acoustic monitoring protocol - firestone...

Tropical Ecology, Assessment, and Monitoring(TEAM) Initiative

Acoustic Monitoring ProtocolT. Scott Brandes, Ph.D., Postdoctoral Researcher, TEAM Initiative

Version 2.1

April 1, 2005

The Tropical Ecology, Assessment and Monitoring (TEAM) InitiativeThe Center for Applied Biodiversity Science (CABS)Conservation International1919 M Street, NW, Suite 600Washington, D.C. 20036, USA202.912.1000202.912.0773 fax

TEAM Initiative online: www.teaminitiative.orgCABS online: www.biodiversityscience.org Conservation International online: www.conservation.org

Conservation International is a private, non-profi t organization exempt from federal income tax under section 501 c(3) of the Internal Revenue Code.

AcknowledgementsPiotr Naskrecki contributed to the methodology for collecting Orthoptera stridulations, as well as the basic ideas behind data analysis, particularly with the idea of focusing on sono-types. The Bioacoustics Research Program (BRP) at the Cornell Lab of Ornithology (CLO) has contributed by allowing TEAM to use and develop extensions within their Extensible Bioacoustics Toolbox (XBAT) to facilitate algorithm development for automatic call recognition.

3Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative

Table of Contents

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4

Spatial Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Equipment List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6

Data Forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Data Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Data Checking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Literature Cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

Recomended Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Appendix 1: Equipment and suppliers . . . . . . . . . . . . . . . .10

Appendix 2: PDA basics for the HP iPac 5500 series . . .11

Appendix 3: Installation instructions for Potoo v. 2.0

on a HP iPAC running Pocket PC 2002 . . . . . . . . . . . . . . .12

Appendix 4: Installation instructions for Potoo v. 2.0 on a HP iPac running Pocket PC 2003 . . . . . . . . . . . . . . . .13

Appendix 5: Checklist for servicing the PDA recorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Appendix 6: Checklist for servicing the Cornell

recorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

4 Acoustic Monitoring Protocol, v. 2.1

Introduction

Terrestrial animals communicate acoustically all over the planet. No where is this more apparent than in the tropics, where species-richness is several times greater than in higher latitudes. A large percentage of birds, frogs, bats and insects create sounds that are often species-specifi c. This abun-dance of sound provides a ready made source of information that can be used to explore the composition of this diversity in particular regions of interest.

Acoustic surveying lends itself to rapid assessment programs (RAP) which quickly assess the biodiversity of specifi c regions (Riede, 1998). This is largely because numerous animals are heard more often than seen or trapped. This translates into not only higher species counts, but also faster estimations of biodiversity. Parker (1991) describes how in 7 days he recorded the vocalizations of 85% of the 287 species of avifauna his team of 7 ornithologists inventoried after 54 days of intensive fi eld work within a 2km2 area in Amazonian Bolivia, which included 36,804 mist-net hours. If this is representative of the advantages of monitor-ing birds acoustically, then the same is likely true for both stridulating insects and vocalizing anurans, particularly since they are even less visually conspicuous. Although no comparative numbers are provided, Fischer et al. (1997) and Riede (1993, 1996, 1998) found it more fruitful to moni-tor insects acoustically than by physically collecting them. Likewise, Peterson and Dorcas (1992) as well as Crouch III and Paton (2002) strongly advocate acoustic monitoring to better study anuran activity and species presence. This trend also holds true for fi eld sampling of bats. O’Farrell and Gannon (1999) compared acoustic sampling of bats simul-taneously with mist nets and double-frame harp traps, in 57 locations. They found that 86.9% of the combined species present were detected acoustically, where as only 63.5% of the species detected were captured.

This research supports the idea that visual and trapping surveys should be supplemented with acoustic surveys for added robustness. Acoustic surveys, though, can be done in several ways. One straightforward way is for researchers to conduct acoustic surveys by walking transects with recording equipment, or taking notes as to what they hear. However, more systematic and less intrusive, acoustic surveys could be done with remote monitoring stations. Such stations can be set up to record sound for designated intervals of time and left for a period of weeks, depending on data storage capac-ity and how often sound is recorded. Additionally, acoustic monitoring stations can be set up for long term monitor-ing to establish baselines of biodiversity measurements or examine biodiversity trends for a region. It is of this second type of acoustic monitoring, that of remote stations, that the remainder of this document will address.

The acoustic monitoring described in this protocol is one aspect of a much larger undertaking to assess and moni-tor biodiversity in tropical regions throughout the world. Within this TEAM Initiative, the goal is not to assess bio-diversity by doing complete bio-inventories in each study site, but instead, to generate baseline data about biodiversity composition within groups of taxa at multiple levels, by implementing specifi c protocols. As part of that assessment, the acoustic monitoring will be used to provide baseline information about specifi c groups of acoustically active biota, and perhaps to generate an index of biodiversity based on the complexity of calls recorded within a region. The taxonomic groups of interest, in order of suggested develop-ment, are insects, anurans, birds, and bats, each with unique requirements. In general, diurnal communities consist of birds, cicadas and grasshoppers, and nocturnal communities are predominately crickets, Katydids, frogs, and bats. Dusk choruses frequently contain species from all these groups (Riede, 1997).

