pocketlai: a smartphone app. for estimating leaf area index

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 CO2 sequestration

o assimilation of exogenous information in simulation models

o forecasting purposes


How to derive LAI?

• It can be measured

1. collection of leaves

2. measurement of their area

dedicated instruments

acquiring and processing leaf images


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 cameraSuitable for extensive campaigns


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!


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


Indirect methods

Light transmittance models relating gap fraction (P0) 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)


LAIkeP 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 - flowchartPocketLAI – IRRI, 8-11 October 2013

STOP

START

Specify a code for themeasure and start the acquisition procedure

Rotate the device along its main axis starting with the display oriented downward

and concluding withit in vertical position

Wait 5 sec. to allow theuser to put the device

below the canopy. Thengive a signal to user

Is the angle betweenthe vertical and the normal to the

screen = 57.5°?

NO

YES

Acquire information

Process information

Storedata

Export datain tabular and

GIS format

Put the device above the canopy

Visualize results on the display

(only for App-L)

segmentationluminance

Two methods:

PocketLAIPocketLAI – IRRI, 8-11 October 2013

An integrated quick manual is available


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)


we’ve seen that angles are important for indirect methods…

we used the device accelerometer to derive an inclinometer

1

0

0

RRg

G

G

G

G

pz

py

px

p

cossin0

sincos0

001

xR

cos0sin

010

sin0cos

yR

100

0cossin

0sincos

zR

22cossintan

pzpy

px

pzpy

pxxyz

GG

G

GG

G

pz

pyxyz G

Gtan

imagesautomatically acquired at 57.5° while the user is rotating the device


Images are acquired in live-preview mode

Baret et al. (2010) Agr. For. Met. 150, 1393-1401

ProcessingPocketLAI – IRRI, 8-11 October 2013

)5.57cos(5.0

0 5.57LAI

eP

1) segmentation

2) Luminance (L, candela m-2) … using device “exposimeter”

St

kNL

2

above

below

L

LP0

• 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


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


0

2

4

6

8

media = 4media = 4mean = 4mean = 4

0

2

4

6

8

media = 4media = 6

mean = 4mean = 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


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


trueness

repeatability

linearity

reproducibility


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


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)


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


tsr r 2tsR R 2

t = critical value of the Student t distribution (2 tails) at 95% confidence level for n-1 freedom

degrees

PocketLAI – Tests (1), resultsPocketLAI – IRRI, 8-11 October 2013

• App-L is the most accurate

• The other methods present similar performances


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 (sr set equal to sR in case sr > sR; Orwitz, 1995; Scaglia et al., 2011). 6

• App-G:one of themost precise

• App-L: decidedly the less precise


• 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”


Rice canopies do not deviate so much……but others do!


• 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


10 cm10 cm


Measurement protocols (1):

• ceptometer

o maize: Facchi et al. (2010)

o giant reed & grassland:

• PocketLAI

o maize:

o giant reed & grassland:


Facchi et al. (2010) J. Ag. Eng. 1, 33-40

× 2 replicates

5 readings below × 2 replicates

5 readings × 2 replicates


maize giant reed grassland

Giant reed (& maize):• overestimation for low values (big leaves + clumping effect)• underestimation for values higher than 5 m2 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 – 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


Pocket… NPocketLAI – IRRI, 8-11 October 2013

…coming soon


Simplicity is complexity resolved

(C. Brâncuşi)

Thanks so much for the invitationand for your kind attention

pocketlai: a smartphone app. for estimating leaf area index

Documents

secondary pocketlai

pocketlai segmentation

cassandra lab pocketlai

commercial tools lai

angle betweenthe vertical

pixels intensity

probe angles

zenith angle warrenwilson