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Assessments of individual animal health alerts to early signs of population level effects in wildlife but often rely on logistically complex wild animal captures, hindering our understanding of the wellbeing of populations in regions with limited resources. Here, we tested photogrammetry methods using small aerial drones for accurate morphometric measurements of Antillean manatee (Trichechus manatus manatus) body size and body condition. We flew drones to collect aerial imagery of captive manatees in Quintana Roo, Mexico and compared manatee body size measurements from scaled aerial imagery with physically measured body sizes. To assess optimal altitude for imaging, body size measurements acquired with an out-of-the-box drone were compared to measurements from the same drone model equipped with a LiDAR for precision altimetry flown at three altitudes (30 m, 50 m, 70 m). The accuracy of body size measures was similar for all drone models but improved with the addition of LiDAR. Difference in body size estimates between manual and drone-based measurements indicate a correction factor may be needed to account for disparities. We then used body size measurements to develop a body condition index for Antillean manatees. Our findings highlight the strength of low-cost aerial drones for morphometric measurements and assessments of manatee body condition.
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Vol.:(0123456789)
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Mammalian Biology
https://doi.org/10.1007/s42991-022-00228-4
ORIGINAL ARTICLE
Drone‑based photogrammetry assessments ofbody size andbody
condition ofAntillean manatees
EricAngelRamos1 · SarahLandeo‑Yauri1 · NatalyCastelblanco‑Martínez1,2,3 · MariaRenéeArreola4·
AdamH.Quade5· GuillaumeRieucau5
Received: 12 October 2020 / Accepted: 5 January 2022
© The Author(s) under exclusive licence to Deutsche Gesellschaft für Säugetierkunde 2022
Abstract
Assessments of individual animal health alerts to early signs of population level effects in wildlife but often rely on logisti-
cally complex wild animal captures, hindering our understanding of the wellbeing of populations in regions with limited
resources. Here, we tested photogrammetry methods using small aerial drones for accurate morphometric measurements of
Antillean manatee (Trichechus manatus manatus) body size and body condition. We flew drones to collect aerial imagery
of captive manatees in Quintana Roo, Mexico and compared manatee body size measurements from scaled aerial imagery
with physically measured body sizes. To assess optimal altitude for imaging, body size measurements acquired with an
out-of-the-box drone were compared to measurements from the same drone model equipped with a LiDAR for precision
altimetry flown at three altitudes (30m, 50m, 70m). The accuracy of body size measures was similar for all drone models
but improved with the addition of LiDAR. Difference in body size estimates between manual and drone-based measurements
indicate a correction factor may be needed to account for disparities. We then used body size measurements to develop a
body condition index for Antillean manatees. Our findings highlight the strength of low-cost aerial drones for morphometric
measurements and assessments of manatee body condition.
Keywords Body condition· Health indices· Photogrammetry· Trichechus manatus· Unmanned aerial vehicles
Introduction
Wild animal health is often evaluated through assessment of
their body condition, i.e., the accumulation of energy stores
in the form of higher lipid content relative to lean tissue
(e.g., McKinney etal. 2014; Norkaew etal. 2018; Christian-
sen etal. 2020a, b). Individuals in good body condition can
have higher survivability, reproductive success, and better
ability to cope with environmental stressors compared to
animals in poor condition, all of which confer fitness benefits
(Stevenson and Woods 2006; Clutton-Brock and Sheldon
2010). Poor body condition and population health in wildlife
have been associated with major losses of available habi-
tat impacting animal reproduction and survival (Preen and
Marsh 1995; Harwood etal. 2000). Body condition assess-
ments in wild populations help to determine the baseline
health status of individuals, detect animals in poor health,
and estimate survival and mortality rates. Additionally, they
can provide insights into the environmental and anthropo-
genic causes and the consequences of these effects within
and across populations (Stamper and Bonde 2012).
Handling editors: Stephen C.Y. Chan and Leszek Karczmarski.
This article is a contribution to the special issue on “Individual
Identification and Photographic Techniques in Mammalian
Ecological and Behavioural Research – Part 1: Methods and
Concepts”—Editors: Leszek Karczmarski, Stephen C.Y. Chan,
Daniel I. Rubenstein, Scott Y.S. Chui and Elissa Z. Cameron.
* Guillaume Rieucau
grieucau@lumcon.edu
1 Fundación Internacional para la Naturaleza y la
Sustentabilidad, Chetumal, QuintanaRoo, Mexico
2 Consejo Nacional de Ciencia y Tecnología, Chetumal,
QuintanaRoo, Mexico
3 División de Desarrollo Sustentable, Universidad de Quintana
Roo, Chetumal, QuintanaRoo, Mexico
4 Dolphin Discovery Group, Cancún, QuintanaRoo, Mexico
5 Louisiana Universities Marine Consortium, Chauvin, LA,
USA
E.A.Ramos et al.
1 3
Body condition indices typically include a variety of
insitu and laboratory-based measures of morphology, blood
chemistry, and physiological condition linked to animal
health (Stevenson and Woods Jr 2006; Morfeld etal. 2016;
Booth etal. 2020). These assessments can be logistically
complex in free-ranging animals, particularly in marine
mammals where most species are fully aquatic (e.g., ceta-
ceans, sirenians) and are impractical to capture and measure
insitu. Collecting physiological data including blood chem-
istry and morphometrics on wild marine megafauna often
relies on the direct capture and release of free-ranging ani-
mals (Wells and Scott 1990; Lanyon etal. 2010; Bonde etal.
2012) or on stranded animals (Larrat and Lair 2021). Live
capture and release methods for wild animals are expensive
and complicated undertakings, requiring teams of trained
experts in animal handling and veterinarians to safely cap-
ture animals (e.g., Alves-Stanley etal. 2010; Bonde etal.
2012; Sulzner etal. 2012). Collecting data to develop robust
condition indices for evaluating the health of wild marine
mammals, and, therefore, assessing their body condition is
a pressing challenge.
Body size is an important characteristic of animals asso-
ciated with their reproduction, energetics, and survival
(Speakman 2005).Photogrammetry (i.e.,measurements
throughtheuse of photographs) provides a non-invasive
alternative for remote acquisition of morphometric meas-
urements of animals(Booth etal. 2020), and has been suc-
cessfully used to estimatethe age, sex, body size and mass in
several terrestrial and aquatic mammals (Karczmarski etal.
2022a, b). In marine mammals, photogrammetry techniques
have been applied broadly for measuring body size and esti-
mating body condition of several species of baleen whales
(Best and Rüther 1992; Pettis etal. 2004; Christiansen etal.
2016; Johnston etal. 2022), dolphins (Perryman and Lynn
1993; Fearnbach etal. 2018), pinnipeds (Goebel etal. 2015;
Pomeroy etal. 2015), and sirenians (Flamm etal. 2000).
These methods produce reliable body length estimates in a
variety of species (Webster etal. 2010; Wong and Auger-
Méthé 2018) and can be used to reveal trends in growth and
survival (Cheney etal. 2018), and to identify regional differ-
ences in morphometric patterns (van Aswegen etal. 2019).
The basic methods for acquiring these data on individual
animals require at least one camera positioned from a boat,
aircraft, or land, paired with a method for acquiring a reli-
able scale in images (Cheney etal. 2018). Scaling imagery to
precisely estimate animal body size can be accomplished in
multiple ways, including the use of a scaled reference object
of known size, calibrated cameras (Dawson etal. 2017), or
two parallel lasers mounted to a camera body projecting two
points of a calibrated distance onto animal bodies (Durban
and Parsons 2006; Rohner etal. 2015).
Unmanned aerial vehicles (hereafter “drones”) are ideal
platforms for low-cost and non-invasive morphometric
measurements of marine mammal body size because of their
capacity for precision flight, and the ability to carry numer-
ous sensor packages for scaling and observation (Smith etal.
2016; Schofield etal. 2019). Drone-based photogrammetry
has been applied to investigating the health, body condition,
energetics, and reproductive biology of large-bodied marine
animal species including pinnipeds (Allan etal. 2019), killer
whales (Orcinus orca) (Durban etal. 2015), blue whales
(Balaenoptera musculus) (Durban etal. 2016), and hump-
back whales (Megaptera novaeangliae) (Dawson etal. 2017;
Christiansen etal. 2019; Aoki etal. 2021). These studies can
provide compelling data needed for identifying the causes of
population impacts such as mortality events. For example,
Christiansen etal. (2021) identified poor body condition of
eastern North Pacific gray whales (Eschrichtius robustus)
associated with an unusual mortality event likely driven by
starvation of animals. Studies developing and testing basic
photogrammetry techniques using low-cost small multirotor
aircrafts can improve our ability to derive meaningful body
condition indices for monitoring cryptic and endangered
species.