There are 4 distinct categories of biotic groups we would like to address with our acoustic monitoring (insects, anurans, birds, and bats) each with it’s own set of problems to consider. A short overview of these groups is provided, but at this time the scope of this acoustic monitoring protocol only includes crickets, and the sections on spatial layout and methods will need to be developed for each group that is targeted.

InsectsInitially, the focus will be on recording Orthoptera in the 2kHz-9kHz range. This bandwidth should effectively iso-late cricket calls (Naskrecki, 2002). In previous studies, Orthoptera recording stations were set 20m apart (Riede, 1993) and 30m apart (Riede, 1997). Fischer et al. (1997) found that 12 of 14 species of grassland Orthoptera exam-ined were acoustically undetectable by humans beyond 20m. The other 2 were acoustically detectable up to 55m. Riede (1997) found that more Orthoptera can be recorded by placing the microphone within the mid-canopy, as opposed to the ground. From the mid-canopy, both arboreal and ground Orthoptera are heard, whereas, from the ground, fewer arboreal species are recorded. Since our goal is not to comprehensively monitor acoustically throughout the study array, we don’t need to stick to such close spacing of recording devices, but would benefi t from placing the mi-crophones mid to low-canopy.

We are initially targeting crickets. No libraries of cricket calls exists for many of the areas TEAM plans to work. Much work can be done initially by walking around each site and recording the variety of cricket calls with a hand held microphone and recorder; a Sennheiser shotgun micro-phone (ME67) and preamp (K6-C) along with a PDA or Marantz PDM 670 digital recorder works well for this. In 2


weeks at a site in Costa Rica, I was able to collect numerous high-quality cricket and katydid calls. These initial record-ings are then used to develop algorithms for automatic call recognition of the different calls for the area. Even though in many cases the sample recordings do not have species labels, they are distinct enough to be classifi ed as belonging to particular sono-types, analogous to the way unidentifi ed insects can be classifi ed as morpho-species. At a later date, once singing specimens are collected for each sono-type, taxonomic species can be assigned to each sono-type.

Once automated sono-type recognition is developed, base-line information about detected Orthoptera diversity as a function of time can be generated. This can be compared among study sites, seasonally and altitudinally, and used to build a reference from which to compare regions of interest outside the study areas. By looking at the ratio of sono-type diversity to recognize species diversity within the study ar-rays, a better approximation of Orthoptera diversity can be derived when examining new regions, particularly if new sites contain unknown sono-type.

AnuransAnuran vocalizations might not be as easy to isolate in fre-quency as Orthoptera, but likewise, individual species have consistent acoustic patterns and low repertoire size. In large choruses it might be diffi cult to resolve individuals, but Taylor et al. (1996) got encouraging results with a machine learning process focused on patterns of local spectral peaks. Zimmerman (2003) suggests that in the neotropics, vocal frogs congregate around ponds, whereas in Southeast Asia they are found near streams. Furthermore, she recommends that acoustic censusing be done within the neotropics, only from sunset to midnight during the fi rst 2 or 3 months of the rainy season. Crouch III and Paton (2002) suggest that single 10 minute surveys at New England breeding ponds are suffi cient to detect 90% of the anuran diversity at each pond. In the neotropics, Zimmerman recommends at least 20 minutes per night, for as many nights as possible during the beginning of the rainy season.

BirdsA large percentage of bird vocalizations are know and cata-logued. The diffi culty with this group lies in their vocal complexity. Not only do some species have repertoire sizes of more than 300 calls, but numerous species are capable of vocal mimicry, and others have distinct regional dialects. To facilitate automated detection of particular calls, perhaps

the most fruitful approach would be to focus on Suboscines since many have relatively simple vocalizations and limited repertoires. Additionally, they are well distributed through-out South American forests.

BatsBats present a unique challenge in that their echolocations are predominately ultrasonic. To detect these high frequen-cies, ultrasonic transducers instead of standard microphones are required. Additionally, either a single board computer or a laptop computer with a high sampling analog to digital converter (200kHz) or a standard recording device coupled with a heterodyne circuit to generate a beat frequency is needed to capture the high frequency signals. Heterodyned systems will have narrow frequency windows, and individual echolocations will be truncated, folded, and non-uniformly altered due to their varied Doppler shifts. Many species have unknown or weak search echolocations, but others are well known and distinct.

Spatial Layout

Each Integrated Monitoring Array (IMA) will have one sound recording unit placed within it, within the grid location of (04, 600), the same grid in which one of the butterfl y traps is placed. This is done so that the recording devices can be serviced along with the butterfl y traps, minimizing the per-son hours needed to implement each protocol. Since we are using too few recorders to measure density, sites with fewer than 6 IMA’s should distribute the PDA recorders within the number of IMA’s available, placing them at various butterfl y trip grid locations. To avoid confusion, fl agging for different groups of variables is color coded. All acoustic sampling loca-tions associated with this protocol should be marked with red fl agging only.

