ACOUSTIC PROTO.ver.2.1_3.31.05.indd

Tropical Ecology, Assessment, and Monitoring
(TEAM) Initiative
Acoustic Monitoring Protocol
T. Scott Brandes, Ph.D., Postdoctoral Researcher, TEAM Initiative
Version 2.1
April 1, 2005
The Tropical Ecology, Assessment and Monitoring (TEAM) Initiative
The Center for Applied Biodiversity Science (CABS)
Conservation International
1919 M Street, NW, Suite 600
Washington, D.C. 20036, USA
202.912.1000
202.912.0773 fax
TEAM Initiative online: www.teaminitiative.org
CABS online: www.biodiversityscience.org
Conservation International online: www.conservation.org
Conservation International is a private, non-profit organization exempt from federal
income tax under section 501 c(3) of the Internal Revenue Code.
Acknowledgements
Piotr 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.
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
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
3
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-specific. This abundance 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 specific
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 field work within a 2km2 area
in Amazonian Bolivia, which included 36,804 mist-net
hours. If this is representative of the advantages of monitoring 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 monitor 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 field sampling of bats. O’Farrell and
Gannon (1999) compared acoustic sampling of bats simultaneously 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 capacity and how often sound is recorded. Additionally, acoustic
monitoring stations can be set up for long term monitoring 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.
4
The acoustic monitoring described in this protocol is one
aspect of a much larger undertaking to assess and monitor biodiversity in tropical regions throughout the world.
Within this TEAM Initiative, the goal is not to assess biodiversity 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 specific protocols. As part of that assessment,
the acoustic monitoring will be used to provide baseline
information about specific 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 development, 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.
Insects
Initially, the focus will be on recording Orthoptera in the
2kHz-9kHz range. This bandwidth should effectively isolate 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 examined 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 benefit from placing the microphones 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 microphone (ME67) and preamp (K6-C) along with a PDA or
Marantz PDM 670 digital recorder works well for this. In 2
Acoustic Monitoring Protocol, v. 2.1
weeks at a site in Costa Rica, I was able to collect numerous
high-quality cricket and katydid calls. These initial recordings 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 classified as belonging
to particular sono-types, analogous to the way unidentified
insects can be classified 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, baseline 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 arrays, a better approximation of Orthoptera diversity can be
derived when examining new regions, particularly if new
sites contain unknown sono-type.
the most fruitful approach would be to focus on Suboscines
since many have relatively simple vocalizations and limited
repertoires. Additionally, they are well distributed throughout South American forests.
Bats
Bats present a unique challenge in that their echolocations
are predominately ultrasonic. To detect these high frequencies, 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
Anurans
Anuran vocalizations might not be as easy to isolate in frequency as Orthoptera, but likewise, individual species have
consistent acoustic patterns and low repertoire size. In large
choruses it might be difficult 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 first 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 sufficient 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.
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 butterfly traps
is placed. This is done so that the recording devices can be
serviced along with the butterfly traps, minimizing the person 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 butterfly
trip grid locations. To avoid confusion, flagging for different
groups of variables is color coded. All acoustic sampling locations associated with this protocol should be marked with red
flagging only.
Equipment List
For each IMA
Birds
A large percentage of bird vocalizations are know and catalogued. The difficulty 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
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
•
•
1PDA canopy recorder (see Appendix 1 for
parts list)
50 meters of rope to hoist canopy recorders (the
recorders weigh < 2 kg)
For each field station
•
•
•
USB flash card reader
Large (144 GB/year) external hard drive
NiMH battery charger
5
•
•
•
•
•
•
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 monofilament fishing line
1 oz. (25-30 g) fishing weights
red flagging tape
For field sampling
•
•
•
•
1 additional compact flash 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 construction
The recording devices are currently constructed at
Conservation International’s headquarters in Washington,
DC and then sent out to the field 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 in
Appendix 1.
Recording device placement within canopy
Enter the grid square location from a main trail approximately mid-way between the 2 stakes. In the opposite direction of the path to the nearby butterfly 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
6
up by a rope over a branch so that the recorders can be readily 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 slingshot (as with the butterfly traps).
To use a sling shot, shoot monofilament line with a lead
fishing weight attached to the end over a tree limb. It helps
to tie a small piece of flagging 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 monofilament 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 secure the device at that height, and tie a piece of red flagging
tape on the tree the rope is tied to. To more easily find the
recording device, also tie a piece of red flagging tape on the
main trail at the location from which to go off trail to find
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 sampling
For 6 IMA’s, field work requires 1 person for 8-10 hours
a month (if this person is also assisting with the butterfly
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 devices should be serviced during the same day that butterfly
traps or leaf litter traps in the same grid are visited. They
should be serviced once every 14 days (we are in the process of extending this to a 1 month interval). A check list
of what to bring for each field 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 recharge all 9 batteries.
