Leaf area index and optical
properties
measurements of raspberry in Hyytiälä, 2013
(+ some GNSS observations in Hyytiälä & Siikaneva)
Measurements conducted June 24 - July 22, 2013.
Last modified 22.7.2013
Note: All image files and raw data not available in the web version.
Photographs taken during the campaign (folder).
1. Specific leaf area measurements
All the samples collected from one
4-yr-old seedling stand (
kansalaisen
karttapaikka)
Leaf samples were weighed,
scanned and dried in 80 °C oven.
Raspberry has leaves containing 3/5 leaflets, connected by a petiole,
weighing separately for the leaflets and the petioles, in order to
determine the proportion of the petiole from the leaf dry weight.
Scanned images thresholded at blue channel using Otsu's method, and the
projected leaf area was determined from the thresholded image.
a. Samples #1
Collected on 24.6.2013
10 shoots in total, 5
1st year and 5 2nd year shoots.
Each 1-yr/2-yr pair is from the same location.
From each shoot, 3 samples of leaves were selected (from upper,
middle and lower 1/3 of
the leaf-containing part of the shoot).
b. Samples #2
Additional samples
collected on 27.6.2013.
20 shoots in total, 10 1st year and 10 2nd year shoots, from
different locations.
One leaf sample from each shoot was collected, from the upper
2/3 of the leaf-containing part.
Measurement data for both samples (
xlsx),
see the sheet 'sla'.
Scanned images, samples #1 (
folder)
Scanned images, samples #2 (
folder)
Image thresholding, Matlab code (
file)
2. Sample shoots for determining
intershoot leaf area variation
Measurements conducted 25.-26.6.2013.
One 1×1 m area selected, same
stand as for specific leaf area samples.
40 shoots from the area randomly selected (20/20, 1st/2nd yr).
Leaves from each shoot dried and weighed to determine the leaf area.
The leaf-containing part in the shoot was divided into 3 sections of
equal length, and the leaf area determined for each section separately.
Results in the excel file (
xlsx),
see the sheet 'shoot_leaf_area'.
3. LAI measurements from sample areas
Measurements conducted 28.6.-4.7.2013.
Circular areas (50) of homogeneous raspberry canopies (minimum LAI and
height variation within the area) were marked in
the field.
Each area is defined by its center, and a radius
(65-100 cm).
A rectangular plot (1×1 m) was established at the center of each
area.
Shoots collected from each plot, and brought to
the laboratory for analysis.
Two types of measurements were conducted on the plots.
Type 1 measurements (21 plots):
- visual canopy cover estimate (0-100 %)
- maximum height
- weighing all shoots (fresh weight, 1st year and 2nd year
shoots separately)
- selecting a sample of shoots for leaf area determination,
separate samples for 1st year and 2nd year shoots
- sampling ratio dependent on the total number of shoots
<60 shoots --> 2/3
60-90 shoots --> 1/2
>90 shoots --> 1/3
- aimed at 30-45 sample shoots (<10% standard error of LAI,
based on
simulations)
- leaves were picked from the sample shoots and weighed
fresh weight --> oven drying (80
°C)
--> dry weight
- leaf area for the plot calculated using dry weight of the
leaves, and the sample ratio
- the fresh/dry weight of leaves includes the petiole that
connects the leaflets, its mass was reduced from the measured
value using regression models from 1)
- height measured for each sample shoot
Type 2 measurements (29 plots):
- visual canopy cover estimate (0-100 %)
- maximum height
- weighing all shoots (fresh weight, 1st year and 2nd year
shoots separately)
- LAI predicted with regression models, using the fresh weights
of 1st year and 2nd year shoots
The center of each sample plot was positioned with GNSS on 15.7. 2013.
In addition, the plot corners were positioned on the type 1 plots.
Results in the excel file (
xlsx)
(LAI measurements: sheet 'LAI_data'; heights of the sample shoots:
'shoot heights'; GNSS observations: 'GNSS_obs').
Sampling simulator (
R-code).
Photographs of the plots 1-14 (
folder)
4. Leaf optical properties
measurements
Measurements conducted 19.-21.7.2013.
Optical and structural properties of raspberry leaves (and a small
sample of fireweed).
4.1 Sample locations
Four (4) locations of raspberry, and
three (3) of fireweed were selected. The stand was the same as used for
collecting specific leaf area samples in 1).
Selected fresh-looking, green canopies. The leaves were already
yellowish in most parts of the stand due to the dry season.
Shoots (1-3) from each location were cut and brought to the laboratory.
For raspberry, separate samples of 1st year and 2nd year shoots were
selected.
While waiting for the measurements, the shoots were kept in a cooling
room (7 ºC), in a bucket of water, the lights on.
The maximum time between cutting the shoots and making the measurement
was ~4 hours.
Coordinates of the sample points measured with GNSS (
csv).