Equipment List

For each IMA• 1PDA canopy recorder (see Appendix 1 for

parts list)

• 50 meters of rope to hoist canopy recorders (the recorders weigh < 2 kg)

For each fi eld station• USB fl ash card reader

• Large (144 GB/year) external hard drive

• NiMH battery charger


• Desiccant packs (1oz) (200 packs)

• Trapping adhesive paste to exclude ants (e.g. Tanglefoot or Tangle-trap)

• Wrist slingshot

• 100m spool of 7-10 kg test strength monofi la-ment fi shing line

• 1 oz. (25-30 g) fi shing weights

• red fl agging tape

For fi eld sampling• 1 additional compact fl ash card (2GB)

• Extra set of rechargeable battery packs (1 D-cell 4-pack, 1 D-cell 5-pack)

• Waterproof notebooks

• 1 additional microphone for each PDA canopy recorder

Software for data analysis• MATLAB ® with the Signal Processing and

Image Processing toolboxes (Math Works, Inc.).

• TEAM written detectors.

• Raven sound analysis software (Cornell University).

Method

Recording device constructionThe recording devices are currently constructed at Conservation International’s headquarters in Washington, DC and then sent out to the fi eld stations. The software used by the devices for recording sound at scheduled intervals of time (Potoo) has been written by Conservation International. A list of parts needed to build the device is found inAppendix 1.

Recording device placement within canopyEnter the grid square location from a main trail approxi-mately mid-way between the 2 stakes. In the opposite direc-tion of the path to the nearby butterfl y trap, walk at least 20 meters and begin looking for a branch in the canopy that is horizontal enough to hold the line in place, high enough that the trap opening will be in the main canopy level, and with a clear enough area around it such that the device (and any weight and line used by a sling shot) will not get tangled in leaves and can be pulled through.The recording units should be placed mid to low-canopy, with their microphones pointed to the ground, and at least 1 meter away from any tree trunks. They should be hoisted

up by a rope over a branch so that the recorders can be read-ily pulled up into the canopy for deployment, or brought down to the ground for servicing. The rope can initial be placed over a mid-canopy branch via a climber or a sling-shot (as with the butterfl y traps).

To use a sling shot, shoot monofi lament line with a lead fi shing weight attached to the end over a tree limb. It helps to tie a small piece of fl agging tape to the lead weight so that it can be seen in the canopy. Make sure that the tree limb does not have any wasp nests or other things good not to disturb. Tie the end of the monofi lament to the nylon rope that will be attached to the recording device, and pull the rope over the branch and to the ground.

Once the rope is placed over the chosen branch, hoist the recording device up to the desired height, suspending at mid to low-canopy. Tie the end of the rope to a tree to se-cure the device at that height, and tie a piece of red fl agging tape on the tree the rope is tied to. To more easily fi nd the recording device, also tie a piece of red fl agging tape on the main trail at the location from which to go off trail to fi nd the recording device.

When returning to service the recording unit each month, untie the rope and lower the recording unit to the ground. Follow the checklist of things to do (Appendix 5), then hoist the recording device back up to the same height as it was, and tie it to the tree again.

Field samplingFor 6 IMA’s, fi eld work requires 1 person for 8-10 hours a month (if this person is also assisting with the butterfl y traps), 12 months a year.

The PDA recorders should be set to record for 10 minutes each night, 1 hour after sunset. The sound recording de-vices should be serviced during the same day that butterfl y traps or leaf litter traps in the same grid are visited. They should be serviced once every 14 days (we are in the pro-cess of extending this to a 1 month interval). A check list of what to bring for each fi eld visit as well as a checklist of what to do to service each unit is given in Appendix 5.

2 or 3 days prior to visiting the recorders, start recharging the D-cell batteries. They begin to slowly discharge once taken out of the recharger; however, 4 batteries might take 24 hours to fully charge, so prepare enough time to fully re-charge all 9 batteries.When revisiting a recording unit, check for any visible prob-lems with it. The most likely parts to need to replace are the microphone screen and the microphone stick. Check the state of the furry windscreen covering the microphone. If it


is damaged or covered in algae, try to gently clean it without damaging the microphone inside. Write down the condi-tion of the windscreen in the fi eld notebook. If it needs to be replaced, do so when you next have a chance to.

Data Forms

During each visit to a recording device, fi ll in the follow-ing information in the designated acoustic monitoring fi eld notebook (see Excel fi le):

Field technicians (names):Date (day/month/year):IMA (1-6):Grid coordinates (04, 600):PDA recorder identifi cation number:What condition is the furry windscreen for the microphone in?Which, if any, replacement parts are installed?Is a fresh silicate pack required? Was the device deployed again to collect a new set of recordings?Any additional notes:

Data Entry

Each wav-fi le needs to be logged. The following fi elds need to be put in a spread sheet as columns, with a new line for each wav-fi le (see Excel fi le):

wav-fi le nameRecorder identifi cation numberDate collected (day/month/year)Time (24hr:min)Recording duration (min)IMA (1-6)Grid coordinates (04, 600)Air temperature during recording (deg C) – from TEAM Climate monitoring data loggers.