The West Indian manatee (Trichechus manatus) — com-
prised of two subspecies, the Antillean manatee (T. m.
manatus) and the Florida manatee (T. m. latirostris) — are
threatened by extensive exploitation and high mortality rates
from current human impacts. The Antillean subspecies is
considered Endangered (Self-Sullivan and Mignucci-Gian-
noni 2008), and inhabits diverse coastal and riverine habitats
throughout the Caribbean Sea, Mexico, Central America,
and northern South America (Quintana-Rizzo and Reynolds
III 2010). Their populations are generally small and display
limited genetic diversity and dispersal (GarciaRodriguez
etal. 1998; Hunter etal. 2012), with an estimate of less than
5700 individuals for the entire subspecies (Deutsch etal.
2008; Self-Sullivan and Mignucci-Giannoni 2008). Mana-
tees face high levels of mortality from natural phenomena
(e.g., algal blooms, epizootic diseases; Foley etal. 2019;
Rodríguez etal. 2019), intensive hunting and other anthropo-
genic causes (e.g., watercraft collision, bycatch; O'Shea etal.
1985; Bonde etal. 2004). These impacts have led to local
extirpation of manatees (e.g., in some areas of the Veracruz
State, Mexico; Serrano etal. 2017) exposing the subspecies
to major population-level threats and causing species-wide
decline (Domning 1982; Castelblanco-Martínez etal. 2012).
Investigations into the health and body condition of West
Indian manatees have been greatly facilitated by several
long-term capture and release efforts providing researchers
with the data needed to assess animal health in systematic
regional studies (Bonde etal. 2012; Stamper and Bonde
2012). Body condition indices (BCIs) based on length,
umbilical girth, and mass have been developed for assess-
ing individual health and evaluating the condition of Flor-
ida manatees (Harshaw etal. 2016) and Antillean manatees
Drone-based photogrammetry assessments ofbody size andbody condition ofAntillean manatees
1 3
(Castelblanco-Martinez etal. 2021). Flamm etal. (2000)
demonstrated that aerial video photogrammetry from a teth-
ered airship was effective for determining the size of Florida
manatees and estimating their life-stage structure. However,
aerial imaging of free-ranging manatees is complicated by
the small proportion of time manatees spend lying flat at
the surface in a position where body size can be reliably
estimated, and by the challenge of validating aerial estimates
to the actual body size of wild animals. Thus, the accuracy
of different aerial photogrammetry methods for studies of
manatee health and biology should be tested on novel plat-
forms with good control data of animals of known size.
Few studies have used aerial drones to study manatees. In
clear shallow waters, small aerial drones improved the detec-
tion of Antillean manatees and enabled observations of their
behavior (Ramos etal. 2018), and photo-identification of
individuals (Landeo-Yauri etal. 2020). Behavioral reactions
to the overhead drone during approaches and stable hovering
were most prevalent at low altitudes (< 20m) suggesting
non-invasive use of these systems should prioritize higher
altitude flight (Ramos etal. 2018). Using the same dataset,
Landeo-Yauri etal. (2020) developed a visual classification
method for photo-ID of individual manatees demonstrating
its use for reidentifying a portion of the population. The
long-term conservation and protection efforts of manatee
populations would benefit from small drone surveys and
advancements of image/video post-processing techniques
for developing non-invasive platforms for manatee health
assessments (Raoult etal. 2020).
Here, we conducted a series of experiments to test the
efficiency of photogrammetry using small aerial drones to
estimate body size and body condition of Antillean mana-
tees. Our goals were: (1) to test if photogrammetry meas-
urements from drones provide reliable estimates of manatee
body size using a scaled reference object compared to the
ground sampling distance and onboard sensor data; (2) to
examine if the addition of a LiDAR sensor for altimetry
improves accuracy in body size estimates; and (3) to use
these data to investigate the resulting differences in BCI pro-
duced by manual measurements and drone-based methods
for health assessments of Antillean manatees.
Methods
Study design
We conducted two experiments to assess the accuracy of
drone-based methods for measuring manatee body size and
using these measures to estimate their body condition. We
provide a detailed workflow outlining steps undertaken in
this study in Fig.1. In Experiment 1, we examined the differ-
ences in accuracy of manatee body size estimates acquired
from drone-based photogrammetry of manatees with and
without a reference object of known size to scale imagery.
In Experiment 2, we compared the accuracy of photogram-
metry between a drone equipped with a LiDAR package for
accuracy altimetry to a drone without LiDAR. The data from
Experiment 1 were then used to develop preliminary body
condition estimates for manatees using manual straight-
line measures of body length and curvilinear measures of
umbilical girth (Fig.2) compared to photogrammetry-based
straight-line measures of body length and maximum width.
Study site andsubjects
We conducted our experiments with 18 captive Antillean
manatees of various ages of both sexes (Table1) at four
Dolphin Discovery facilities in the state of Quintana Roo on
the Caribbean Sea coast of Mexico (Fig.2). Manatees were
classified based on total straight-line body length as adults
(> 225cm), juveniles (176–225cm), or calves (< 175cm)
(Mignucci-Giannoni etal. 2000). All manatees were housed
in the same pool with at least one other manatee (Table1).
The health and welfare of all animals were regularly assessed
during veterinary exams and all manatees were estimated to
be in the good physical condition and in good health.
Equipment
Two different consumer-grade multirotor drone models
were used: a DJI Phantom 4 Professional V1.0 (“Phantom
4” hereafter) in Experiment 1; and one DJI Mavic Pro 2 was
used as is (“Mavic” hereafter); and a second Mavic equipped
with a custom-built LiDAR/GPS sensor package (Dawson
etal. 2017) in Experiment 2 (Fig.2). The LiDAR package’s
data-logging system was powered by a 4500-mw lithium
battery and recorded altitude and a GPS location through-
out flights (Dawson etal. 2017). The package was mounted
to the bottom of the body of the aircraft, oriented straight
down aligned with the onboard camera to ensure a reliable
match from the drone imagery to the sensor data for precise
altimetry (Fig.2). Altitude measures from the altimeter were
time-synced with drone flights using a stopwatch in GMT.
Aircraft were manually flown by experienced pilots
(EAR, SLY, GR) via remote control and a mounted tablet
(i.e., Apple iPad or the DJI built-in screen on the remote of
the Mavic) to monitor flight parameters and animal behav-
ior through the live-streaming aerial video. All drones were
equipped with gimbal-mounted high-resolution cameras
filming in 3840 × 2160 pixels at 24 frames per second. Video
imagery was later examined to extract individual frames
at specific times. Drones were launched from the ground
(Experiment 1) or from atop two plastic crates (take-off
height: 0.5m; Experiment 2) from a location ~ 50m from
manatee pools to avoid animal disturbance. The aircraft was
E.A.Ramos et al.
1 3
flown directly over target animals for ~ 15min with the cam-
era pointed straight down to film continuous video footage
of manatees at the surface, most importantly lying flat and
parallel with the water’s surface (Fig.2). All fights were
performed under wind conditions that never exceeded 5m/s.
Body size measurements
We obtained manatee body size derived from manual measure-
ments (indicated by the superscriptM) and from drone-based
photogrammetry (indicated by the superscriptD). Manual
measures include straight-line body length (SLM) and umbili-
cal girth (UGM): SLM is the straight-line measure from the
tip of the snout to the medial notch of the fluke, while UGM
is defined as the circumference at umbilical level and is typi-
cally considered the maximum girth of the manatee body (e.g.,
Harshaw 2012; Erdsack etal. 2018). Manual morphometric
measures of manatee body size were collected following stand-
ard manual methods (Lima etal. 2005), as part of regular phys-
ical monitoring in the week prior to drone flights. Manatees
were trained to stay in place and lay fully extended at the water
surface, while several people collected the measures using a
measuring tape (Fig.2). Drone-based measures obtained were
straight-line body length (SLD) and maximum width (MWD).
Straight-line body length was gathered in drone imagery (SLD)
by tracing a line from the snout to the medial notch. MWD was
defined as the maximum width of the manatee body, and was
subsequently used to obtain the UGD by applying the following
equation (adapted from Harshaw etal. 2016):
UG =MW ×𝜋.
