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PocketLAI

A smartphone app for estimating leaf area
index


Roberto Confalonieri, Marco Foi
University of Milan, Cassandra lab
PocketLAI – IRRI, 8-11 October 2013
Leaf area index

• Total one-sided area of leaf tissue per unit ground surface
• Key variable for analyzing the interaction between plants
and atmosphere
o amount of radiation intercepted
o plant water requirements
o CO
2
sequestration
o assimilation of exogenous information in simulation
models
o forecasting purposes
PocketLAI – IRRI, 8-11 October 2013
How to derive LAI?

• It can be measured
1. collection of leaves
2. measurement of their area
 dedicated instruments
 acquiring and processing leaf images
PocketLAI – IRRI, 8-11 October 2013
How to derive LAI?

• It can be estimated
o allometric relationships
o inversion of light transmittance models
 LAI-2000, LAI-2200
 ceptometers (AccuPAR, SUNSCAN)
 CI-100
 hemispherical camera

Suitable for extensive campaigns
PocketLAI – IRRI, 8-11 October 2013
Context: commercial tools

LAI-2000 (now LAI-2200) and ceptometers
• quite expensive (4500 - 10000 $)
• characterized by low portability (12×24×109 - 65×14×43 cm;
4.15 - 6.5 kg – with cases)
• long and expensive maintenance services in case of
damages
…field campaigns can be interrupted!
PocketLAI – IRRI, 8-11 October 2013
Context: smartphones

• Production volumes a bit larger than those of LAI-2000 and
ceptometers…
• Competing pressure is leading producers to provide
devices with wonderful hardware
• High quality sensors and computational capability for a few
hundred dollars (games!)
• …the possibility of making/receiving telephone calls is
becoming somehow secondary
PocketLAI – IRRI, 8-11 October 2013
Indirect methods

Light transmittance models relating gap fraction (P
0
) and LAI
• Poisson model for random spatial distribution of infinitely
small leaves



o θ is the probe angle
o k is the extinction coefficient, function of θ and χ
(Campbell „s ellipsoidal leaf angle distribution)
PocketLAI – IRRI, 8-11 October 2013
( )
( ) LAI k
e P
· ÷
=
u
u
0
How LAI is estimated?

Solutions: modified versions of the model
• Ceptometers
o information on canopy structure & direct/diffuse
radiation
• LAI-2000
o five probe angles: no other information needed

• …57.5° zenith angle (Warren-Wilson, 1963; Baret et al., 2010)
o neither information on canopy structure, nor different
angles are needed
o we started from here
PocketLAI – IRRI, 8-11 October 2013
PocketLAI - flowchart


PocketLAI – IRRI, 8-11 October 2013
STOP
START
Specify a code for the
measure and start the
acquisition procedure
Rotate the device along its main axis starting
with the display oriented downward
and concluding with
it in vertical position
Wait 5 sec. to allow the
user to put the device
below the canopy. Then
give a signal to user
Is the angle between
the vertical and the normal to the
screen = 57.5°?
NO
YES
Acquire information
Process information
Store
data
Export data
in tabular and
GIS format
Put the device above
the canopy
Visualize
results
on the
display
(only for App-L)
segmentation
luminance
Two methods:
PocketLAI


PocketLAI – IRRI, 8-11 October 2013
An integrated quick manual
is available
PocketLAI


PocketLAI – IRRI, 8-11 October 2013
PocketLAI – IRRI, 8-11 October 2013
PocketLAI


segmentation based on
pixels intensity (leaves
darker than cloudy sky)
segmentation based on
pixels chromatic values in
an HSB color space (blue
pixels detected)
PocketLAI


PocketLAI – IRRI, 8-11 October 2013
we‟ve seen that angles
are important for indirect
methods…
we used the device
accelerometer to derive
an inclinometer
|
|
|
.
|

\
|
= =
|
|
|
.
|

\
|
=
1
0
0
R Rg
G
G
G
G
pz
py
px
p
( )
|
|
|
.
|

\
|
÷
=
| |
| | |
cos sin 0
sin cos 0
0 0 1
x
R ( )
|
|
|
.
|

\
| ÷
=
u u
u u
u
cos 0 sin
0 1 0
sin 0 cos
y
R
( )
|
|
|
.
|

\
|
÷ =
1 0 0
0 cos sin
0 sin cos
¢ ¢
¢ ¢
¢
z
R
2 2
cos sin
tan
pz py
px
pz py
px
xyz
G G
G
G G
G
+
÷
=
|
|
.
|

\
|
+
÷
=
| |
u
pz
py
xyz
G
G
= | tan
images
automatically acquired at 57.5°
while the user is rotating the device
PocketLAI


PocketLAI – IRRI, 8-11 October 2013
Images are acquired in
live-preview mode
Baret et al. (2010) Agr. For. Met. 150, 1393-1401
Processing


PocketLAI – IRRI, 8-11 October 2013
( )
|
|
.
|

\
|
°
÷
= °
) 5 . 57 cos(
5 . 0
0
5 . 57
LAI
e P

1) segmentation
2) Luminance (L, candela m
-2
) … using device “exposimeter”
S t
k N
L
·
·
=
2
| · =
above
below
L
L
P
0
• N is the f-number or focal ratio
• t (sec) is the exposure time
• S is the ISO sensitivity
• k is the reflected-light constant
• β correction factor for scattered radiation below
the canopy
PocketLAI – Tests

1. Evaluation of PocketLAI and other indirect methods
(AccuPAR ceptometer, LAI-2000) for rice by adapting the
ISO 5725 protocol for the validation of analytical methods