Sounds from the PDA’s should be stored on both a work sta-tion hard drive for analysis, and backed up on an external hard drive. The sound fi les should be stored with the follow-ing folder structure:Put all sounds in a folder titled “TEAM Acoustic Monitoring”. Within that folder, create folder for each PDA recorder identifi cation number. Put all wav fi les in the folder that corresponds to the PDA that they came from.

The fi le names for the sound fi les have the following naming convention:identifi cation number..day.month.year..hour.minute.wavFor example, a sound fi le created by recorder number 1 at 7:05 pm on August 6, 2004 should be named:ID01..6.8.2004..19.05.wavThe PDA recorder should do this automatically.

A log fi le of all the recordings done with the PDA is stored on the fl ash memory card. Move this fi le, “PDA_log.txt” to the same location that the wav-fi les are archived. This fi le can be opened in Excel and used to quickly and accurately transcribe the fi lenames into the Excel acoustic monitoring data entry forms.

Data Checking

Raw dataThe raw data needs to be checked to make sure that the re-cording device is working properly. Keep a log of any days that full length recordings were not collected by the device. Listen to part of the last recording made to verify that the microphone is still working properly. If only quiet sound is recorded or the sounds are softer than they should be, go back and listen to previous recordings. If the natural sounds recorded are all very soft or silent for the last week or more of the recordings, the microphone should be replaced as soon as possible.

Data Analysis

From the fi les of the temperature logged at each IMA, extract the temperatures corresponding to the times closest to when the sounds are recorded for each IMA that a sound recorder is in. Add these values to the wav-fi le log.

The TEAM-written ACR software is still in development.Run the TEAM-written software to scan each wav-fi le for tar-get sounds. A log of target sound will be generated and can be opened as an event viewer in Raven, sound analysis software (http://www.birds.cornell.edu/brp/raven/RavenFullVersion.html). Open some of the processed wav-fi les and their corre-sponding events in Raven, and confi rm that the right sounds are being detected. More on this as software is developed.

With one recording device per IMA, recording nightly, basic presence/absence of target sounds can be tracked to look for both seasonal and long-term trends.


Literature Cited

Crouch III, W. B., and P. W. C. Paton. 2002. Assessing the use of call surveys to monitor breeding anurans in

Rhode Island. Journal of Herpetology 36:185-192.

Fischer, P.F., U. Schulz, H. Schubert, P. Knapp , and M. Schmöger. 1997. Quantitative assessment of grassland

quality: acoustic determination of population sizes of Orthopteran indicators species. Ecological Applications

7:909-920.

Naskrecki, P. 2002. Personal communications.

O’Farrell, M. J., and W. L. Gannon. 1999. A comparison on acoustic verses capture techniques for the inventory of

bats. Journal of Mammalogy 80:24-30.

Parker, T. A. III. 1991. On the use of tape recorders in avi-faunal surveys. Auk 108:443-444.

Peterson, C. R., and M. E. Dorcas. 1992. The use of auto-mated data acquisition techniques in monitoring

amphibian and reptile populations. Pages 369-378 in D. McCullough, editor. Wildlife 2001: Populations. Elsevier Applied Science, New York.

Riede, K. 1993. Monitoring biodiversity: analysis of Amazonian rainforest sounds. Ambio 22:546-548.

Riede, K. 1996. Diversity of sound-producing insects in a Bornean lowland rain forest. Pages 77-84 in D. S.

Edwards, W. E. Booth, and S. C. Choy, editors. Tropical rainforest research – current issues. Kluwer Academic

Publishers, Netherlands.

Riede, K. 1997. Bioacoustic monitoring of insect commu-nities in a Bornean rain forest canopy. Pages 442-452 in

N. E. Stork, J. Adis, and R. K. Didham, editors. Canopy Arthropods. Chapman and Hall, London.

Riede, K. 1998. Acoustic monitoring of Orthoptera and its potential for conservation. Journal of Insect

Conservation 2:217-223.

Taylor, A., G. Watson, G. Grigg, and H. McCallum. 1996. Monitoring frog communities: an application of

machine learning. Pages 1564-1596. Proceedings of the 8th Innovative Applications of Artifi cial Intelligence

Conference.

Zimmerman, B. L. 2003. Personal communications.

Recomended Reading

Ahlen, I., and H. J. Baagoe. 1999. Use of ultrasound detectors for bat studies in Europe: experience from fi eld identifi cation, survey, and monitoring. Acta Chiropterologica 1:137-150.

Chesmore, E. D., O. P. Femminella, and M. D. Swarbrick. 1998. Automated analysis of insect sounds using time-encoded signals and expert systems – a new method for species identifi cation. Pages 273-287 in P. Bridge, P.

Jeffries, D. R. Morse, and P. R. Scott, editors. Information technology, plant pathology and biodiversity. CAB International, Wallinford, UK.

Eyring, D. F. 1946. Jungle acoustics. Journal of the Acoustical Society of America 18:257-270.

Gold, B., and N. Morgan. 2000. Speech and audio signal processing, processing and perception of speech and mu-sic. John Wiley & Sons, Inc., New York.

Jelinek, F. 1998. Statistical methods for speech recognition. MIT Press, Cambridge, Mass.