Manual
body size
measurements
Drone flights
with DJI
Phantom 4 Pro
Images
extracted
from videos
Reference
object to
scale size
Barometer
altitude to
scale size
Measurement
of body size in
ImageJ
Body
size
values
Body
size
values
Body
size
values
Calculate body
condition index
Calculate body
condition index
Comparison
Drone flights
with DJI Mavic
Pro 2 with
LiDAR
Images
extracted
from videos
Barometer
altitude to
scale size
Body
size
values
Body
size
values
Body
size
values
Measurement
of body size in
MorphoMetrix
LiDAR
altitude to
scale size
Manual
body size
measurements
Drone flights
with DJI Mavic
Pro 2 with
LiDAR
Experiment 1 Experiment 2
Comparison
Comparison ComparisonComparison
Fig. 1 Detailed workflow outlining the various steps we undertook
in both photogrammetry experiments with captive Antillean mana-
tees at several Dolphin Discovery facilities in Quintana Roo, Mex-
ico. In Experiment 1, we flew a DJI Phantom 4 Pro recording video
over captive manatees to compare their effectiveness of the drone’s
onboard sensors compared to the use of a reference object of known
size. In Experiment 2, we flew a DJI Mavic Pro 2 and the same model
equipped with a LiDAR GPS sensor package (LiDAR drone) for pre-
cision altimetry to determine if the use of body size measures with
LiDAR improved size estimates. Images were extracted from videos
to measure manatee body size. Images in Experiment 1 were meas-
ured using ImageJ. Images in Experiment 2 were measured with Mor-
phoMetriX software (Torres and Bierlich 2020) to facilitate marine
megafauna photogrammetry. Data from Experiment 1 were then used
to calculate two body condition indices using the manual measures
and drone-based photogrammetry measures of body size
Drone-based photogrammetry assessments ofbody size andbody condition ofAntillean manatees
1 3
Experiment 1: Scaling withareference object
compared toonboard altimeter
We flew the Phantom 4 on 30 March, 31 March, and 01 April
2019 over 18 individuals (12 adults, 4 juveniles, 2 calves)
(Table1). A white polystyrene block (1m L × 0.25mW)
used as a reference object of known size was placed in the
pool floating at water level to accurately scale aerial imagery
(Fig.2). The drone was hovered for several minutes at a time
at different altitudes from 5 to 101m. Altitude data was
obtained from the onboard data storage of flight records.
Manual measurements of animal body size (standard length
and umbilical girth) were performed by the on-site veterinar-
ians within the same week of the flights.
Aerial videos filmed with the Phantom 4 were reviewed
using VideoPad v.7.4 NCH software and to extract a minimum
of 10 high-quality screenshot images (3840 × 2160 pixels)
from aerial video of manatees close to the water’s surface in a
nearly horizontal and straight position as possible for further
analysis. Straight-line body length (SL) and maximum width
(MW) of each manatee visible in drone images were meas-
ured in pixels using ImageJ software (Abràmoff etal. 2004).
Drones
Body size measurements
DJI Phantom 4 Pro
DJI Mavic Pro 2
DJI Mavic Pro 2 with
LiDAR
UG
(a) (d)
(b)
MW
Reference object
SL
SL Exp.#1
Exp.#2
Exp.#2
(c) MorphoMetriX
MDD
M
Fig. 2 Elements of the photogrammetry experiments. a Straight-
line body length (SLD) and maximum width (MWD) of each mana-
tee were measured in individual images of manatees extracted from
high-resolution aerial drone video recordings. Straight-line total
body length (SLM) and umbilical girth (UGM) were measured manu-
ally during veterinary exams. The veterinary team at Dolphin Dis-
covery used a measuring tape held over the stationary animal lying
flat at the surface to determine the straight-line total body length of a
manatee. Manatees were trained to perform this behavior (Lima etal.
2005), ensuring less variability due to animal curvature and position.
b A white polystyrene block (1m L × 0.25 m W) placed in manatee
pools during flights served as a reference object to scale animal size
in aerial video imagery. c Output of MorphoMetriX illustrating body
size measurements of Julieta at Puerto Aventuras collected with a
DJI Mavic Pro 2 at a flight altitude of 50m. In MorphometriX, the
number of width segments (yellow-colored segments) was set to 10,
representing 10% increments of the length measurement. d Images of
each of the drones used in this study: DJI Phantom 4 Pro in Experi-
ment 1 and two DJI Mavic Pro’s in Experiment 2, one equipped with
a custom LiDAR/GPS package and the other without
E.A.Ramos et al.
1 3
A reference object (RO) was used to scale manatee size in
aerial imagery (e.g., if the length of the reference object in the
image was equal to 100 pixels, the obtained rate was 0.01m/
pix). An alternate method, using flight altitude data from the
onboard altimeter, image size (in pixels), camera sensor width,
and focal distance, was also applied to calculate the ground
sampling distance (GSD), which is another form of image rate
(m/pix) used to scale manatee size:
To determine how accurate each measure was relative to
SLM, we calculated the differences between SLM and values
produced with a reference object (SLD,RO) and ground sam-
pling distance (SLD,GSD).
Experiment 2: Comparison ofLiDAR equipped drone
versusnon‑LiDAR equipped drone
Flights with the Mavics were conducted on 16 and 17 Octo-
ber 2019 (Table1). For these flights, we selected a single
adult manatee (Julieta) as representative of a healthy indi-
vidual for which the straight-line body length (SLM) was
measured by on-site veterinarians following standardized
GSD = [
sensor width(mm)× f light alt itude(m)
]
[
focal lengt h(mm)× image width(pix)
].
procedures. We flew over Julieta the day of the first series
of flights using the Mavic (no-LiDAR drone) and the Mavic
with the custom-built LiDAR/GPS sensor package (LiDAR
drone). To examine the effect of imaging manatee bodies
at different altitudes on size measurements, each drone was
flown at altitudes of 70m, 50m, and 30m twice (first during
descent flight and second during ascent flight) where it was
kept in a stationary hovering position for two consecutive
minutes.
Individual frames were extracted from video files
from both Mavics using VLC media player (VideoLAN
organization) and saved as .tiff files to preserve resolu-
tion. Twenty images were created per altitude per flight,
resulting in 40 images per altitude and 120 images per
flight totaling 600 images. Three flights were conducted
using the LiDAR mounted drone and two flights were
conducted with the standard drone without LiDAR. As a
result, 360 images were analyzed for the drone equipped
with the altimeter, and 240 images for the drone without
LiDAR. Analysis was restricted to images in which the
focal individual was in a nearly parallel position to the
surface presenting minimal body curve.
Aerial manatee body size measurements were extracted
with the software MorphoMetriX (Torres and Bierlich
2020). MorphoMetriX allows the user to input flight and
Table 1 Information on the study location, drone flights, and the Antillean manatees (n = 18) imaged during our photogrammetry tests at Dol-
phin Discovery facilities in the Mexican Caribbean
A adult, J juvenile, C calf, F female, M male. No. of images = Number of images used in photogrammetry experiment. “-” indicates that the indi-
vidual was not included due to insufficient images of high-quality
Exp. no Facility Date No. of flights Name Age Age class Sex No. of images
1 Isla Mujeres 2019-Mar-30 4 África 2 J F 14
César > 11 A M 45
Fabián 9 A M 54
Sabina > 11 A F 23
Puerto Aventuras (Pool 1) 2019-Mar-31 3 Bombom 3 J F 16
Dorothy 15.6 A F 22
Julieta 17.9 A F 28
Michelin 0.9 C M 28
Nohoch 2 A M 18
Puerto Aventuras (Pool 2) 2019-Mar-31 1 Conchis 4.6 J F
Claudia 4.3 A F 10
Dreams 2019-Mar-31 1 Lorenzo 6.5 A M
Pablo 21.1 A M
Quijote 11 A M –
Cozumel 2018-Apr-01 2 Angel 16 A M 25
Edgar 8 A M 25
Roberto 8 A M –
Yoltzin 10 A M –
2 Puerto Aventuras (Pool 1) 2019-Oct-16 2 Julieta 17.9 A F 240
2019-Oct-17 3 Julieta 17.9 A F 360
Drone-based photogrammetry assessments ofbody size andbody condition ofAntillean manatees
1 3
sensor parameters including Image ID, focal length (mm),
altitude (m), and pixel dimension (mm/pixel). Focal length
of the DJI Mavic Pro 2 camera was 26mm (DJI: www.
dji. com/ mavic/ inf o# sp ecs) and pixel dimension was set to
0.008666mm/pixel following Torres and Bierlich (2020).
Each image was individually uploaded and processed in
MorphoMetriX to measure manatee body length. Straight-
line body length measurements began at the tip of the
snout and ended at the medial notch of the fluke. Data
were then exported as CSV files.
