Land Processes Field Work and Projects at sites in

the southern Sierra Nevada Mountains

Tuolumne River

Professor Susan Ustin

Department of Land, Air and Water Resources
University of California Davis
NASA Student Airborne Research Program, June 17, 2015

Critical Zone Observatory

(NSF Hydrology program)

Teakettle
2500m

National Ecological
Observatory Network
(NEON)

HyspIRI Preparatory Program

and SARP Sites:
SJER (foothill

woodland)

Lower Soaproot Saddle

Upper Teakettle

Evapotranspiration and Carbon fluxes are Measured by Eddy Covariance at Several CZO
Sites and are under construction at NEON sites

Measure fluxes of CO2, H2O and Temperature

And standard weather station information:
Net Radiation ( shortwave, longwave),
wind speed and direction,
relative humidity,
canopy, soil, and air temperatures.

The Southern Sierra CZO operates eddy covariance flux towers, installed at 4 locations
varying from 400-2700 meters.

2007 NRC Decadal Survey - HyspIRI

HyspIRI: A hyperspectral sensor combined with a multispectral thermal sensor
in low Earth orbit

Visible ShortWave InfraRed

(VSWIR) Imaging Spectrometer
Map dominant trees
species, Bartlett Forest, NH

Map Soil & Canopy C : N Ratio

White Mountain National Forest, NH

Multispectral Thermal InfraRed

(TIR) Scanner
Map evpotranspiration,
temperature and emissivity

Image data

Flightlines flown by NASA for HyspIRI and NSF for the

NEON & CZO; Location of our field Sites

2013, 2014, and 2015

AVIRIS (20m) and MASTER (50m) data
in April, June and September

SARP June 2013, 2014 & 2015

MASTER data (~7m)

U.S. Forest

USGS DEM, DOQs

Yosemite,
Sequoia Nat. For.

NEON 2013 June FW Lidar (1m) and

NEON AVIRIS (3m?)
AVIRIS-next generation, 2014 (2m)
flown at different sun-view angles
USFS Lidar (from NCALM) (1m)
CZO data is available: Lidar, Landsat,
MODIS, flux data (current data not
online)

SARP flightlines
NEON lidar flights
USFS LiDar Data
Flux Towers
HyspIRI flightlines
AVIRIS and MASTER

Reflectance calibration targets:

Flightlines flown by NASA for HyspIRI and NSF for the

NEON & CZO; Location of our field Sites

Soil temperatures (at overflight time),

Soil reflectance, and
Soil emissivity (to be done by you at
JPL this summer)
Field Data
Leaf reflectance and chemistry
for dominant species
Leaf thickness, leaf area, fresh and dry
mass,
LAI (from fisheye photos)
Tree location and species ID from
transects, polygons and plots
(measured over 3 yrs)
Ground lidar measurements of
individual trees
Tree height, crown dimensions
Mapping live, dead trees

U.S. Forest
Yosemite,
Sequoia Nat. For.

SARP flightlines
NEON lidar flights
USFS LiDar Data
Flux Towers
HyspIRI flightlines
AVIRIS and MASTER

AVIRIS (20m pixel) and MASTER flights in lall 2013 and 3

seasons 2014 and 2015(April, June, Sept.)

Data over RIM fire:

AVIRIS C (20m)
Fall 2013
S, S, F 2014
S, S 2015
NCALM lidar data
(1m) 2 lines at FW and
the entire area with
first/last return
USFS vegetation map
USFS fire severity map
DEM, DOQ

October 2013 HyspIRI flew entire

RIM burn area (403 sq. mi)
Center point of
flightline

MASTER Instrument
MASTER flightlines from 2013 and 2014 showing Normalized
Difference Water Index for low and high elevation sites

2013

2014
24 in.

20 in.

NASA MASTER
flights scheduled
June 23rd and 24th

Lower Elevation
(San Joaquin
Experimental Range)

Upper Elevation
(Teakettle)

NASA AVIRIS-next generation instrument flown on Twin

Otter acquired at 4m and 2m pixels in 2014
Multiple orientation of flightlines designed to capture
structure information

Sites and length of lines (2014):

Coachella - 10 km
Kearney 7 km
Loma Ridge - 1km
Tonzi 3 km or 9 km
San Joaquin 6 km
Lower Teakettle 29 km

Waveform LiDAR

Airborne Observations of Ice in the

Jakobshavn Fjord
Area is 6.5 km long and 750 m wide, color-coded by elevation (red high, blue low)
Unfiltered

10% Noise

Noise
Removed

59
Data Courtesy of SigmaSpace Corp.

 The POLAR
instrument is a
photon-counting
altimeter
Our data will likely
look similar to this

Jeff Thayer, U. Colorado Boulder

Mahsa Moussavi et al. 2014. Int. J. Remote Sensing

Pictures of our Field Sites

SJER is a savanna with Grey pine and blue oak

Quercus douglasii
(Blue oak savanna)