Kogan, J.A., and D. Margoliash. 1997. Automated recogni-tion of bird song elements from continuous recordings using dynamic time warping and hidden Markov models: a comparative study. Journal of the Acoustical Society of America 103:2185-2196.

Marten, K., D. Quine, and P. Marler. 1977. Sound trans-mission and its signifi cance for animal vocalization. II. Tropical forest habitats. Behavioral Ecology and Sociobiology 2:291-302.

Rabiner, L., and B. H. Juang. 1993. Fundamentals of speech recognition. Prentice-Hall, Englewood Cliffs, NJ.

Rand, A. S., and G. E. Drewry. 1994. Acoustic monitor-ing at fi xed sites. Pages 150-153 in W. R. Heyer, M. A. Donnelly, R. W. McDiarmid, L. C. Hayek, and M. S. Foster, editors. Measuring and monitoring biological di-versity: standard methods for amphibians. Smithsonian Institute Press, Washington, DC.

Schwenker, F. and C. Dietrich. 2000. Initialization of Radial Basis Function Networks by Means of Classifi cation Trees. Neural Network World 10:473-482.


Schwenker, F., C. Dietrich, H. A. Kestler, K. Riede, and G. Palm. 2002. Radial Basis Function Neural Networks and Temporal Fusion for the Classifi cation of Bioacoustic Time Series. Neurocomputing (in press).

Wiley, R. H. and D. G. Richards. 1982. Adaptions for acoustic communication in birds: sound transmission and signal detection. Pages 131-181 in D. E. Kroodsma, and E. H. Miller, editors. Acoustic communication in birds, vol I: production, perception, and design features of sounds. Academic Press, New York.

Glossary

ACR – Automatic Call RecognitionACR – Automatic Call RecognitionACR – software used to rec-ognize specifi c sounds.

IMA – Integrated Monitoring Array (1 km x 1 km)

PDA – Personal Digital Assistant – a type of hand-held PDA – Personal Digital Assistant – a type of hand-held PDAcomputer.

Sono-type – an animal sound that is distinct enough to be repeatedly categorized the same way, and is presumed to be-long to a particular genus or species.

Appendix 1: Equipment and suppliers

TEAM provides the PDA recorders, since they are built in-house. TEAM has written the software (Potoo) that runs the PDA sched-uled recordings. The parts list for building the PDA recorders and prices are listed below (Table 1, Table2). The MatLab software mentioned is to run the TEAM-written automatic call recognition software (still being developed). To be safe, budget $2000/year for replacement parts for 6 PDA recorders. Photo shown in Figure 1

Vendors:www.bhPhotoVideo.com 1-800-606-6969 www.CasesbyPelican.com 1-800-882-4730www.cyberguys.com 1-800-892-1010 www.Digikey.com 1-800-344-4539www.drierite.com 937-376-2927 www.hp.com 1-800-999-4747www.mathworks.com 508-647-7000 www.radioshack.com1-800-843-7422http://www.birds.cornell.edu/brp/raven/RavenFullVersion.html

Figure 1. PDA recorder.


Parts needed for Acoustic Recorder Vendor Part # quantity price for 1 Total Price

HP iPac 5555 HP 264493-002 1 $ 600.00 $ 600.00

expansion pack for CFII card HP 170339-B22 1 $ 40.00 $ 40.00

Compact Flash Card (2GB) B&H Photo Video Lexor 2 $ 200.00 $ 400.00

1 D-cell battery holder Digi-Key BHDL-ND 2 $ 0.71 $ 1.42

4 D-cell battery holder Digi-Key BH24DL-ND 4 $ 1.71 $ 6.84

weather proof con, female panel (4-term) Digi-Key SC1167-ND 1 $ 4.32 $ 4.32

weather proof con, male inline (4-term) Digi-Key SC1159-ND 2 $ 3.12 $ 6.24

weather proof con, female inline (4-term) Digi-Key SC1177-ND 1 $ 5.88 $ 5.88

weather proof connector, dust cap Digi-Key SC1174-ND 1 $ 0.92 $ 0.92

audio transducer Digi-Key P9965-ND 1 $ 4.44 $ 4.44

4-term cable with male jack Digi-Key CP-354S-ND 1 $ 4.38 $ 4.38

DC plug, male, 5.5 x 2.1mm Radio Shack 274-1569 1 $ 2.59 $ 2.59

DC plug female, 5.5 x 2.1 mm Radio Shack 274-1582 1 $ 2.59 $ 2.59

DC plug, male, 4.0 x 1.7mm Radio Shack 274-1532 1 $ 2.59 $ 2.59

Pelican case, 1200 Pelican 1200 1 $ 32.09 $ 32.09

18 rechargable D-cells, 8500 mAh Cyberguys 141 0365 9 $ 22.60 $ 203.40

microphone Cornell University 16-elements 1 $ 120.00 $ 120.00

misc. PVC parts, cement, and silicone for mic housing

Home Depot 1 $ 25.00 $ 25.00

Total $ 1,462.70

Table 1. Parts needed for Acoustic Recorder.