When revisiting a recording unit, check for any visible problems 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
Acoustic Monitoring Protocol, v. 2.1
is damaged or covered in algae, try to gently clean it without
damaging the microphone inside. Write down the condition of the windscreen in the field 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, fill in the following information in the designated acoustic monitoring field
notebook (see Excel file):
Field technicians (names):
Date (day/month/year):
IMA (1-6):
Grid coordinates (04, 600):
PDA recorder identification 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-file needs to be logged. The following fields need
to be put in a spread sheet as columns, with a new line for
each wav-file (see Excel file):
wav-file name
Recorder identification number
Date 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 station hard drive for analysis, and backed up on an external
hard drive. The sound files should be stored with the following folder structure:
Put all sounds in a folder titled “TEAM Acoustic
Monitoring”. Within that folder, create folder for each PDA
recorder identification number. Put all wav files in the folder
that corresponds to the PDA that they came from.
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
The file names for the sound files have the following naming
convention:
identification number..day.month.year..hour.minute.wav
For example, a sound file created by recorder number 1 at
7:05 pm on August 6, 2004 should be named:
ID01..6.8.2004..19.05.wav
The PDA recorder should do this automatically.
A log file of all the recordings done with the PDA is stored
on the flash memory card. Move this file, “PDA_log.txt” to
the same location that the wav-files are archived. This file
can be opened in Excel and used to quickly and accurately
transcribe the filenames into the Excel acoustic monitoring
data entry forms.
Data Checking
Raw data
The raw data needs to be checked to make sure that the recording 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 files 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-file log.
The TEAM-written ACR software is still in development.
Run the TEAM-written software to scan each wav-file for target 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-files and their corresponding events in Raven, and confirm 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.
7
Literature Cited
Recomended Reading
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.
Ahlen, I., and H. J. Baagoe. 1999. Use of ultrasound
detectors for bat studies in Europe: experience from
field identification, survey, and monitoring. Acta
Chiropterologica 1:137-150.
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 avifaunal surveys. Auk 108:443-444.
Peterson, C. R., and M. E. Dorcas. 1992. The use of automated 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 communities 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 Artificial Intelligence
Conference.
Zimmerman, B. L. 2003. Personal communications.
8
Chesmore, E. D., O. P. Femminella, and M. D. Swarbrick.
1998. Automated analysis of insect sounds using timeencoded signals and expert systems – a new method for
species identification. 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 music. 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 recognition 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 transmission and its significance 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 monitoring at fixed 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 diversity: standard methods for amphibians. Smithsonian
Institute Press, Washington, DC.
Schwenker, F. and C. Dietrich. 2000. Initialization
of Radial Basis Function Networks by Means of
Classification Trees. Neural Network World 10:473-482.
Acoustic Monitoring Protocol, v. 2.1
Schwenker, F., C. Dietrich, H. A. Kestler, K. Riede, and
G. Palm. 2002. Radial Basis Function Neural Networks
and Temporal Fusion for the Classification 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 Recognition – software used to recognize specific sounds.
IMA – Integrated Monitoring Array (1 km x 1 km)
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 scheduled 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 1-800-882-4730
www.cyberguys.com 1-800-892-1010
www.Digikey.com 1-800-344-4539
www.drierite.com 937-376-2927
www.hp.com 1-800-999-4747
www.mathworks.com 508-647-7000 www.radioshack.com
1-800-843-7422
http://www.birds.cornell.edu/brp/raven/RavenFullVersion.html
PDA – Personal Digital Assistant – a type of hand-held
computer.
Sono-type – an animal sound that is distinct enough to be
repeatedly categorized the same way, and is presumed to belong to a particular genus or species.
Figure 1. PDA recorder.
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
9
Parts needed for Acoustic Recorder
Vendor
Part #
HP iPac 5555
HP
264493-002
1
$
600.00
$
600.00
expansion pack for CFII card
HP
170339-B22
1
$
40.00
$
40.00
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
1200
1
$
32.09
$
32.09
Cyberguys
141 0365
9
$
22.60
$
203.40
Cornell University
16-elements
1
$
120.00
$
120.00
1
$
25.00
$
25.00
Compact Flash Card (2GB)
Pelican case, 1200
18 rechargable D-cells, 8500 mAh
microphone
misc. PVC parts, cement, and silicone for
mic housing
Home Depot
quantity
price for 1
Total
Total Price
$ 1,462.70
Table 1. Parts needed for Acoustic Recorder.
10
Acoustic Monitoring Protocol, v. 2.1
One time purchases for site
USB microdrive reader for lab 6-in-1
reader
Battery Charger
Desiccant packs (1oz) (200 packs)
Vendor
Part #
Cyberguys
204 0674
1
$
35.49
$
35.49
Cyberguys
141 0348
1
$
59.95
$
59.95
60011
1
$
28.97
$
28.97
W.A. Hammond
Drierite Co.LTD
quantity
price for 1
Total Price
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
1
$
200.00
$
200.00
1
$
400.00
$
400.00
200 GB External hard drive (144GB each
year)
Raven sound analysis software
Cornell University
Total
$ 4324,41
Table 2. One time purchases for sites (independent of the number of recorders).