Low elevation site

San Joaquin
Experimental
Range

San Joaquin Experimental Range (SJER) was established in 1934 and was California's first
range science research station; Remodeled 2010 with stimulus money

Low elevation woodland/savanna

Pinus sabinana
Gray pine

Canopy Structure & Reflectance

San Joaquin:
Quercus douglasii
(blue oak)

4500
4000
3500

2500
2000
1500
1000
500
0

366
443
521
599
655
733
811
889
966
1,043
1,120
1,196
1,253
1,333
1,412
1,492
1,572
1,651
1,731
1,811
1,866
1,946
2,027
2,107
2,187
2,267
2,346
2,426

Reflectance

3000

Wavelength

How do we analyze or model mixed pixel data to retrieve species

identification, chemistry or other biophysical products?

San Joaquin Experimental Range

San Joaquin Experimental Range

Green veg
Dry veg
Soil

Reflectance * 10000

GV
NPV
Soil

Wavelength (nm)

Best Endmembers selected using CoB, EAR, and MASA techniques.

Color Infrared (NIR=red display,

red=green display, green=blue display

Structure and composition of

a Mid-Elevation Mixed
Conifer Forest
Soaproot Saddle Site

Mid elevation conifer forest

Canopy Structure & Reflectance

Soaproot Saddle:

Pinus ponderosa
(ponderosa pine)
How do shadows impact retrieval of
canopy chemistry?
Can shade fraction aid in characterization
of structure?

How does understory impact

interpretation of the forest species
composition?
Can shadows (or albedo) be used to
estimate biomass or other structure
parameter?

Soaproot Saddle

Soaproot Saddle
GV
NPV
Soil

Reflectance * 10000

Green veg
Dry veg
Soil

Wavelength (nm)

Best Endmembers selected using CoB, EAR, and MASA

techniques.

Mid-elevation Mixed Conifer Forest

(mixed yellow pine forest)

Upper Teakettle (upper elevation forest)

Upper elevation conifer forest

SARP Land Group 2014

Canopy Structure & Reflectance

Teakettle:
Abies concolor
Abies magnifica
6000
5000

3000
low % shadow
high % shadow

2000
1000
0
366
463
560
658
733
831
927
1,024
1,120
1,215
1,293
1,392
1,492
1,592
1,691
1,791
1,866
1,966
2,067
2,167
2,267
2,366
2,466

Reflectance

4000

Wavelength

Teakettle (upper elevation)

Teakettle
GV
NPV
Soil

Reflectance * 10000

Green veg
Dry veg
Soil

Wavelength (nm)

Best Endmembers selected using CoB, EAR, and MASA

techniques.

Changing Plant Functional Types in California from 1934 to 1996

Grasslands
Mixed oak-pine
savanna
Ponderosa pine forest
Mixed Montane
Hardwod & Conifer
Mixed conifer
Lodgepole pine,
red fir
Subalpine conifers

Lake Tahoe

Analyzed by James Thorne,

UC Davis based on the
Wieslander VTM Project,
1934

We know General Information about the Distribution of species in these

Forests Under Different Water Regimes
High

Water Supply

(deep soils, no rain shadow)

Low

(shallow soils or rain shadow)

Elevation (meters)

3500

3000

2500

2000

1500

Can we apply this information in a species map of these forests?

Scaling Plan
PROSPECT-5 +4SAIL2

Trait syndromes

Leaf Chemistry, ,
Pigments, water, C, N, LMA

Plot Data
Woody Species
Canopy Dominants, different structures
Define Structure:
LAI, % Green foliage, %NPV, % Soil
Sites
Timing, magnitude P, R, ET
Flux towers, other Research Sites
D
High Fidelity Spectroscopy

Evaluation of HyspIRI

Canopy
depth
LAI, gap
structure

NEON AOP
FW LiDAR
AVIRIS-NG
NASA ER2
AVIRIS
MASTER

Ht.
USFS LiDAR and WV2 data

MEASUREMENTS
Spectra
Hemispherical leaf reflectance and
transmittance
Directional leaf reflectance
Reflectance for soil, rock, understory
vegetation, & dry plant materials (leaves,
stems, bark)

Leaf Traits
Leaf water content
Leaf mass area
Leaf thickness
Leaf pigments
Leaf carbon & nitrogen

Structure & Composition

leaf area index or biomass
canopy cover or gap fraction
plot-level inventory (forested sites)
species
ground cover fraction
diameter at breast height
canopy height
canopy base height
crown width

Measuring Forest Inventory

50m tape
100 m tape

Crown Diameter

Tree diameter at
breast height (DBH)

DBH tape

Fisheye photography used to estimate Leaf Area Index and canopy gap size distribution

Fisheye photos

Annual solar tracks superimposed on FY photos

Calculate the fPAR penetrating the canopy to the ground

Measuring Tree Height and Distance

Inclinometer

Measuring reflectance of foliage in the field

ASD measurements
LI-COR 1800 Integrating Sphere

Leaf
clip

Different
Model
ASD

Spectralon panel for

calibrating
reflectance

Trimble
GPS

Sample Collection
Measure with leaf clip or
integrating sphere?
Leaf Clip (RF only)