Statistical analysis
For Experiment 1, comparisons between manual and drone
measures were made using only body length (SL) to evalu-
ate the accuracy of drone-based measurements, because the
drone-based umbilical girth (UGD) introduces an additional
bias since it is calculated as a perfect circumference based on
the linear maximum width (MWD). A student's t-test was used
to compare the ΔSLmanual-drone obtained with both methods
employed for scaling (RO and GSD). The mean and standard
deviation (SD) were calculated on manual and drone-based
body size measures (SL and UG) to compare their relative
variability in measurements.
For Experiment 2, a linear mixed model (LME) was used to
examine whether body length estimates differed between the
LiDAR drone vs. the non-LiDAR drone and between different
flight altitudes. Drone types (LiDAR and non-LiDAR) and
flight altitudes (30m, 50m, and 70m) as well as the interac-
tion between the two factors were included as fixed effects in
the LME. As it is possible that our selected aerial images may
not have been satisfactory units of replication, we included
Image ID nested in a flying altitude of a flight as a random
effect in our LME to control for pseudoreplication and the
likely non-independence of the series of images analyzed. The
LME was conducted using the nlme package in R version 3.6.1
(The R Foundation for Statistical Computing: www.r- proje ct.
org).
Body condition index
Morphometric measurements of manatee body size taken dur-
ing veterinary exams were used to calculate a body condition
index (BCI) for Antillean manatees according to Harshaw etal.
(2016) and Castelblanco-Martinez etal. (2021):
BCI is calculated as a ratio, SLD and UGD are expressed in
metric units. The resulting BCI values are expected to range
from approximately 0.6–1 for manatees in good health, and
individuals with BCI values close to 1 were considered poten-
tially overweight (Harshaw etal. 2016).
BCI = UG
SL
.
To determine the accuracy of the photogrammetry-based
measures of manatee body size, we compared BCI values
derived from manual body size measurements (BCIM) and
drone-based photogrammetry measurements (BCID).
Results
Experiment 1
During 11 flights performed with the Phantom 4, we recorded
173min of aerial video recordings. We obtained suitable
images (straight position close to the water surface; n = 308)
for 12 of the 18 manatees (Table1). The mean flight alti-
tude for the selected images was 28.5m (SD = 21.6 m,
mode = 30m, range = 5–101m) and the most useful images
(84%) were captured below 40m.
Accuracy ofdrone‑based size measures withareference
object andwithanonboard altimeter
For most animals, SLD estimated with both methods were
normally distributed (Fig.3a and b). The difference between
SLM (actual body size) and SLD (estimated) was not statisti-
cally significantly different when comparing the methods used
(t-test: n = 308; t = 1.553; p = 0.121). SLD were similar in size
and deviations from SLM in all manatees measured with the
reference object or with GSD (Fig.3). The difference was
marginally lower when using a reference object (RO) to scale
imagery (mean ± SD = 21.3 ± 11.59cm) t han when calculated
with GSD (mean ± SD = 22.8 ± 12.40cm). The relative er ror
(|SLM–SLD|/SLM) (Fig.3c and d) obtained with the reference
object was similarly lower (mean ± SD = 8.2 ± 3.83%) than
when using GSD (mean ± SD = 8.7 ± 4.31%). Thus, we used
the reference object-based values to present information of
manatee body size values.
Manual anddrone‑based manatee body size values
The mean values (± SE) of SLD,RO and UGD,RO were calculated
for adults (SL: 253.8 ± 1.75cm; UG: 191.3 ± 1.46cm), juve-
niles (SL: 210.7 ± 1.17cm; UG: 151.5 ± 1.00cm) and calves
(SL: 162.2 ± 1.56cm; UG: 125.2 ± 2.16cm). The values of SL
and UG from manual and drone-based measurements (RO-
based values, mean ± SD) are presented in Table2 for all man-
atees (n = 12). Across all animals combined, SLM values were
higher and more variable (mean ± SD = 252.7 ± 48.38cm) than
values for SLD,RO (mean ± SD = 231.1 ± 42.16cm). UGM val-
ues were lower (mean ± SD = 167.3 ± 33.59cm) than values
for UGD,RO (mean ± SD = 173.2 ± 33.18cm). In general, mana-
tee body size estimates from photogrammetry overestimated
umbilical girth and underestimated body length (Table2,
Fig.4).
E.A.Ramos et al.
1 3
Fig. 3 Split violin plots and overlapping boxplots displaying photo-
grammetry-based estimates of the straight-line body length (cm) of a
female and b male manatees per individual and sex using a scaled ref-
erence object compared to the ground sampling distance (GSD), and
the relative differences between these two measures from actual body
size (SLM) for c females and d males. Data were collected at altitudes
of 5–40m. Black dots represent outliers. The black bar in the boxplot
represents the median. The bottom of the box represents the 25th per-
centile and top represents the 75th percentile. Body length measure-
ments were similar when using a reference object or GSD. Body size
measurements were more variable in males than females when using
barometric values of altitude to scale imagery (onboard altimeter) as
compared to a reference object. The number of photos analyzed for
body size is listed in Table1
Table 2 Values for manual body
size measurements (cm) and
resulting body condition indices
of Antillean manatees
Manual size measurements: straight-line total body length (SLM) and umbilical girth (UGM). Photogram-
metry-based size measurements: straight-line total body length (SLD) and umbilical girth (UGD). A adult, J
juvenile, C calf, F female, M male. BCIM = Body condition index using SLM and UGM; BCID = Body con-
dition index using SLD and UGD. Standard deviations of drone-based body size estimates and body condi-
tion indices are listed in parenthesis. Manual measurements were not replicated per individual
Name Age Age class Sex SLMSLDUGMUGDBCIMBCID
Africa 2 J F 188 174.1(± 6.80) 138 142.2 (± 8.26) 0.73 0.82 (± 0.06)
Bombom 3 J F 220 210.6 (± 6.87) 154 150.1 (± 7.08) 0.70 0.71 (± 0.04)
Claudia 4.3 A F 241 201.6 (± 3.20) 142 146.8 (± 4.18) 0.59 0.73 (± 0.02)
Dorothy 15.6 A F 319 280.0 (± 4.55) 234 208.5 (± 5.89) 0.73 0.75 (± 0.02)
Julieta 17.9 A F 332 292.8 (± 7.01) 220 232.4 (± 8.43) 0.66 0.79 (± 0.03)
Sabina > 11 A F 280 264.2 (± 7.20) 189 210.2 (± 9.05) 0.68 0.80 (± 0.03)
Angel 16 A M 276 258.7 (± 6.42) 178 190.3 (± 5.26) 0.65 0.74 (± 0.03)
Cesar > 11 A M 280 258.8 (± 5.33) 160 180.2 (± 6.76) 0.57 0.70 (± 0.03)
Edgar 8 A M 259 242.9 (± 10.46) 157 173.4 (± 5.53) 0.61 0.715 (± 0.05)
Fabian 9 A M 237 217.1 (± 9.42) 166 172.9 (± 6.95) 0.70 0.798 (± 0.05)
Michelin 0.9 C M 170 156.2 (± 4.70) 117 116.7 (± 6.34) 0.69 0.748 (± 0.04)
Nohoch 2 A M 230 215.7 (± 5.56) 152 155.4 (± 5.13) 0.66 0.721 (± 0.03)
Drone-based photogrammetry assessments ofbody size andbody condition ofAntillean manatees
1 3
Experiment 2
Body length estimates significantly differed between drone
type (F1,594 = 140.67; p < 0.0001) and flight altitudes
(F2,594 = 48,36; p < 0.0001) (Fig.5), however, the interac-
tion between the two factors was not significant (Drone type
× flight altitudes: F2,594 = 2.94; p = 0.054).
When compared to the known body length of the mana-
tee Julieta (314cm), estimates obtained through analysis
of images collected with the standard drone (non-LiDAR
drone) always overestimated body length with greater dif-
ferences reported for 50m and 70m flight altitudes (mean
Δ SLmanual-drone: at 30m = 0.14m; at 50m = 0.37m; at
70m = 0.29 m) (Fig. 6). Greater accuracy was obtained
for lower altitude flights (30m) with the standard drone.
Body length estimates calculated using the LiDAR-equipped
drone equipped were more accurate (mean Δ SLmanual-drone:
at 30m = − 0.19m; at 50m = 0.16m; at 70m = − 0.03m).
Smaller differences in body length estimates were obtained
for images collected during 70m altitude drone flights
(Fig.6).
Assessment ofmanatee body condition index
The BCI values obtained from manual body size measure-
ments (BCIM) were lower for all individuals compared to
BCID (Table2, Fig.7). The average BCID for all individu-
als was 0.75 ± 0.05 (mean ± SD) and ranged from 0.70 to
0.82. The average BCIM for all individuals was 0.66 ± 0.05
(mean ± SD), ranging from 0.57 to 0.73.