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 blinking, 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 simultaneously 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 holding them all depressed for 10 seconds. Following that, hard
reset the iPAQ and it should start up in a tutorial.
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
Determine PDA operating system version number:
Remove the PDA from the black plastic compact flash 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 files onto the Storage
Card, with the same folder names:
Note: To make the dll files visible on the PC, open the “File
Explorer” and select Tools->Folder Options->View->Show hidden filed and folders
The installation files are in a folder with the following files
and folders:
11
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
Start->Programs->File Explorer.
Make sure all files are visible on the PDA by going to the bottom of the “File Explorer” window, below the last file or folder
listed, and click and hold on the background white area and
select “View All Files”. This will make the dll files visible on
the screen (see step 1).
Next, run the following 2 cab files 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 finished, the following files should be in
these locations:
My Device\Windows\nyctibius.dll
My Device\Windows\mfcce300d.dll
My Device\Windows\SunRiseSunSet.dll
My Device\Windows\quick.exe
My Device\Program Files\Potoo\Potoo.exe
My Device\Program Files\Potoo\ReadMe.txt
Getting the PDA ready
When setting up a PDA from the “out of the box” or “new”
state, there are several settings to check/adjust:
1) Make DLL files visible. Start by opening the File
Explorer, Start->Programs->File Explorer, and going to the
“My Device\” folder, scroll to the bottom of the file list so
that you can see a blank area below the files, press on the
12
blank area and select “View all files” This should allow
DLL’s to be visible everywhere in the file system.
2) Set the proper time Zone and Time. Click the DATE
just 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 first 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 file 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 file
explorer, and go to Start->Settings->Personal->Buttons, and
select the arrow button (Button 4). Then select the file 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 finished.
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 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 levels to their lowest setting for both “On Battery”
Acoustic Monitoring Protocol, v. 2.1
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
it is visible.
Appendix 4: Installation instructions for Potoo v.
2.2 on a HP iPAC running Pocket PC 2003
Installing the software
From the PC, place the following 3 files 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 files are visible on the PDA by going to the bottom of the “File Explorer” window, below the last file or folder
listed, and click and hold on the background white area and
select “View All Files”.
Getting the PDA ready
When setting up a PDA from the “out of the box” state,
there are several settings to check/adjust:
1) Make DLL files visible. Start by opening the File
Explorer, Star->Programs->File Explorer, and going to the
“My Device\” folder, scroll to the bottom of the file list so
that you can see a blank area below the files, press on the
blank area and select “ View all files” This should allow
DLL’s to be visible everywhere in the file system.
to Start->ActiveSync->Tools->Options. Make sure that both
check boxes are UNCHECKED on the “PC” tab: “Use mobile 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 file for it to point to in the
scroll box below. “Potoo” should be one of the choices.
Click “OK” and “Close” when you’ve finished.
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 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 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
sure it is visible.
2) Set the proper time Zone and Time. Click the DATE
just 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
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
13
When servicing the PDA in the field:
⃞ Make a new entry in the field notebook for this
device (See: Method, Field Sampling, for
more information).
⃞ Visually inspect the furry windscreen surrounding 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 flash memory card.
⃞ Reset Potoo (the recording software – see
instructions below).
⃞ Check the silicate drying pack, and replace if
necessary.
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 field deployment. The lights on the
recharger flash during recharging, and are on steadily once
recharging is finished. If a light is off, it indicates that a battery is no longer working and needs to be thrown away.
Erase previous sounds on the replacement flash-memory
card to free up storage space. I like to keep a very small file,
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 current one in use is saturated.
Bring with you:
⃞
⃞
⃞
⃞
⃞
14
battery holder with 4 recharged D-cell batteries.
battery holder with 5 recharged D-cell batteries.
empty flash memory card.
fresh silicate drying pack, in a zip lock bag.
flat-head screwdriver (to remove furry windscreen for microphone, 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 files
from the full flash memory card to both the
computer used for TEAM audio monitoring
and the external hard drive back-up, then erase
the flash memory card, preparing it for the next
PDA deployment.
How to reset Potoo
Hard-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 parameters. 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 field station
should be written in the Acoustic Monitoring field notebook). 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.
Acoustic Monitoring Protocol, v. 2.1
How to collect the data from the ARU
Bring back to the station:
⃞ 2 battery holders with 9 used D-cell batteries.
⃞ Full flash memory card.
⃞ Used silicate drying pack.
When changing out the microphone gain board, set the dip
switches to the following settings, providing the lowest setting of gain, 25 dB:
switch 1 = 1
switch 2 = 0
switch 3 = 0
switch 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 field:
⃞ 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
Bring the ARU and battery back to the field 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 files should then be archived as TEAM
sound files, and a short text file 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 “Prefill” 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 = 0
switch 2 = 0
switch 3 = 0
switch 4 = 1
How to set up the ARU
The 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 file for more specific details). The important 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.
Tropical Ecology, Assessment, and Monitoring (TEAM) Initiative
15