, 15 and 30 cm of water respectively. We decided to use 5, 15 and 30 cm of water for our experiment for several reasons: i) we were able to replicate realistic scenarios where mangrove mud is exposed and fully covered with water; ii) if 15 or 30 cm of water have an effect on the spectral reflectance of mangrove leaves, a more thorough experiment should be proposed; however, if there is no effect at these depths, no effect could be expected from other tidal heights; and iii) the containers used limited our ability to simulate the entire tidal range of the Cairns region (i.e. 3.6 m). We also collected mud from the study site and used it to create a 5 cm coating for the bottom of the containers. We did this for two main reasons: i) to better simulate the mangrove environment in our study site (turbid water) and ii) to prevent the bottom of the container from contributing to the spectral readings from the leaves. With the mud in place, water was poured into the container and left for 24 h to ensure any solids would settle, though water remained turbid throughout the experiment, as it is often the case in our study area. Lastly, our design allowed us to isolate the effects of tidal height on FVC estimation from the interference of stems, branches and dead leaves commonly found in mangrove ecosystems.

    Hyperspectral imagery acquisition and pre-processing: We obtained hyperspectral imagery over the leaf arrangement using a Headwall NANO Hyperspectral Scanner (Headwall Photonics Inc.), with a spectral resolution of 270 bands between 400–1000 nm (spectral bandwidth of 1.4–2 nm) and a Field of View equal to 15.3 degrees. The spectral range of this pushbroom scanner incorporates the visible (400–650 nm), red edge (650–750 nm) and NIR regions (750–1000 nm), which are often used to discriminate plant species. The scanner was turned on and left to warm up for 3 min before the first scan. Dark signal measurements were taken before and after the scans by completely covering the sensor and recording the signal in each spectral band. The samples were illuminated by direct sunlight and the scanner was positioned two meters above the samples, centered above the leaf arrangement. A 75% white Spectralon® panel was scanned alongside all images, thereby ensuring that any corrections due to changing illumination could be made during the image pre-processing stages. This set-up allowed us to i) reduce to the minimum any bidirectional reflectance distribution effects, ii) attain imagery of the mangrove leaves such that each pixel represented approximately 1 x 1 mm, and iii) isolate the effects of tidal height on mangrove leaves to assess FVC.

  • Other Descriptors
  • Data type dataset
  • Keywords
    • fractional vegetation cover
    • beta regression
    • linear regression
    • tidal influence
    • tidal height
    • water effect size
    • remote sensing
  • Funding source
  • Research grant(s)/Scheme name(s)
  • Research themes
    Tropical Ecosystems, Conservation and Climate Change
    FoR Codes (*)
    • 059999 - Environmental Sciences not elsewhere classified
    • 040699 - Physical Geography and Environmental Geoscience not elsewhere classified
    SEO Codes
    • 960503 - Ecosystem Assessment and Management of Coastal and Estuarine Environments
    Specify spatial or temporal setting of the data
    Temporal (time) coverage
  • Start Date 2017/04/17
  • End Date 2017/04/17
  • Time Period
    Spatial (location) coverage
  • Locations
    • Jack Barnes Bicentennial Mangrove Boardwalk, Cairns
    • James Cook University, Smithfield, QLD
    Data Locations

    Type Location Notes
    URL https://cloudstor.aarnet.edu.au/plus/s/Q8ut85SkXnbSoid
    Physical Location Research Data JCU secure CloudStor account
    The Data Manager is:
    College or Centre
    Access conditions Open: free access under license
  • Alternative access conditions
  • Data record size 6 files: 3.4 GB
  • Related publications
      Name Younes, Nicolas, Joyce, Karen E., Northfield, Tobin D., and Maier, Stefan W. (2019) The effects of water depth on estimating Fractional Vegetation Cover in mangrove forests. International Journal of Applied Earth Observation and Geoinformation, 83. 101924.
    • URL https://doi.org/10.1016/j.jag.2019.101924
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    Citation Younes, Nicolas (2020): Hyperspectral scan of simulated mangrove forest. James Cook University.