Fig. 4 Scatterplot of the manatee umbilical girth (cm) and body
length (cm) measured manually versus from drone-based imagery
(mean ± SD). Trend lines were positive and similar for body size esti-
mates from both methods
Fig. 5 Comparison of differences in measurements of the body length
of a single adult Antillean manatee imaged from a DJI Mavic Pro 2
(no-LiDAR drone:n30 meters = 80; n50 meters = 80; n70 meters = 80) and the
same model drone equipped with a custom-built LiDAR package for
precision altimetry (LiDAR drone: n30 meters = 120; n50 meters = 120;
n70 meters = 120). Body length was defined as the straight-line body
length (SLD) measured from the tip of the snout to the medial tip of
the tail using a measuring tape extended lengthwise next to the ani-
mal lying flat at the surface. The red dotted line represents straight-
line total body length (SLM) acquired during regular veterinary
exams. Flights with the LiDAR drone flown at an altitude of 70m
produced the most precise measurements of body size
Fig. 6 Comparison of the accuracy of body length measurements of
a single adult Antillean manatee (Julieta) imaged with a DJI Mavic
Pro 2 (no-LiDAR drone) and the same model equipped with a cus-
tom-built LiDAR system for precision altimetry (LiDAR drone). Δ
SLmanual-drone represents the difference in meters between straight-line
body length measured manual with a tape ruler (SLM) or from aerial
drone imagery (SLD). The manatee graphic is scaled to SLM. The
LiDAR drone provided more precise body length measurements of
manatees than the no-LiDAR drone
E.A.Ramos et al.
1 3
Discussion
Advancing new methods for assessing marine mammal
health is critical to supporting wildlife management and
conservation efforts. In this study, we flew small consumer-
grade drones with and without a custom LiDAR-based altim-
eter and compared methods for estimating the body size and
body condition of Antillean manatees. Using a scaled refer-
ence object resulted in a similar error when compared to the
use of the ground sampling distance derived from imagery
and the drone’s onboard sensors, hence, using a reference
object is equally efficient when flight data is unavailable
or when the drone altimeter data is unreliable. Imaging
from the drone equipped with the LiDAR altimeter showed
improved accuracy in body size measurements compared
to that from an out-of-the-box drone. Drone-based size
measures of manatees used to calculate a photogrammetry-
based body condition index for Antillean manatees enabled
a preliminary assessment for drone-based BCI studies of the
subspecies. Our study provides strong support for the use
of small drones for robust measurement of the body size of
Antillean manatees.
The LiDAR-equipped aircraft provided more reliable esti-
mates of manatee body size than the built-in altimeter of the
Mavic Pro 2 with a resulting suitable accuracy to measure
individual manatees. Consumer-grade DJI drones use baro-
metric pressure and built-in GPS to determine altitude, and
these methods introduced major inaccuracies into altitude
estimations in drones without LiDAR. Drift in DJI barom-
eter can skew altitude readings in a single flight (Colefax
etal. 2019). Thus, in flights conducted without the LiDAR,
erroneous altitude readings from DJI sensors are likely con-
tributors to less precise body size measurements and BCI
values. Additionally, pixel issues in imagery acquired at
high altitudes may have impacted the accuracy of measure-
ments in all flights in the non-LiDAR drone compared to the
LiDAR-equipped drone. These findings support the use of
LiDAR as a low-cost enhancement to research using small
drones for photogrammetry that enables improvements in the
accuracy of altitude data, increasing the reliability of body
size measurements of animals (Dawson etal. 2017).
Collecting reliable drone-based morphometric measure-
ments of manatees was hindered by several factors inherent
in the use of overhead imagery in place of manual meas-
urements of animal body size. Differences in body length
(SL) in drone-based measurements likely arose from the
differences in measuring the straight-line length of mana-
tees from above during drone flights, where animal bodies
are naturally curved downward at the posterior and anterior
ends and result in shorter body lengths as compared to the
length measured manually when the animals were station-
ary at the surface and fully extended (a trained behavior in
these animals). Considering the differences between meas-
ures from drone-imagery and manual measures, developing
a correction factor to account for the disparity is essential.
We calculated the difference between body size values
obtained through photogrammetry and manual methods
(ΔSLmanual-drone), resulting in a correction factor that should
be considered preliminary due to our small sample size. The
umbilical girth (UG) was not used for comparisons between
manual and drone-based methods, as it could not be meas-
ured directly in the drone imagery, but obtained using the
Africa Bombom Claudia Dorothy Julieta Sabina AngelCesar EdgarFabian Michelin Nohoch
0.65
0.75
0.85
0.95
Body condition index
Female Male
Manatee
Fig. 7 Violin plots and overlapping boxplots depicting body condi-
tion index (BCI) values for female and male manatees. The plots rep-
resent straight-line photogrammetry-based measurements of mana-
tee body size (BCID). Black dots mark outliers. The black bar in the
boxplot represents the median. The bottom of the box marks the 25th
percentile and top marks the 75th percentile. The single red bar repre-
sents the BCI value derived from the single set of manual size meas-
ures of manatees (BCIM) using straight-line body length (SLM) and
umbilical girth (UGM). BCID measurements resulted in overestima-
tion in manatee body size by approximately 10% compared to BCIM
Drone-based photogrammetry assessments ofbody size andbody condition ofAntillean manatees
1 3
straight-line maximum width (MWD) assuming width as the
diameter of the circle UG. The use of MWD to estimate UGD
resulted in slight overestimation compared to UGM and sub-
sequent differences regarding drone-based BCI values com-
pared to BCI values derived from manual measurements.
The development of 3D models of manatees similar to those
created for harbor porpoises (Phocoena phocoena) (Irschick
etal. 2021) and right whales (Eubalaena sp.) (Christiansen
etal. 2019) will enable volumetric estimation of animals in
the wild, potentially providing the ability to test other BCIs
in use with manatees (Harshaw etal. 2016; Castelblanco-
Martínez etal. 2021).
In addition, future efforts should also be directed at deter-
mining the variance introduced by environmental factors and
strategies for overcoming their effects. In our data, the time
of day of overhead imaging was a critical choice for success-
ful photogrammetry. High levels of glare from late morning
to mid-afternoon and shadows cast by manatee bodies made
it challenging to capture high-quality imagery. Similarly, the
presence of water surface ripples may limit the efficiency of
the imagery method as the shape of the manatee bodies can
be distorted by the ripples. Additionally, the behavior, habi-
tat use, and environmental factors must be considered when
using photogrammetry to study wild aquatic animals; for
example, manatees do not usually spend much time in a flat,
straight position while near the surface, which hindered our
efforts to obtain suitable images from all individuals evalu-
ated. Manatees also occupy a variety of turbid habitats with
poor visibility that may be unsuitable for drone imaging.
This illustrates the difficulties associated with aerial pho-
togrammetry applied to our target species, and the need for
further tests and improved protocols to successfully imple-
ment drones for photogrammetry of manatees in their natu-
ral habitats. Despite these difficulties, approaching animals
in the wild is logistically challenging and pinpointing their
location is often infeasible, thus, drone-based assessments
offer a non-invasive alternative with the capacity to collect
higher volumes of data at lower costs.
Body condition for captive manatees (mean = 0.66) was
similar to the average BCI (UG/SL) in healthy wild Antil-
lean manatees from the Mexican Caribbean (Castelblanco-
Martínez etal. 2021). Florida manatees (0.75; Harshaw
etal. 2016) had higher BCIs than Antillean manatees. The
Florida subspecies is larger than the Antillean subspecies
with stockier body size (Wong etal., 2012) with differing
shape (Johnson 2019) and growth rates (Castelblanco-Mar-
tínez etal. 2014) resulting in a higher average BCI. Body
size and shape differences between the subspecies such as
the larger size of Florida manatees (Domning and Hayek
1986) may be driven by thermoregulatory adaptations to
colder habitats (e.g., Allen’s rule; Allen 1877, Bergmann’s
rule; Bergmann 1847), which should be taken into account
in the comparison of morphometric BCIs between the two
subspecies. Differences in the BCIs between two manatee
subpopulations may have been attributable to the need to
increase body fat in the colder northern waters relative to
more southern areas (Harshaw etal. 2016).