Raspberry 1
Height 1.55 m, canopy cover (visual esimate) 80%
Next to the road, slope towards NW, open area. |

Raspberry 2
Height 1.20 m, canopy cover 85%
Fertile site, alongside a ditch, open area.
|

Raspberry 3
Height 1.1 m, canopy cover 75%
Next to a mature forest stand, trees partly shading from the S side.
|

Raspberry 4
Height 1.3 m, canopy cover 75%
Next to a mature forest, trees on the S side, 7 m from the sample point.
|

Fireweed 1
Height ~1.5 m, canopy cover 80%
Open area, dense canopy.
|

Fireweed 2
Height ~1.5 m, canopy cover 80%
Open area, dense canopy.
|

Fireweed 1
Height ~1.5 m, canopy cover 70%
Open area, less dense.
|
|
4.2 Optical properties
Measured directional-hemispherical
reflectance and transmittance factors (DHRF/DHTF) at 350-2500 nm, using
ASD FieldSpec 3 PRO spectroradiometer and ASD RTS-3ZC integrating
sphere.
Notation for naming the samples:
- sample location
- year class (1 = 1st year, 2 = second year; for raspberry
only)
- canopy position (E = sun exposed, S = shaded)
Example:
Raspberry: 1.2.E = location 1, 2nd year shoot, sun exposed
Fireweed: 1.S = location 1, shaded
One fresh-looking leaf representing each sample was selected,
detached from the shoot and measured right after the detachment.
4 measurements per sample were taken (reflectance and transmittance,
both sides of the leaf).
Work order in the measurements was following:
- putting on the spectrometer, heating the lamp (~30 min
before the measurements)
- optimization of the spectrometer i.e. the integration time
is adjusted so that the whole DN range (16-bit) is used<>
- measuring the samples:
- for each measurement, 30 readings were taken and
averaged
- each measurement stored in a separate file, see
the measurement log for file names
- transmittance measurement was repeated 5 times for each
sample, by detaching and attaching the leaf to the sample port at each
time (this was done because variation was observed between
transmittance measurements)<>
- calculation of the reflectance/transmittance factors:
DHRF/DHTF = (measured DN - nearest stray light) / (nearest white
reference - nearest stray light)
- stray light was measured at the beginning and at the end of
measurements
- white reference (separately for each measurement mode) was
measured for every other sample
In addition to the basic samples, effect of moisture on raspberry leaf
reflectance was tested by spraying the leaf with water.
Measurement log (
xlsx).
Port configuration of the integrating sphere and the measurement
modes (
xlsx) (
illustration).
Matlab code for processing the samples (
file).
Reflectance spectra of raspberry (
fig),
transmittance spectra of raspberry (
fig),
reflectance and transmittance spectra of fireweed (
fig).
Effect of moisture on raspberry leaf reflectance (
fig)
Measurement data (ASD raw files and exported ASCII). ASD raw files
can be readed with ViewSpecPro software (
download).
Calculated spectra for the samples (
xlsx), calculated after
the measurements, no smoothing or cleaning of the outliers. Especially
in the transmittance data should be studied more carefully.
4.3 Specific leaf area
Specific leaf area was measured for the
same sample shoots as for optical properties measurements. Same
notation in sample naming used.
Weighing of the leaves,
scanning, drying in 80 °C oven for at least 24 hours.
Scanned images thresholded at blue channel using Otsu's method, and the
projected leaf area was determined from the thresholded image.
Specific leaf areas for the samples (
xlsx).
5. Other GNSS observations from
Hyytiälä
VRS-GPS
(Trimble R8) used.
Data in excel file (
xlsx)
Raw data, can be read with Trimble Business Center software (
folder).
- samples n:o
144-318: Point
samples of sand road surface near the raspberry stands, for radiometric
calibration of LiDAR signals. Samples contain pure sand/gravel, and no
grass. The radius of each sample in centimeters (30-50 cm) is recorded.
The LiDAR pulses inside the radius are safe to use for radiometric
tests.



