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A Macroscope in the Redwoods

A Macroscope in the Redwoods

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Published by Gilman Tolle
(Published in ACM SenSys 2005) The wireless sensor network "macroscope" offers the potential to advance science by enabling dense temporal and spatial monitoring of large volumes. This paper presents a case study of a wireless sensor network that recorded 44 days in the life of a 70-meter tall redwood tree, at a density of every 5 minutes in time and every 2 meters in space.
(Published in ACM SenSys 2005) The wireless sensor network "macroscope" offers the potential to advance science by enabling dense temporal and spatial monitoring of large volumes. This paper presents a case study of a wireless sensor network that recorded 44 days in the life of a 70-meter tall redwood tree, at a density of every 5 minutes in time and every 2 meters in space.

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Published by: Gilman Tolle on Jun 08, 2010
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A Macroscope in the Redwoods
Gilman Tolle,Joseph Polastre,Robert Szewczyk, andDavid Culler
Computer Science Division,University of California,BerkeleyBerkeley, CA 94720
Neil Turner, Kevin Tu,Stephen Burgess, andTodd Dawson
Department of IntegrativeBiology, University ofCalifornia, BerkeleyBerkeley, CA 94720
Phil Buonadonna,David Gay, and Wei Hong
Intel Research BerkeleyBerkeley, CA 94704
The wireless sensor network “macroscope” offers the po-tential to advance science by enabling dense temporal andspatial monitoring of large physical volumes. This paperpresents a case study of a wireless sensor network that recorded44 days in the life of a 70-meter tall redwood tree, at adensity of every 5 minutes in time and every 2 meters inspace. Each node measured air temperature, relative humid-ity, and photosynthetically active solar radiation. The net-work captured a detailed picture of the complex spatial vari-ation and temporal dynamics of the microclimate surround-ing a coastal redwood tree. This paper describes the de-ployed network and then employs a multi-dimensional anal-ysis methodology to reveal trends and gradients in this largeand previously-unobtainable dataset. An analysis of systemperformance data is then performed, suggesting lessons forfuture deployments.
Categories and Subject Descriptors
C.2.1 [
Computer - Communication Networks
]: Net-work Architecture and Design—
Wireless communication 
; C.3[
Special-Purpose and Application-Based Systems
]: Real-time and embedded systems; J.3 [
Life and Medical Sci-ences
]: Biology and genetics
General Terms
Design, Experimentation, Measurement, Performance
Wireless Sensor Networks, Microclimate Monitoring, Macro-scope, Application Analysis
Permission to make digital or hard copies of all or part of this work forpersonal or classroom use is granted without fee provided that copies arenot made or distributed for profit or commercial advantage and that copiesbear this notice and the full citation on the first page. To copy otherwise, torepublish, to post on servers or to redistribute to lists, requires prior specificpermission and/or a fee.
November 2–4, 2005, San Diego, California, USA.Copyright 2005 ACM 1-59593-054-X/05/0011 ...
Wireless sensor networks offer the potential to dramati-cally advance several scientific fields by providing a new kindof instrument with which to perceive the natural world. Asthe telescope allowed us to perceive what is far away andthe microscope what is very small, some refer to sensor net-works as “macroscopes” [5] because the dense temporal andspatial monitoring of large volumes that they provide offersa way to perceive complex interactions. As the technologyhas progressed, we have gotten ever closer to obtaining suchmacroscopic views of previously unrecorded phenomena[9,11, 15]. This paper reports on a case study of microclimaticmonitoring of a coastal redwood canopy, a case study thatwe believe has clearly crossed that threshold. Using a largenumber of wireless micro-scale weather stations we have ob-tained an unprecedented picture of environmental dynamicsover such a large organism. Here we describe the study,present an overview of the data that has been obtained, anduse a multidimensional analysis methodology to more deeplyunderstand the dense and wide-ranging spatiotemporal dataobtained from the macroscope.