Our ability to capture drone-based body measurements
of captive manatees and compare them with physical size
measurements of the same animals provided a rare opportu-
nity to ground-truth our photogrammetry methods. Despite
our limited sample size, captive manatees in this study
were native to Mexico and in good health. BCI values var-
ied across our sample of manatees highlighting the need
to account for individual variability in manatee body size
and health condition based on age and other possible factors
(e.g., percentage of body fat, volume of gas). The BCI we
calculated was used to compare to a large database of animal
morphometric data of Antillean manatees from populations
throughout their range revealed potential ecotypes with dif-
ferent BCIs across riverine and marine coastal ecosystems
(Castelblanco-Martínez etal. 2021). To effectively ground-
truth drone-based photogrammetry for wild Antillean mana-
tees, comparisons of morphometric measurements and other
BCI values of individually tracked manatees sampled over
time and in different regions to reveal temporal trends (e.g.,
seasonal, yearly) regarding their health would be useful. The
relative ease of flying drones over manatees and waiting for
surfacings where most of their body is visible can facilitate
assessments of large numbers of animals when manatees are
clustered together, for example, with hundreds of Florida
manatees at their warm-water aggregation sites.
Assessments of BCI for manatees will be improved
with the use of visual indices now associated with quanti-
fied BCI values of Antillean manatees captured in health
assessments (Castelblanco-Martínez etal. 2021). For
example, emaciated manatees exhibit extensive weight loss
and depletions in muscle and fats, detectable in the low
nuchal fat deposits around the neck (i.e., “peanut head”)
and the visible protrusion of skeletal structure of the ribs,
scapulae, pelvis, spine, and head (Harvey etal. 2019).
Precise measurement of scars and wounds of injured
manatees facilitates an understanding of how many indi-
viduals in populations survive vessel collisions (Langtimm
etal. 1998) and provide insight into the level of threats
manatees face from boating activity (Beck etal. 1982).
All three species of manatee regularly live-strand from
health-related issues due to natural causes and anthro-
pogenic impacts like boat strikes (Adimey etal. 2012).
Stranded manatees are typically underweight and in poor
health, requiring extensive short- to long-term rehabilita-
tion and eventual release, a task recognized as essential to
their conservation (e.g., Adimey etal. 2012; Normande
etal. 2015; Ball etal. 2020). Drone observations provide
a useful way to remotely track animal health following
release according to its measured BCI, reducing the need
E.A.Ramos et al.
1 3
for close boat approaches to document animal condition
in post-release monitoring. For example, non-standardized
methods of viewing animal condition through aerial drone
videos are regularly employed by Wildtracks in Belize—a
manatee rescue and rehabilitation center—to monitor man-
atees during releases and remotely observe the animal in
the following months for visually detectable signs of poor
health (e.g., abnormal movement, weight loss; Z. Walker,
personal communication). Drones can also be applied to
determine the size and age of calves relative to their stages
of dependency and to track the pregnancy status of adult
females, data essential for local population management in
areas with small populations (Self-Sullivan and Mignucci-
Giannoni 2012).
The development of novel, reliable, non-invasive, low-
cost methods for photogrammetry opens new avenues for
measuring the body size and assessing the health condi-
tion of rare and endangered marine megafauna like Antil-
lean manatees. We foresee the combination of photo-
grammetry-based health and body condition assessments,
physiological sampling (e.g., blood samples, urine, blow
sampling), and information on local population character-
istics and behavior (e.g., size, food availability, preferred
species) to help inform on regional threats and produce
a more robust picture of the effectiveness of visual body
condition examinations at identifying underlying health
issues. Comparisons within and across populations will
help to elucidate differential impacts faced by manatees
and to provide critical insights into their welfare and con-
servation needs regionally and species-wide.
Supplementary Information The online version contains supplemen-
tary material available at https:// doi. org/ 10. 1007/ s42991- 022- 00228-4.
Acknowledgements We are very grateful to Dolphin Discovery Aquar-
iums for allowing us to perform our tests in their facilities. Thanks to
Chris and Iain Kerr at Ocean Alliance for building the LiDAR sensor
for us. Big thanks to all the staff and manatee caretakers for their help
during our tests, especially to Adriana Mingramm, Rocío Fraustro and
Luz Garduño, who provided the biometrics data for the manatees they
have under their care. Thanks to Carlos Niño-Torres for comments on
the first phase of the experiments. We also thank RIU hotels and the
Lowry Park Zoo for supporting our field stays and trips.
Author contributions All authors contributed to the study conception
and design. Drone flights, data collection and analysis were performed
by SLY, EAR, AHQ, MRA, and GR. The first draft of the manuscript
was written by EAR, SL-Y, NC-M, and GR and all authors commented
and edited previous versions of this manuscript. All authors read and
approved the final manuscript.
Funding No funding was received for conducting this study.
Availability of data and material The datasets generated during and/or
analyzed during this study are not publicly available due to their use in
multiple studies in preparation but are available from the corresponding
author on reasonable request.
Declarations
Conflict of interest The authors have no relevant financial or non-fi-
nancial interests to declare.
Ethics approval This was an observational study and received ethics
approval from the internal veterinary leadership at the Dolphin Dis-
covery aquarium facilities in Mexico.
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... This is contrary to other studies that have similarly assessed how altitude affects UAV-based image length measurements. For instance, Ramos et al. (2022) compared the size measurements of DJI Mavic 2 video frame (3840 × 2160, 24 frames per second) length measurements of captive manatees to actual measured lengths [41]. They observed a quadratic relationship between altitude and relative error, where low (30 m) UAV altitudes overestimated manatee body lengths by 15 cm and high (70 m) UAV altitudes overestimated lengths by 25 cm. ...
... They observed a quadratic relationship between altitude and relative error, where low (30 m) UAV altitudes overestimated manatee body lengths by 15 cm and high (70 m) UAV altitudes overestimated lengths by 25 cm. The most overestimation they observed, however, was when the drone was at 50 m and they observed an overestimation of 35 cm [41]. Interestingly, they also only observed overestimation instead of underestimation as observed in our study. ...
... Putch (2017) observed a maximum error of 1.14% error when measuring the distances between targets (11.8 m, 14.9 m, and 30.4 m) on a rooftop across 20 m, 30 m, 60 m, and 120 m UAV altitude [48]. It is important to note that these studies differed significantly from our methods by using a 1 m × 0.25 m polystyrene in-frame reference object [41], combining transect survey images into an orthomosaic map to make measurements of land-based targets [47], or used ground control points at known distances apart within the frame to calibrate images [48]. While this significantly reduces the error for measurements, these methods are not often feasible for highly mobile aquatic animals like sharks. ...
Article
Full-text available
Drones are an ecological tool used increasingly in shark research over the past decade. Due to their high-resolution camera and GPS systems, they have been used to estimate the sizes of animals using drone-based photogrammetry. Previous studies have used drone altitude to measure the target size accuracy of objects at the surface; however, target depth and its interaction with altitude have not been studied. We used DJI Mavic 3 video (3960 × 2160 pixel) and images (5280 × 3960 pixel) to measure an autonomous underwater vehicle of known size traveling at six progressively deeper depths to assess how sizing accuracy from a drone at 10 m to 80 m altitude is affected. Drone altitudes below 40 m and target depths below 2 m led to an underestimation of size of 76%. We provide evidence that accounting for the drone’s altitude and the target depth can significantly increase accuracy to 5% underestimation or less. Methods described in this study can be used to measure free-swimming, submerged shark size with accuracy that rivals hand-measuring methods.
... Consequently, traditional aerial surveys have typically categorized dugongs as either "mothercalf pairs" or "solitary individuals" (Hines et al., 2005;Garrigue et al., 2008;Ichikawa et al., 2012;Marshall et al., 2018). Advancements in drone technology have paved the way for swift individual identification and body length estimation in other sirenian species in recent years (Landeo-Yauri et al., 2020Ramos et al., 2022). The body length of dugongs serves as an indicator of their growth stage because they are born, weaned, and reach sexual maturity within distinct body length ranges (Marsh, 1980;Marsh et al., 1984;Kwan, 2002). ...
... The snout coordinates were calculated based on the location and yaw direction of the drone at the time of capture, both of which were extracted from the EXIF metadata of the images. The distance between the image center and snout was scaled based on the flight height, image size (in pixels), camera sensor width, and focal distance of the drone (Ramos et al., 2022). The software MATLAB R2023a (MathWorks Inc., Natick, MA, USA) was used for the analysis. ...
... Examples of rated photographs are provided in Figure 2. The length of the straightline from the tip of the snout to the medial notch of the fluke was measured. The body length of the dugong was scaled using flight altitude data, image size, camera sensor width, and the focal distance of the drones (Ramos et al., 2022). ...
