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. 2016 Nov 18;16(11):1948.
doi: 10.3390/s16111948.

Extracting Plant Phenology Metrics in a Great Basin Watershed: Methods and Considerations for Quantifying Phenophases in a Cold Desert

Keirith A Snyder  1 , Bryce L Wehan  2 , Gianluca Filippa  3 , Justin L Huntington  4 , Tamzen K Stringham  5 , Devon K Snyder  6
Affiliations

Extracting Plant Phenology Metrics in a Great Basin Watershed: Methods and Considerations for Quantifying Phenophases in a Cold Desert

Keirith A Snyder et al. Sensors (Basel). .

Abstract

Plant phenology is recognized as important for ecological dynamics. There has been a recent advent of phenology and camera networks worldwide. The established PhenoCam Network has sites in the United States, including the western states. However, there is a paucity of published research from semi-arid regions. In this study, we demonstrate the utility of camera-based repeat digital imagery and use of R statistical phenopix package to quantify plant phenology and phenophases in four plant communities in the semi-arid cold desert region of the Great Basin. We developed an automated variable snow/night filter for removing ephemeral snow events, which allowed fitting of phenophases with a double logistic algorithm. We were able to detect low amplitude seasonal variation in pinyon and juniper canopies and sagebrush steppe, and characterize wet and mesic meadows in area-averaged analyses. We used individual pixel-based spatial analyses to separate sagebrush shrub canopy pixels from interspace by determining differences in phenophases of sagebrush relative to interspace. The ability to monitor plant phenology with camera-based images fills spatial and temporal gaps in remotely sensed data and field based surveys, allowing species level relationships between environmental variables and phenology to be developed on a fine time scale thus providing powerful new tools for land management.

Keywords: PhenoCam network; StarDot cameras; camera-based repeat digital photography; pinyon and juniper; sagebrush steppe; semi-arid meadows.

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Conflict of interest statement

The authors declare no conflict of interest. The funding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Figures

Figure A1
Figure A1
Porter Canyon meadow vegetation types and monitoring locations. Meadow phenocam focuses on the T2 transect of monitoring wells (see Figure 3 for alternate angle).
Figure A2
Figure A2
Phenology analyses of an individual pinyon canopy. (a) Image set contained all filtered images, including images with snow; (b) Image set contained the same images as (a), with all snow images removed.
Figure A3
Figure A3
Initial spatiotemporal analysis that was confounded by interspace, which lead to the filtering described in Figure 8. The red and yellow colors closely map with sagebrush canopy, while green and blue closely map with interspace but have a negative growing season length.
Figure A4
Figure A4
Cumulative distribution frequency (CDF) of data shown in Figure 9c, with histograms of the two ranges after splitting the original CDF.
Figure 1
Figure 1
Regions of Interest (ROI) at three site locations. (a) Meadow site of wet, mesic and dry meadow sagebrush canopy in red, pink and orange respectively; (b) ROI for upland sagebrush steppe in white, canopy in green and interspace in blue; (c) Pinyon and juniper canopy site with 3 pinyon ROIs in cyan and 3 juniper ROIs in green.
Figure 2
Figure 2
An example from the wet meadow of processing raw RGB values. (a) Raw GCC values acquired from extracting the per-pixel RGB digital numbers averaged across the ROI; (b) Three filters were applied in the order: night, spline, max. Max filtered GCC values calculated from sub-daily data after night and spline filters are applied. Raw GCC values at daily time steps are also shown as gray dots; (c) Filtered data fitted with uniform distribution of residuals around the observed data points to estimate uncertainty (1000 replications, gray lines); (d) The fitted line and median phenophase dates (vertical lines) upturn date (UD), stabilization date (SD), downturn date (DD) and recession date (RD) and the 10th to 90th confidence intervals around those dates.
Figure 3
Figure 3
Analyses of the wet meadow to demonstrate snow/night filter. (a) Cumulative distribution frequency of GCC for all images, with the red line being the first break in slope and data below this was removed with snow/night filter; (b) raw data (red dots) with snow/night filter shown as blue dots, and black line is with the max filter applied; (c) Fitted and threshold seasonal GCC values obtained with the snow/night filter; (d) Fitted and threshold seasonal GCC values obtained on manually filtered images.
Figure 4
Figure 4
Seasonal course of GCC (black) and phenophase dates of (a) the wet meadow and (b) the mesic meadow, plotted with 3-day average daily air temperature (red) and average daily groundwater depth (blue).
Figure 5
Figure 5
Seasonal course of GCC and phenophase dates are shown for (a) the dry meadow sagebrush canopy and (b) for the upland sagebrush canopy, plotted with 3-day average air temperature and soil water content. The dry meadow sagebrush had a longer growing season and increased greenness relative to the upland sagebrush canopy.
Figure 6
Figure 6
Seasonal course of GCC and phenophase dates for (a) pinyon and (b) juniper plotted with 3-day average daily soil temperature at 5 cm and soil volumetric water content (VWC). Note data gaps in soil VWC were caused by datalogger malfunction. Pinyon and juniper had a similar growing season. However, there was greater seasonal variation in greenness for juniper and a close tracking of green up with soil temperature in juniper.
Figure 7
Figure 7
Fitted curves for 3 regions of interest (ROIs): sagebrush steppe community, sagebrush canopy, and interspace. ROIs are shown in Figure 1b.
Figure 8
Figure 8
The manual filtering method used to determine pixels in the spatiotemporal analyses. Tick marks below bottom panel apply to all panels and are DOY for (a,b) and number of days for (c). (a,b) Vertical red lines represent lower and upper limits where pixels were removed due to bimodal distributions for upturn date (UD) and recession date (RD). Red bars are removed data. (c) Growing season length (GSL) calculated as the difference between RD and UD. Red bars illustrate pixels that characterized interspace and gray bars are pixels that characterized vegetation and were predominately sagebrush canopy. These data are used in the analyses in Figure 9.
Figure 9
Figure 9
(a) Growing season length (GSL) illustrated for pixels of vegetation, data are from the gray bars in Figure 8c; (b) Seasonal GCC range of vegetation, pixels of vegetation were determined from the gray bars in Figure 8c; (c) Seasonal GCC range of the interspace, interspace pixels were determined from red bars in Figure 8c. Interspace pixels were as follows: green to red match bark and shadows and violet to blue match bare ground. (b,c) scales were kept fixed from 0.01–0.1 to highlight the two distributions.
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