Integrating Sphere
(RF & TM)

Spectralon: Approved NIST Standard for Calculating Reflectance

Gray panels of known reflectance
Rare Earths used to Calibrate
Wavelength
Holmium Oxide for UV-VIS-NIR
Dysprosium Oxide for NIR
Erbium Oxide - for VIS-NIR
Note it is not a perfect

99% White Reflecting

Panels
Reflector
(calibration

provided with each

panel)

Used to calibrate wavelength and albedo

Levels keep fiber optic

entrance pointed at nadir

Measuring Invariant Targets for

Calibrating the optical spectral bands

Camera next to ASD fiber optic probe

Record field of view

of spectrometer

Levels keep fiber optic

entrance pointed at nadir

Calibrated Radiance

Derived Reflectance of
Plant after RTM calibration

We use the field

spectra to evaluate the
calibration from
radiance to
reflectance, which is
done using a radiative
transfer model that
accounts for the
scattering and
absorption of light in
the atmosphere
40

Components of Photosynthesis Revealed in the Solar Radiance Data

Components of Photosynthesis in Radiance Spectrum

Carotenoids

Absorption Spectrum of Chloroplast Pigment Molecules

430 nm
453 nm

662 nm

652

Senescence sequence of a leaf

42

Reflectance, Transmittance, and Absorptance from Fresh and Dry Leaves

Fresh leaf

Dry leaf

(a)

(b)

0.9

0.9

0.8

0.8

Transmittance

0.7

Transmittance

0.7

0.6

0.6

0.5

0.5

Absorptance
Absorptance
0.4

0.4

Reflectance

0.3
0.2

0.2

0.1

0.1

0
400

600

800

1000 1200 1400 1600

Reflectance

0.3

1800 2000 2200 2400

Wavelength (nm)

0
400

600

800

1000 1200 1400 1600

1800 2000 2200 2400

Wavelength (nm)

Absorption by Water Vapor, Liquid Water and Solid Phases in the Solar
Reflected Spectrum

Water Vapor
Liquid Water
Solid (ice)

Near 1000 nm absorption spectra for three phases of water overlap but maxima are
displaced by wavelength

Robert O. Green

Palo verde

Leaf Absorption Coefficients

Water
Chlorophyll a & b

Tamarix
Leaf water absorptions

Dry
Residues

NDWI = R860 R1240 /R860 R1240

AVIRIS

45

Canopy Water Content Estimated from MODIS

0.6

Band4
R858.5nm

0.5

MODIS Water
Index (SRWI):

Reflectance

0.4

SRWI

cw=0.001
0.3

Band5
R1240nm

0.2
0.1

cw=0.03
0
400

900

1400

1900

2400

Wavelength (nm)
cw=0.001

cw=0.002

cw=0.003

cw=0.015

cw=0.02

cw=0.03

cw=0.01

(Pablo Zarco-Tejada et al., 2001 IEEE; Rem. Sens. Env. 2003)

R858
R1240

Absorption Spectra of Non-Pigment Plant

Materials

CAI = 0.5 (R2000-R2200)/R2100

Craig S.T. Daughtry. 2001. Agronomy Journal 93: 125-131

47

HIGH

AGU Poster Presentation

Tree Crown Delineation using
Watershed Techniques and Forest
Metrics on NEON LiDAR Data
By Kimberly Luong

LOW

LIDAR OVERLAID ON AERIAL IMAGERY KIMBERLY LUONG 2014

Potential Student Projects:

1. Mapping species distribution for the oak woodland community, mixed conifer forest or the upper elevation forest
2. Mapping plant functional types by growth form
3. Estimating leaf area index from MASTER data (change in LAI with the drought)
4. Estimating biomass from ground lidar and MASTER data
5. Mapping emissivity and surface temperatures for soil types
6. Quantify ecologically important canopy structure properties (tree height, canopy area, tree spacing, % cover)
7. Quantifying ecologically important canopy physiological properties (water content, pigment content, dry biomass)
8. Investigate links between topography (DEMs, contours) and vegetation using lidar data from NEON.
9. Scaling from NEON AVIRIS to HyspIRI AVIRIS or HyspIRI AVIRIS to MASTER data
10. Evaluating drought impact from time series of MASTER data
11. Identify dead and/or dying trees from MASTER
12. Investigating the new POLAR lidar data for vegetated sites
Past SARP Projects:
1. Estimate ET with different models
2. Separate emissivity and surface temperatures
3. Calibrate the TIR sensor on MASTER
4. Calibrate optical bands from radiance to reflectance
5. Calculate CWC and FMC (used in fire risk models)
6. Vegetation and community type mapping
7. Estimating chemistry from inversion of PROSPECT
8. Creating a DEM from lidar data

How do you
contribute to the
drought in
California?

June 5, 2015