Appendix 2: PDA basics for the HP iPAC 5500 series

A “hard reset” is accomplished by pressing in the tiny button at the bottom right of the PDA with the stylus.

A “sleep to awake” transition is accomplished by pressing what looks like a power button at the upper right. A little power is consumed when the PDA is in the sleep state, so don’t leave the PDA unattended for weeks at a time in this state, without an external battery pack.

To store the PDA long term, remove the Li-ion battery in the back of the PDA, after fully recharging it.

When connected to external power, the Li-ion battery is charging when the orange light at the upper right is blink-ing, and it is fully charged when it is on continuously.

The PDA can be restored to its “out of the box” condition, where all of its settings and additional software are removed, if necessary. This can be accomplished manually by simul-taneously holding down the calendar button (lower left) and the arrow button (lower right) and pushing in the tiny reset button at the bottom right with the stylus, and hold-ing them all depressed for 10 seconds. Following that, hard reset the iPAQ and it should start up in a tutorial.

One time purchases for site Vendor Part # quantity price for 1 Total Price

USB microdrive reader for lab 6-in-1 reader

Cyberguys 204 0674 1 $ 35.49 $ 35.49

Battery Charger Cyberguys 141 0348 1 $ 59.95 $ 59.95

Desiccant packs (1oz) (200 packs)W.A. Hammond Drierite Co.LTD

60011 1 $ 28.97 $ 28.97

MatLab MathWorks 1 $ 1,900.00 $ 1,900.00

MatLab Signal Processing Toolbox MathWorks 1 $ 800.00 $ 800.00

MatLab Image Processing ToolBox MathWorks 1 $ 900.00 $ 900.00

200 GB External hard drive (144GB each year)

1 $ 200.00 $ 200.00

Raven sound analysis software Cornell University 1 $ 400.00 $ 400.00

Total $ 4324,41

Determine PDA operating system version number:Remove the PDA from the black plastic compact fl ash card holder. There is a sticker on the bottom of the back of the PDA with the version number of the operating system. It should read “Pocket PC 2002” or Pocket PC 2003 Prem”.

Another way to tell the version number is to remove the Li-ion battery from the back and read the Model number of the PDA. Models h5450 and h5455 run on Pocket PC 2002Models h5550 and h5555 run on Pocket PC 2003.

Appendix 3: Installation instructions for Potoo v. 2.0 on a HP iPAC running Pocket PC 2002

When installing onto a PDA in the “New” condition:

From the PC, place the following 8 fi les onto the Storage Card, with the same folder names:Note: To make the dll fi les visible on the PC, open the “File Explorer” and select Tools->Folder Options->View->Show hid-den fi led and folders

The installation fi les are in a folder with the following fi les and folders:

Table 2. One time purchases for sites (independent of the number of recorders).


In the “root”directory:• netcf.core.ppc3.arm.cab• system_SR_enu.cab

In the “forWin” folder:• nyctibius.dll• mfcce300d.dll • SunRiseSunSet.dll• quick.exe

In the “Potoo” folder:• Potoo.exe• ReadMe.txt

Put the storage card into the PDA.

Note: To open File Explorer on the PDA, go to File Explorer on the PDA, go to File ExplorerStart->Programs->File Explorer.

Make sure all fi les are visible on the PDA by going to the bot-tom of the “File Explorer” window, below the last fi le or folder listed, and click and hold on the background white area and select “View All Files”. This will make the dll fi les visible on the screen (see step 1).

Next, run the following 2 cab fi les by “clicking” them in this order:• netcf.core.ppc3.arm.cab• system_SR_enu.cab

Copy over the contents of the “forWin” folder into the “My Device\Windows” folder. Copy over the Potoo folder and it’s content into the “My Device\Program Files” folder. When you have fi nished, the following fi les should be in these locations:

My Device\Windows\nyctibius.dllMy Device\Windows\mfcce300d.dll My Device\Windows\SunRiseSunSet.dllMy Device\Windows\quick.exeMy Device\Program Files\Potoo\Potoo.exe My Device\Program Files\Potoo\ReadMe.txt

Getting the PDA readyWhen setting up a PDA from the “out of the box” or “new” state, there are several settings to check/adjust:

1) Make DLL fi les visible. Start by opening the File Explorer, Start->Programs->File Explorer, and going to the “My Device\” folder, scroll to the bottom of the fi le list so that you can see a blank area below the fi les, press on the

blank area and select “View all fi les” This should allow DLL’s to be visible everywhere in the fi le system.

2) Set the proper time Zone and Time. Click the DATEjust below “Start”. Adjust the home time zone, time, and date. Click “OK” when done.

3) Set the Microphone Gain. Start->Settings->System->iPAQ Audio->Microphone AGC then select “Disable Automatic Gain Control, and set the Microphone gain to its lowest setting, -3. Then click “OK” then “Close”.

4) Active Sync. Start->ActiveSync->Tools->Options->Schedule-> then UNCHECK the fi rst 2 boxes: “When connected to my PC”, and “When not connected to my PC”, and CHECK the last box “When synchronized remotely”. Then click “OK” then “Close”.