- samples n:o
319-1040: Point
samples for evaluating z-accuracy of LiDAR data. The points are
selected so that the surface is as level and smooth as possible within
50 cm radius from the sample center. If the radius is smaller, this is
mentioned in the radius-column.
319-482: asphalt road
483-545: sand road
546-738: sand road, may contain some grass
739-765: sand road
766-887: sand road, may contain some grass (Note! When compared against
Z data from LiDAR, the points 782-808 have 0.6 m bias. They are clearly
erroneous, DO NOT USE THOSE POINTS!. Reason is unknown. Probably the
poor visibility of satellites.)
888-1040: asphalt road
- samples
1041-1145,
1231-1400,
1501-1525: Samples of fireweed and
birch
Each sample has attributes: radius [cm]
(measured for fireweed, 0 for birch samples), species [1=birch,
2=fireweed], visual canopy cover estimate [%], height [cm]
Fireweed has almost certainly gained height after the 16.6. LiDAR
campaign. Example pictures from the burned stand near the SMEAR station
In total, 215 birches and 160 m2
(85 samples) of fireweed measured.
:
- samples
1146-1167,
1171-1230,
1401-1500: Sample points for
evaluating the accuracy of the GPS equipment
Sample point 1 (Pilkotun tie):
Trees blocking the view, measured using
tolerance of 0.03 m in horizontal, 0.05 m in vertical direction
Measured on 16.6. (1146-1167), repeated on 17.7. (1401-1432)
Sample point 2 (Pilkotun tie):
Trees blocking the view, measured using
tolerance of 0.03 m in horizontal, 0.05 m in vertical direction
Measured on 16.6. (1171-1200), repeated on 17.7. (1433-1469)
Sample point 3 (Hyytiälä station):
Open area, good accuracy, tolerance
0.015 m in horizontal, 0.03 m in vertical direction
Measured on 16.6. (1201-1230), repeated on 17.7. (1470-1500)
6. GNSS-mittauksia Siikanevan
ilmakuvien ja laserkeilauksen (28.5.2013) laadun tarkistukseen
Mittaukset tehty 17.7.2013 Siikanevan
mittaustornien (Siikaneva 1 ja 2) ympäristöstä VRS-GPS
laitteistolla (Trimble R8).
Pisteet excel-tiedostossa (
xlsx).
- pisteet 1-21 (Siikaneva 1), 83-102 (Siikaneva 2): Pitkospuiden ja
paalujen kulmia ilmakuvien orientoinnin tarkastamiseen
- pisteet 22-82 (Siikaneva 1), 123-172
(Siikaneva 2): Suon pintapisteitä laserkeilauksen z-tarkkuuden
arviointiin.
Valittu pisteitä, joissa
pintakasvillisuus vähäinen ja maanpinta mahdollisimman
tasainen 20 cm säteellä pisteestä. Esimerkkikuvat alla.


GPS-antennia kannateltu mitattaessa kevyesti: antennitangon alaosa
koskettaa maanpintaa, mutta antenni ei uppoa turpeeseen.
Siikaneva 1:llä mittaukset tehty pitkospuiden vierestä,
pitkospuilla seisten. Siikaneva 2:lla mittauksia myös
pidemmältä pitkospuiden ulkopuolelta.
- pisteet 103-122: Testimittauksia
yhdestä mittauspisteestä Siikaneva 1:lla: selvitetty
mittausten hajontaa.