2. Comparison with AccuPAR ceptometer for canopy
structures deviating from the assumption behind the light
transmittance model implemented in PocketLAI
PocketLAI – IRRI, 8-11 October 2013
Confalonieri et al. (2013) Comput. Electron. Agric. 96, 67-74
Francone et al. (2013) Field Crop. Res. in press
PocketLAI – Tests (1), methods


ISO 5725-2: Accuracy
PocketLAI – IRRI, 8-11 October 2013
0
2
4
6
8
media = 4
media = 4
mean = 4
mean = 4
0
2
4
6
8
media = 4
media = 6
mean = 4
mean = 6
Trueness
Precision
Repeatability
(variability just due to
the replicate effect)
Reproducibility
(variability due to
different users, etc.)
Inter-laboratory tests
or ring tests
or ring trials
PocketLAI – Tests (1), methods

Inter-laboratory tests (ISO 5725):
• different laboratories
• different operators for each laboratory
• different levels for the analyte
• different replicates for level, lab, operator
• presence of reference materials
PocketLAI – IRRI, 8-11 October 2013
trueness
repeatability
linearity
reproducibility
PocketLAI – Tests (1), methods

Inter-laboratory tests (ISO 5725):
• different laboratories
• different operators for each laboratory
• different levels for the analyte
• different replicates for level, lab, operator
• presence of reference materials
PocketLAI – IRRI, 8-11 October 2013
4 groups, each composed of 4 students
• different sowing densities
• different moments during crop cycle
• homogeneous (small) plots
split in quadrants
• each quadrant corresponds
to a single replicate (to
avoid trampling effects)
LAI from destructive method (20 plants plot
-1
)
PocketLAI – Tests (1), methods

Inter-laboratory tests:
1. outliers detection (among laboratories for each level)
• Cochran‟s test (variances)
• Grubbs‟ test (means)
2. trueness (RMSE, ME, CRM), linearity
3. Precision
• standard deviation, limit ( ) of repeatability
• standard deviation, limit ( ) of reproducibility
PocketLAI – IRRI, 8-11 October 2013
t s r
r
2 · =
t s R
R
2 · =
t = critical value of the Student t distribution (2 tails)
at 95% confidence level for n-1 freedom degrees
PocketLAI – Tests (1), results


PocketLAI – IRRI, 8-11 October 2013
• App-L is the most accurate
• The other methods present similar performances
PocketLAI – Tests (1), results


PocketLAI – IRRI, 8-11 October 2013
a
: repeatability limit. 1
b
: relative standard deviation of repeatability. 2
c
: reproducibility limit. 3
d
: relative standard deviation of reproducibility. 4
e
: laboratory 3 is an outlier according to the Cochran test. 5
f
: corrected value (s
r
set equal to s
R
in case s
r
> s
R
; Orwitz, 1995; Scaglia et al., 2011). 6
• App-G:
one of the
most precise
• App-L:
decidedly the
less precise
PocketLAI – Tests (1), results


PocketLAI – IRRI, 8-11 October 2013
• No relationships between repeatability and LAI limit
• Only App-L (luminance) presents a significant relationship
between reproducibility and LAI
Repeatability Reproducibility
PocketLAI – Tests (2)

Assumption behind models for light transmittance into the
canopy:
“Small leaves randomly distributed within the canopy”
PocketLAI – IRRI, 8-11 October 2013
Rice canopies do not deviate
so much…
…but others do!
PocketLAI – Tests (2), methods

• Three canopies markedly deviating from the assumption
behind light transmittance model
o maize: big leaves, row seeded
o giant reed: big leaves, row-planted, plants far from
each other, marked tillering aptitude
o grassland: often not homogeneous (no random
distribution)
• We just compared PocketLAI estimates with those provided
by the AccuPAR ceptometer
PocketLAI – IRRI, 8-11 October 2013
10 cm 10 cm
PocketLAI – Tests (2), methods

Measurement protocols (1):
• ceptometer
o maize: Facchi et al. (2010)
o giant reed & grassland:
• PocketLAI
o maize:
o giant reed & grassland:
PocketLAI – IRRI, 8-11 October 2013
Facchi et al. (2010) J. Ag. Eng. 1, 33-40
× 2 replicates
5 readings below × 2 replicates
5 readings × 2 replicates
PocketLAI – Tests (2), results

PocketLAI – IRRI, 8-11 October 2013
maize giant reed grassland
Giant reed (& maize):
• overestimation for low values (big leaves + clumping effect)
• underestimation for values higher than 5 m
2
m
-2
Grassland:
• no systematic under/overestimations
• more replicates needed (heterogeneity, AccuPAR 80 cm-probe)
PocketLAI – Conclusions

• PocketLAI resulted comparable – for rice – to commercial
tools for both trueness and precision
• It represent a nice solution
o in contexts characterized by low availability of
resources
o when portability is an important requisite
o in cases when a large number of instruments is needed
PocketLAI – IRRI, 8-11 October 2013
• PocketLAI – Remarks

• It presented a device-effect (especially for low-cost
products), thus requiring to apply calibration facilities
(…and the need for developing automatic calibration
facilities)
• It resulted less robust in cases of canopies markedly
deviating from the assumptions behind light transmittance
models are (maize, giant reed, grassland)
• An automatic selection of the segmentation algorithm
would
o improve user experience and
o reduce subjectivity in evaluating how cloudy the sky is
PocketLAI – IRRI, 8-11 October 2013
Pocket… N


PocketLAI – IRRI, 8-11 October 2013
…coming soon



PocketLAI – IRRI, 8-11 October 2013


Simplicity is complexity resolved
(C. Brâncuşi)
Thanks so much for the invitation
and for your kind attention

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