5) Set the Arrow button on lower right to launch Potoo. Potoo must be installed for this to work. Start by opening the fi le explore, Start->Programs->File Explorer, creating a shortcut of Potoo.exe in “My Device\Program Files\Potoo” (hold down on Potoo.exe and select “copy”), and putting it in “My Device\Windows\StartMenu” (push down on blank background and select “Paste Shortcut”. Then, close the fi le explorer, and go to Start->Settings->Personal->Buttons, and select the arrow button (Button 4). Then select the fi le for it to point to in the scroll box below. “Shortcut to Potoo” should be one of the choices. Click “OK” and “Close” when you’ve fi nished.

6) Go to Start->Settings->System->Power->Main. CHECK “On Battery Power: Turn off device if not used for ‘1 min-ute’”. UNCHECK “On external power: Turn off device if not used for” If this is not unchecked, the recording will not work properly. There are no adjustments for the “Standby” and “USB Charging” tabs. Click “OK” and “Close” when done.

7) Adjust power and backlight settings. Start->Settings->System->Backlight->

a) Battery Power. CHECK “Turn off backlight if device is not used for” and select the shortest setting, 30 sec. CHECK the other box “Turn on backlight when a button is pressed”

b) External Power. CHECK “Turn off backlight if device is not used for” and select the shortest setting, 1 min. CHECK the other box “Turn on backlight when a button is pressed”

c) Brightness. Make sure “Automatic” check box is UNCHECKED and adjust the brightness lev-els to their lowest setting for both “On Battery”


and “On Power”. Note, these settings will not remain at their lowest settings after the device “wakes up” again, but they will remain low enough.

8) View the storage card with the File Explorer to make sure File Explorer to make sure File Explorerit is visible.

Appendix 4: Installation instructions for Potoo v. 2.2 on a HP iPAC running Pocket PC 2003

Installing the softwareFrom the PC, place the following 3 fi les onto the Storage Card and run them in this order on the PDA by “clicking” on them:

• System_SR_enu.cab• PotooSetup.cab• PotooSetupFiles.exe

A screen-shot of Potoo is shown in Figure 1.

Note: To open File Explorer on the PDA, go to Start->Programs->File Explorer.

Make sure all fi les are visible on the PDA by going to the bot-tom of the “File Explorer” window, below the last fi le or folder listed, and click and hold on the background white area and select “View All Files”.

Getting the PDA readyWhen setting up a PDA from the “out of the box” state, there are several settings to check/adjust:

1) Make DLL fi les visible. Start by opening the File Explorer, Star->Programs->File Explorer, and going to the “My Device\” folder, scroll to the bottom of the fi le list so that you can see a blank area below the fi les, press on the blank area and select “ View all fi les” This should allow DLL’s to be visible everywhere in the fi le system.

2) Set the proper time Zone and Time. Click the DATEjust below “Start”. Adjust the home time zone, time, and date. Click “OK” when done.

3) Set the Microphone Gain. Start-> Settings->System->iPAQ Audio->Microphone AGC then select “Disable Automatic Gain Control, and set the Microphone gain to its lowest setting, -3. Then click “OK” then “Close”.

4) Active Sync. There should be nothing to adjust here, but do these steps to make sure the PDA is set up properly. Go

to Start->ActiveSync->Tools->Options. Make sure that both check boxes are UNCHECKED on the “PC” tab: “Use mo-bile schedule to sync with this PC” and “Sync with this PC during manual sync. Then click “OK” then “Close”.

5) Set the Arrow button on lower right to launch Potoo. Potoo must be installed for this to work. Go to Start->Settings->Personal->Buttons, and select the arrow button (Button 4). Then select the fi le for it to point to in the scroll box below. “Potoo” should be one of the choices. Click “OK” and “Close” when you’ve fi nished.

6) Go to Start->Settings->System->Power->Main. CHECK “On Battery Power: Turn off device if not used for ‘1 minute’”. UNCHECK “On external power: Turn off device if not used for” If this is not unchecked, the record-ing will not work properly. There are no adjustments for the “Standby” and “USB Charging” tabs. Click “OK” and “Close” when done.

7) Adjust power and backlight settings. Start->Settings->System->Backlight->

a) Battery Power. CHECK “Turn off backlight if device is not used for” and select the shortest setting, 30 sec. CHECK the other box “Turn on backlight when a button is pressed”

b) External Power. CHECK “Turn off backlight if device is not used for” and select the shortest setting, 1 min. CHECK the other box “Turn on backlight when a button is pressed”

c) Brightness. Make sure “Automatic” check box is UNCHECKED and adjust the bright-ness levels to their lowest setting for both “On Battery” and “On Power”. Note, these settings will not remain at their lowest settings after the device “wakes up” again, but they will remain low enough.

8) View the storage card with the File Explorer to make File Explorer to make File Explorersure it is visible.


Figure 1. Potoo Screen Shot.

Appendix 5: Checklists for servicing the PDA recorders

Recharge 9 D-cell batteries a few days before deployment. The batteries require up to 24 hours to recharge. They will gradually discharge even if not in use, so they should be recharged just prior to fi eld deployment. The lights on the recharger fl ash during recharging, and are on steadily once recharging is fi nished. If a light is off, it indicates that a bat-tery is no longer working and needs to be thrown away.Erase previous sounds on the replacement fl ash-memory card to free up storage space. I like to keep a very small fi le, titled “Do not erase.txt” on the card so I can verity that the card is working, but this is not necessary.