In meeting with a collection of local biologists, we beganwith the question of what would they like to observe thatthey simply cannot measure today. The responses covereda wide array of interests, including the dispersal patterns of wind-borne seeds, the water profiles experienced by spawn-ing salmon, insect densities across riparian environments,and the microclimate of meadow and woodland transects.In classifying these desires against the requirements theyplace on the underlying technology and the state of the artin the measurement and analysis techniques, we arrived atan initial choice of studying the ecophysiology of coastalredwood forests.The microclimate over the volume of an entire redwoodtree is known to have substantial variation and to have sub-stantial temporal dynamics. When you walk in the forestit is temperate and moist, despite the wide variation inweather conditions. The top of the tree experiences widevariation in temperature, humidity, and, of course, light,whereas the bottom is typically cool, moist, and shaded.This variation was understood to create non-uniform gra-dients, essentially weather fronts, that move through thestructure of the tree. For example, as the sun rises, the topof the canopy warms quickly. This warm front moves downthe tree over time until the entire structure stabilizes or until
cooling at the canopy surface causes the process to reverse.Humidity fronts also move through the canopy, but the pro-cess is complicated by the tree moving so much water upfrom the soil and into the air. At some point, the observedhumidity is driven by the transpiration process and decou-pled from the prevailing climate conditions. The biologistsworking in this area had substantial experience with sensorsfor measuring the relevant climatic factors and had devisedmethods for instrumenting trees using conventional technol-ogy. They would climb the tree to attach a winch near thetop, typically 50m to 70m up, and haul a suite of weathermonitoring instruments up the vertical transect with a verylong serial cable connecting to a battery powered data loggerat the base. With this limited apparatus, they were able tovalidate that there was substantial variation, but they couldnot get a detailed picture of the entire structure over time.This defined our challenge.Together we designed a wireless micro-weather stationbased on the Berkeley Motes manufactured by Crossbow.The requirements and design of the node are described inSection4.1.We built upon the established system, network-ing, and data access technology provided by TinyOS [7],MintRoute[18], and TinyDB[8]. This provided a flexible basis for both the ad hoc multihop routing and the rangeof query processing the biologists might want to explore.However, as this provided much more complex functionalitythan, for example, the dedicated sense-and-send capabilitydeployed on Great Duck Island [17], we provided a simpleinternal data logging backup. We also had to develop aGPRS base-station to provide the transit link between thedeployment site and the Internet. The requirements and de-sign of the network and software architecture are describedin Section4.2.In addition to the base technology, we foundthat we needed to create an experimental methodology thatdescribed how to calibrate a large collection of instrumentsen masse, deploy them, and collect the data. This aspect isoutlined in Section4.3.Having carried out a 44-day study of trees in a study areain Sonoma California, the main thrust of this paper is show-ing the data we were able to obtain: a month in the life of aredwood tree. After the initial excitement of seeing that thedata really showed the kinds of dynamic gradients that thebiologists were hoping to see, we spent months figuring outhow to analyze and present the data systematically. Herewe illustrate one such methodology. We start out by viewingthe entire network as a single instrument. This allows us tosummarize the overall climatic distribution with a substan-tial sampling over space and time. Then we examine timeseries data using the entire network as a distributed instru-ment. We also examine the spatial characteristics, summa-rized over the duration of the study. After understandingthese overall characteristics, it is much more enlightening toexamine the detailed dynamics over space and time. Ideally,this is done by movies, but we present snapshots here.
Several prototype sensor networks have been used to mon-itor environmental parameters within a well-defined spatialregion.Researchers at the Center for Embedded Networked Sens-ing deployed a sensor network called the Extensible Sens-ing System into the James Reserve Forest[4]. The ESShas been organized into various topologies, with up to 40nodes. Directed Diffusion and Tiny Diffusion are used as areliable publish-subscribe middleware system to enable run-time queries for data collection and sensor reconfiguration[14]. Microclimate sensors, and soil temperature, moisture,and nitrate sensors are all present within the ESS. The ESShas been used to monitor temperature and humidity in sixbird nesting boxes for a period of several days.Cardell-Oliver et al. measured waterflow through soil dur-ing periods of active rainfall [3]. This sensing task requireda network that could react to the beginning of a rainstormby beginning to sample at a high temporal frequency, thenreturn to an infrequent monitoring mode after the end of thestorm. Their work shows readings taken from 3 soil moisturesensors over 15 days.In a system called GlacsWeb, researchers at the Universityof Southampton deployed 9 sensor nodes inside a glacier[11]. The nodes monitored pressure, temperature, and tilt,in order to monitor glacier melting behavior. Their workshowed the pressure on a single sensor falling over the courseof seven days as the temperature and tilt remained the same.Additionally, the system was able to track changes in thetilt of the base station over several months as warm weathercaused the shape of the glacier to change.As an experiment in adaptive sampling methods, a hang-ing autonomous vehicle was deployed into the James Reserveby researchers at UCLA and USC[1]. The hanging vehiclemonitored microclimate over a plane perpendicular to theground instead of over a flat area. Using this technology,the researchers interpolated and plotted solar radiation in-tensity over a 70m by 15m transect of the James Reserveforest.To study the movements of nesting birds, researchers atthe University of California, Berkeley deployed 2 networkswith a total of 147 nodes onto an island on the coast of Maine, called Great Duck Island[9]. The GDI deploymentused a combination of ground-emplaced motes to monitormicroclimate, and motes placed in burrows to detect thepresence of birds. The size of this network was steadily in-creased until it covered an 221m by 71m ellipsoidal pattern.The occupancy data collected by this network was verifiedby a superimposed network of cameras. The researchersshowed 16 days worth of temperature readings from a singlebird burrow, and correlated the rises in temperature withthe presence of a nesting bird [9]. Two years later, the re-searchers demonstrated a interpolation of surface tempera-ture and burrow temperature at a single instant in time overthe complete deployment area[16].There is, of course, a wealth of biological studies that usedsmall collections of data loggers and remote sensing to studytemporal and spatial gradients in forest microclimate [10,12, 13]. We apply some of their analysis methods to dataobtained from our wireless sensor network.