Article
In this study, we describe the population characteristics and residency patterns of dugongs (Dugong dugon) across two intertidal seagrass beds in Talibong Island, Thailand: Site A, covering an area of 2.0 × 105 m2, and Site B, covering an area of 2.8 × 105 m2. Transect and individual identification surveys were conducted under clear water conditions using drones: 16 separate days over 11 months at Site A and 10 separate days over 3 months at Site B. Sixty-four individuals were identified from 180 videography sessions. The results confirmed at least two distinct patterns of seagrass habitat utilization among sites located approximately 5 km apart. Site A was characterized by a lower population density, higher year-round site fidelity, occupancy by relatively large individuals, and an absence of feeding aggregations. In contrast, Site B was characterized by a higher population density, lower site fidelity, occupancy by individuals with a wider range of body lengths, and the presence of feeding aggregations. The average population density at Site B was three to five times higher than that at Site A. Site A had a median nearest neighbor distance of 320 m with no significant bias in its distribution, whereas Site B had a median of 20 m with a significant bias. The mean site fidelity index for Site A (0.62 ± 0.08; n = 16) was significantly higher than that for Site B (0.39 ± 0.14; n = 10). Dugongs at Site A might have monopolized this site to some extent, while those at Site B might have benefited from increased opportunities for social interaction provided by aggregations. These findings highlight the importance of fine-scale monitoring of feeding ground utilization by dugongs, taking into consideration individual-specific details such as body lengths and resighting rates for a better understanding of their spatial distribution.
... m. manatus). Applications of UAVs in these studies have included monitoring the occurrence and behaviors of individuals (Hodgson et al., 2013;Ramos et al., 2018;Infantes et al., 2020;Landeo-Yauri et al., 2021), identifying individuals , determining body size and condition of individuals Ramos et al., 2022), and estimating abundance (Edwards et al., 2021). However, these studies have primarily been conducted in clear, shallow waters. ...
... To date, only two previous studies have been conducted using UAVs to detect a sirenian species, the Antillean manatee, in captivity Ramos et al., 2022). The goals of these studies were to assess the effect of UAV flights on the behavior of captive manatees and to evaluate manatee body size and condition for indicators of overall health (Ramos et al., 2022). ...
... To date, only two previous studies have been conducted using UAVs to detect a sirenian species, the Antillean manatee, in captivity Ramos et al., 2022). The goals of these studies were to assess the effect of UAV flights on the behavior of captive manatees and to evaluate manatee body size and condition for indicators of overall health (Ramos et al., 2022). Using the results of this study, and adapting the survey effort accordingly, researchers could explore the use of UAVs to passively monitor the health and behaviors of animals being rehabilitated to be released back into the wild. ...
Article
Detection of many threatened aquatic mammals, such as manatees (Trichechus spp.), using traditional visual observation methods is associated with high uncertainty due to their low surfacing times, cryptic behaviors, and the environmental heterogeneity of their habitats. Rapid advancements in technology provide an opportunity to address these challenges. In this study, we aimed to quantify survey effort of unoccupied aerial vehicles (UAVs) for detecting the Vulnerable Amazonian manatee (T. inunguis). Using a closed population of manatees that is being rehabilitated within a lake at the Rainforest Awareness, Rescue, and Education Center in Iquitos, Peru, we calculated the number of repeat surveys needed to detect at least one individual with 95% (n = 3.10) and 99% (n = 4.76) confidence. We used both generalized linear mixed-effect models and Bayesian single-species and single-season detection models to determine the effects of the environment (water depth, water transparency, cloud cover, wind speed), time of day, and behavior (breathing, foraging, milling) on the time-to-detection and detection probability, respectively. Both models indicated a significant interaction between water depth and water transparency, causing an increase in the time-to-detection (β = 0.032; 95% CI = 0.028, 0.037) and a decrease in the probability of detecting manatees (α = -0.65; 95% CI = -1.3, -0.007), which was calculated to be 0.62 (95% CI = 0.23, 0.94). Due to the similarities between the lake and in situ habitats, the results of this study could be used to design in situ UAV survey protocols for Amazonian manatees or other difficult-to-detect freshwater aquatic mammals and to monitor ex situ animals pre-and post-release, which should ultimately contribute to a better understanding of their spatial ecology and facilitate data-driven conservation efforts.
... The use of unmanned aerial vehicle (UAV) systems is emerging as a promising approach for the non-invasive study of volitional marine animal behavior and biometrics (Gray et al., 2019a;Hodgson et al., 2013;Ramos et al., 2022;Torres and Bierlich, 2020;Torres et al., 2022). Aerial imagery can be used to compute biometrics such as length, body condition, tailbeat frequency, and relative velocities, which can provide key information about animal health (Bierlich et al., 2024), swimming kinematics (Porter et al., 2020), and predator-prey interactions (Hansen et al., 2022). ...
... Ultimately, the quality of the drone aerial imagery has a significant effect on the accuracy of detection and segmentation for any marine and terrestrial species (Ramos et al., 2022). ...
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The recent widespread adoption of drones for studying marine animals provides opportunities for deriving biological information from aerial imagery. The large scale of imagery data acquired from drones is well suited for machine learning (ML) analysis. Development of ML models for analyzing marine animal aerial imagery has followed the classical paradigm of training, testing, and deploying a new model for each dataset, requiring significant time, human effort, and ML expertise. We introduce Frame Level ALIgment and tRacking (FLAIR), which leverages the video understanding of Segment Anything Model 2 (SAM2) and the vision-language capabilities of Contrastive Language-Image Pre-training (CLIP). FLAIR takes a drone video as input and outputs segmentation masks of the species of interest across the video. Notably, FLAIR leverages a zero-shot approach, eliminating the need for labeled data, training a new model, or fine-tuning an existing model to generalize to other species. With a dataset of 18,000 drone images of Pacific nurse sharks, we trained state-of-the-art object detection models to compare against FLAIR. We show that FLAIR massively outperforms these object detectors and performs competitively against two human-in-the-loop methods for prompting SAM2, achieving a Dice score of 0.81. FLAIR readily generalizes to other shark species without additional human effort and can be combined with novel heuristics to automatically extract relevant information including length and tailbeat frequency. FLAIR has significant potential to accelerate aerial imagery analysis workflows, requiring markedly less human effort and expertise than traditional machine learning workflows, while achieving superior accuracy. By reducing the effort required for aerial imagery analysis, FLAIR allows scientists to spend more time interpreting results and deriving insights about marine ecosystems.
... It encompasses the use of both RGB and satellite spectral images [20,21]. As technological developments rapidly advance the versatility and functionality of affordable devices, their potential as a marine aerial survey tool has garnered attention for monitoring aquatic creatures such as humpback whales [22], river dolphins [23], and various manatee species [24,25], among others [26]. For this purpose, machine learning models based on deep convolutional neural networks (DCNNs) have enabled the automatic detection of UAV imagery, mostly only using RGB channels with deep convolutional neural networks (DCNNs). ...
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This study introduces a novel, drone-based approach for the detection and classification of Greater Caribbean Manatees (Trichechus manatus manatus) in the Panama Canal Basin by integrating advanced deep learning techniques. Leveraging the high-performance YOLOv8 model augmented with Sliced Aided Hyper Inferencing (SAHI) for improved small-object detection, our system accurately identifies individual manatees, mother–calf pairs, and group formations across a challenging aquatic environment. Additionally, the use of AltCLIP for zero-shot classification enables robust demographic analysis without extensive labeled data, enhancing model adaptability in data-scarce scenarios. For this study, more than 57,000 UAV images were acquired from multiple drone flights covering diverse regions of Gatun Lake and its surroundings. In cross-validation experiments, the detection model achieved precision levels as high as 93% and mean average precision (mAP) values exceeding 90% under ideal conditions. However, testing on unseen data revealed a lower recall, highlighting challenges in detecting manatees under variable altitudes and adverse lighting conditions. Furthermore, the integrated zero-shot classification approach demonstrated a robust top-2 accuracy close to 90%, effectively categorizing manatee demographic groupings despite overlapping visual features. This work presents a deep learning framework integrated with UAV technology, offering a scalable, non-invasive solution for real-time wildlife monitoring. By enabling precise detection and classification, it lays the foundation for enhanced habitat assessments and more effective conservation planning in similar tropical wetland ecosystems.
... In that regard, 3D photogrammetry and motion capture (MoCap) are providing new opportunities. 3D digital photogrammetry has provided a mechanism for generating intricate digital models of diverse objects (Dixit et al. 2019;Ramos et al. 2022), including living creatures of various sizes, from small frogs to large great whales (Irschick et al. 2020(Irschick et al. , 2022Brown 2022). MoCap, with its ability to capture movements and behaviors with lifelike authenticity (e.g., Stavrakis et al. 2012;Mathis et al. 2020), has been used for recording imperceptible movements of animals (Roy et al. 2011;Marshall et al. 2021) including small reptilian creatures (Kwon, Kim, and Lee 2018;Zong et al. 2018). ...