Bring an extra silicate pack for use in the event that the cur-rent one in use is saturated.

Bring with you:Bring with you:

⃞ battery holder with 4 recharged D-cell batteries.

⃞ battery holder with 5 recharged D-cell batteries.

⃞ empty fl ash memory card.

⃞ fresh silicate drying pack, in a zip lock bag.

⃞ fl at-head screwdriver (to remove furry wind-screen for microphone, if necessary)

When servicing the PDA in the fi eld:When servicing the PDA in the fi eld:

⃞ Make a new entry in the fi eld notebook for this device (See: Method, Field Sampling, for

more information).

⃞ Visually inspect the furry windscreen surround- ing the microphone and write down in the

notebook the condition it is in. Be careful to not damage the microphone. (See: Method, Field Sampling, for more information).

⃞ Replace the 2 battery packs.

⃞ Replace the fl ash memory card.

⃞ Reset Potoo (the recording software – see instructions below).

⃞ Check the silicate drying pack, and replace if necessary.

⃞ Carefully close the pelican case, making sure that the silicate pack isn’t pressing against the PDA front panel, and that no cables are along the inner edge of the box.

⃞ Put the unit back in the canopy.

⃞ Write down all notes in the notebook, includ ing information on parts replaced.

⃞ When back at the lab, transfer the sound fi les from the full fl ash memory card to both the computer used for TEAM audio monitoring

and the external hard drive back-up, then erase the fl ash memory card, preparing it for the next

PDA deployment.

How to reset PotooHard-reset the PDA by pressing the small button on the right side of the base of the PDA with the stylus. Once the PDA boots, launch Potoo by pressing the arrow button on the lower right of the PDA. When Potoo loads, press the “Load” button, to reload the location and recording param-eters. Read over the latitude and longitude as well as the offset start time and record length to make sure the values look correct (the latitude and longitude for the fi eld station should be written in the Acoustic Monitoring fi eld note-book). Adjust them if necessary and save. Press “Sunset” to see if the calculated sunset time looks accurate. Press “Start” to begin the deployment. Read messages in the status bar at the bottom to check for errors. Once the PDA goes into “Sleep” mode, carefully close the pelican case, making sure that the silicate pack isn’t pressing against the PDA front panel.


Bring back to the station:Bring back to the station:

⃞ 2 battery holders with 9 used D-cell batteries.

⃞ Full fl ash memory card.

⃞ Used silicate drying pack.

When changing out the microphone gain board, set the dip switches to the following settings, providing the lowest set-ting of gain, 25 dB:

switch 1 = 1switch 2 = 0switch 3 = 0switch 4 = 0

Appendix 6: Checklists for servicing the Cornell recorders

In some sites, recorders built by Cornell University will be used for longer nightly recording times in order to verify that the nightly 12 minute recording interval used by the PDA recorders is large enough.

Checklist of what to bring to the fi eld:Checklist of what to bring to the fi eld:

⃞ ARU

⃞ Recharged 12Volt deep-cycle or car battery, backpack to carry it, and a plastic cover.

⃞ Laptop computer

⃞ The cable that connects the ARU to the serial port of the Laptop PC

How to set up the ARUThe ARU does not have a back-up clock battery, so it looses its time once disconnected from the main battery. Once it is ready to pull up into the canopy, connect the battery to the ARU and turn on the laptop. Then connect the ARU to the laptop’s serial port. Run the “CrossCut” program (see the ReadMe.txt fi le for more specifi c details). The impor-tant things to do with the CrossCut program are:

• set the clock

• check the recording time settings

• load in new recording time settings if needed

• start the acoustic monitoring program

• Then detach the ARU from the laptop and pull it up into the canopy.

How to collect the data from the ARUBring the ARU and battery back to the fi eld station.Recharge the battery.Open the ARU and extract the hard drive. This will require a small Phillips-head screw driver. Connect the hard drive to the external USB hard-drive adapter. Make certain that the hard-drive is connected in the correct orientation (Pin 1 to Pin 1). If Pin 1 is not labeled as such, it should have a square pattern at its base, instead of a circle. For the unit I brought to Caxiuanã, I think the correct orientation is for the hard drive label to be visible (the circuit board part should face the USB connecting plate). Once the hard drive is connected to a computer, run the “Beast” program.Push “Extract” to transfer the data from the ARU hard-drive to the computer.These extracted fi les should then be archived as TEAM sound fi les, and a short text fi le should be written by the user to explain where and when the recordings where made.Once the data has safely been transferred from the ARU hard drive, select “Prefi ll” to erase the hard drive and prepare it for its next deployment. Put the hard drive back into the ARU, and close it up.

When changing out the microphone gain board, set the dip switches to the following settings, providing a of gain, 51 dB:

switch 1 = 0switch 2 = 0switch 3 = 0switch 4 = 1

acoustic monitoring protocol - firestone...

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