Gathering data on the environmental dynamics around70-meter tall redwood tree for 44 days requires robust sys-tem design and a careful deployment methodology. We se-lected a suite of sensors, integrated them with an existingwireless sensor node platform, and designed a package thatboth resists the elements and allows the sensors access tothe environment. We used the latest TinyOS and TASKsoftware for the node operating system, networking stack,and data collection framework. Finally, we performed two
separate calibration procedures to test the system prior toplacing it in the field, and then spent a day in the forestwith ropes, harnesses, and a notebook.We decided on the following envelope for our deployment:
One month during the early summer, sampling allsensors once every 5 minutes. The early summer con-tains the most dynamic microclimatic variation. Wedecided that sampling every 5 minutes would be suffi-cient to capture that variation.
Vertical Distance:
15m from ground level to 70m fromground level, with roughly a 2-meter spacing betweennodes. This spatial density ensured that we could cap-ture gradients in enough detail to interpolate accu-rately. The envelope began at 15m because most of the foliage was in the upper region of the tree.
Angular Location:
The west side of the tree. The westside had a thicker canopy and provided the most buffer-ing against direct environmental effects.
Radial Distance:
0.1-1.0m from the trunk. The nodeswere placed very close to the trunk to ensure that wewere capturing the microclimatic trends that affectedthe tree directly, and not the broader climate.Figure1shows the final placement of each mote in thetree. We also placed several nodes outside of our angularand radial envelope in order to monitor the microclimate inthe immediate vicinity of other biological sensing equipmentthat had previously been installed.
Figure 1: The placement of nodes within the tree
4.1 Hardware and Network Architecture
The sensor node platform was a Mica2Dot, a repackagedMica2 mote produced by Crossbow, with a 1 inch diameterform factor. The mote used an Atmel ATmega128 micro-controller running at 4 MHz, a 433 MHz radio from Chip-con operating at 40Kbps, and 512KB of flash memory. Themote was connected to digital sensors using I2C and SPIserial protocols and to analog sensors using the on-boardADC.The choice of measured parameters was driven by the bio-logical requirements. We measured traditional climate vari-ables – temperature, humidity, and light levels. Tempera-ture and relative humidity feed directly into transpirationmodels for redwood forests. Photosynthetically active radi-ation (PAR, wavelength from 350 to 700 nm) provides infor-mation about energy available for photosynthesis and tellsus about drivers for the carbon balance in the forest. Wemeasure both incident (direct) and reflected (ambient) levelsof PAR. Incident measurements provide insight into the en-ergy available for photosynthesis, while the ratio of reflectedto incident PAR allows for eventual validation of satelliteremote sensing measurements of land surface reflectance.The Sensirion SHT11 digital sensor provided temperature(
C) and humidity (
3.5%) measurements. The in-cident and reflected PAR measurements were collected bytwo Hamamatsu S1087 photodiodes interfaced to the 10-bitADC on Mica2Dot.The platform also included a TAOS TSL2550 sensor tomeasure total solar radiation (300nm - 1000nm), and anIntersema MS5534A to measure barometric pressure, butwe chose not to use them in our deployment. During cali-bration, we found that the TSR sensor was overly sensitive,and would not produce useful information in direct sunlight.Because TSR and PAR would have told roughly the samestory, and because PAR was more useful from the biologyviewpoint, we decided not to gather data on total solar ra-diation. As for the pressure sensor, barometric pressure issimply too diffuse a phenomenon to show appreciable differ-ences over the height of a single redwood tree. A standardpressure gradient would exist as a direct function of height,but any pressure changes due to weather would affect theentire tree equally. Barometric pressure sensing should beuseful in future large-scale climate studies.The package for such a deployment needs to protect theelectronics from the weather while safely exposing the sen-sors. Our chosen sensing modalities place specific require-ments on the package. Standardized temperature and hu-midity sensing should be performed in a shaded area withadequate airflow, implying that the enclosure must providesuch a space while absorbing little radiated heat. The out-put of the sensors that measure direct radiation is dependenton the sensor orientation, so the enclosure must expose thesesensors and level their sensing plane. The sensors measuringambient levels of PAR must be shaded but need a relativelywide field of view.The package designed for this deployment is shown inFig-ure 2.The mote, the battery, and two sensor boards fit in-side the sealed cylindrical enclosure. The enclosure is milledfrom white HDPE, and reflects most of the radiated heat.The endcaps of the cylinder form two sensing surfaces – onecaptures direct radiation, the other captures all other mea-surements. The white “skirtprovides extra shade, protec-

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