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The study of animals’ activity and behavior in the wild is an extremely challenging task. Although tri‐axial accelerometers are invaluable for behavioral analyses, their use is more frequent in large charismatic endotherms with limited application in ectotherms. The scarce utilization of this methodology on small‐size reptiles is focused on animals’ activity and energetics, showing few records of rapid displays and behavior signals. Here, we present a novel multidisciplinary approach capable of advancing research on reptiles’ behavior. Our proposed approach uses advanced technologies for the digitization, reconstruction and visualization of reptiles and their behavior. We (i) record movement through tri‐axial accelerometers, video cameras, and motion capture systems; (ii) ground‐truth data through the video records; (iii) develop realistically accurate 3D avatars of the recorded movement for visualization purposes, and (iv) archive data on a Behavior Pattern Database. As case studies, we used two small Mediterranean reptiles, the lizard Laudakia cypriaca and the snake Dolichophis jugularis . Through our approach, we successfully recorded, ground‐truthed, and labeled for the first time, several detailed movements and behaviors of the two case study species. We developed an accurate digital overview of those movements using motion capture and 3D animal reconstruction. Finally, we structured a database for archiving all behavioral data and demonstrated how those archives can be used for advancing behavioral research, providing ecological insights into this animal group. Our approach can enhance research on reptiles’ behavior by contributing to the analysis of complex or isolated behaviors, poorly studied, such as signals and social interactions, providing valuable insights and assisting behavioral analysis.
... More recently, drones (unoccupied aircraft systems, UAS, UAV) have revolutionized the ability to obtain aerial photogrammetry data sets on large elusive animals, as they are safer and provide more affordable, accessible, and efficient methods for data collection compared to crewed aircraft (Johnston, 2019). As such, drones serve as a valuable method for obtaining body size measurements on various marine megafauna species (Jech et al., 2020;Piacenza et al., 2022;Ramos, Landeo-Yauri, et al., 2022;Setyawan et al., 2022;Shero et al., 2021), particularly for cetaceans Christiansen et al., 2016Christiansen et al., , 2019Durban et al., 2021;Vivier et al., 2023). For examples, studies using drones detected differences in body length and/or body condition between populations or ecotypes of blue whales (Balaenoptera musculus, B. m. brevicauda; Barlow et al., 2023), killer whales (Orcinus orca; Durban et al., 2021;Kotik et al., 2022), gray whales (Eschrichtius robustus; Bierlich, Kane et al., 2023;L. ...
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Monitoring body length and body condition of individuals helps determine overall population health and assess adaptation to environmental changes. Aerial photogrammetry from drone‐based videos is a valuable method for obtaining body length and body condition measurements of cetaceans. However, the laborious manual processing of drone‐based videos to select frames to measure animals ultimately delays assessment of population health and hinders conservation actions. Here, we apply deep learning methods to expedite the processing of drone‐based videos to improve efficiency of obtaining important morphological measurements of whales. We develop two user‐friendly models to automatically (1) detect and output frames containing whales from drone‐based videos (“DeteX”) and (2) extract body length and body condition measurements from input frames (“XtraX”). We use drone‐based videos of gray whales to compare manual versus automated measurements ( n = 86). Our results show automated methods reduced processing times by one‐ninth, while achieving similar accuracy as manual measurements (mean coefficient of variation <5%). We also demonstrate how these methods are adaptable to other species and identify remaining challenges to help further improve automated measurements in the future. Importantly, these tools greatly speed up obtaining key morphological data while maintaining accuracy, which is critical for effectively monitoring population health.
Article
Although drones are a promising alternative to traditional wildlife monitoring methods, validation efforts are needed to quantify the accuracy of abundance and distribution estimates obtained from using drones. We used drones equipped with high‐resolution Red‐Green‐Blue (RGB) and thermal cameras, coupled with machine learning techniques, to assess the abundance and thermal physiology in northern elephant seals ( Mirounga angustirostris ). Aerial images of 3415 seals and measurements of ambient air temperature, wind speed, and time of day were collected during nighttime and daytime drone flights ( N = 24). Two‐dimensional polygons and surface temperatures of seals were measured from the images. Machine learning algorithms were applied to detect seals in the imagery, and model performance was evaluated. Detection was more accurate using RGB images (machine learning averaged 6.8% lower than human counts) than thermal images (16.6%). However, thermal images were useful for determining that time of day and ambient temperature (but not wind speed or body size) influenced seal external skin temperature. RGB and thermal cameras have different strengths and weaknesses that should be considered when designing research studies. Our study demonstrates that integrating drones, thermal imaging, and machine learning can promote faster, safer, cheaper, less disruptive, and more accurate wildlife monitoring and conservation efforts.
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Techniques for non‐invasive sampling of ecophysiological data in wild animals have been developed in response to challenges associated with studying captive animals or using invasive methods. Of these, drones, also known as Unoccupied Aerial Vehicles (UAVs), and their associated sensors, have emerged as a promising tool in the ecophysiology toolkit. In this review, we synthesise research in a scoping review on the use of drones for studying wildlife ecophysiology using the PRISMA‐SCr checklist and identify where efforts have been focused and where knowledge gaps remain. We use these results to explore current best practices and challenges and provide recommendations for future use. In 136 studies published since 2010, drones aided studies on wild animal body condition and morphometrics, kinematics and biomechanics, bioenergetics, and wildlife health (e.g. microbiomes, endocrinology, and disease) in both aquatic and terrestrial environments. Focal taxa are biased towards marine mammals, particularly cetaceans. While conducted globally, research is primarily led by institutions based in North America, Oceania, and Europe. The use of drones to obtain body condition and morphometric data through standard colour sensors and single camera photogrammetry predominates. Techniques such as video tracking and thermal imaging have also allowed insights into other aspects of wildlife ecophysiology, particularly when combined with external sampling techniques such as biologgers. While most studies have used commercially available multirotor platforms and standard colour sensors, the modification of drones to collect samples, and integration with external sampling techniques, have allowed multidisciplinary studies to integrate a suite of remote sensing methods more fully. We outline how technological advances for drones will play a key role in the delivery of both novel and improved wildlife ecophysiological data. We recommend that researchers prepare for the influx of drone‐assisted advancements in wildlife ecophysiology through multidisciplinary and cross‐institutional collaborations. We describe best practices to diversify across species and environments and use current data sources and technologies for more comprehensive results.
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Body condition is a measure of an animal’s energy reserves relative to its body structure that provides important information about individual- and population-level health. Monitoring the body condition of free-ranging cetaceans has historically been difficult, but in recent years, the unmanned aerial system (UAS, or “drone”) has facilitated noninvasive ways of estimating the cetacean body condition. The Charleston Estuarine System (CES) includes the estuarine and coastal ecosystems surrounding Charleston, South Carolina, and is utilized by Tamanend’s bottlenose dolphins (Tursiops erebennus) throughout the year. The main goals of this study were (1) to test if UASs are suitable for monitoring body condition of dolphins in an estuarine environment, and (2) to determine if site, season, and age class influence the body condition of dolphins in the CES. Land-based UAS surveys were conducted at four sites throughout the CES between September 2022 and May 2023. The body condition of each dolphin was evaluated using images of the individual positioned flat with a straight body at the surface, and a linear mixed effects model was constructed to determine which effects were associated with significant differences in dolphin body condition. After filtering images for quality, 428 images of 174 unique dolphins were included in the final analysis, with repeated body condition estimates of 24 dolphins from multiple seasons. Both season and age class were significant predictors of dolphin body condition, but site was not. In addition, individual dolphins were catalogued in a Drone Dolphin ID database, which allowed some dolphins’ unique body condition changes to be tracked over time. These findings provide an important baseline for dolphin body condition in the CES that can be built upon in future studies to better understand how body condition changes in response to environmental and anthropogenic stressors or for different age classes.
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After near extirpation by nineteenth century whaling, New Zealand's southern right whales (Eubalaena australis) are recovering strongly, calving almost exclusively at the subantarctic Auckland Islands. Right whales are capital breeders; body condition is an important driver of their breeding success. Here we use unmanned aerial vehicles to characterise variation in individual size and shape, and to quantify the size structure of the subset of the population we sampled. Of 108 whales photographically identified we gained a comprehensive set of measurements from 63 individuals, as well as length measurements for 29 calves and six non-calf whales for which the full suite of measurements were not obtainable. Lactating females (n = 32) ranged in length from 11.84 to 15.22 m, apparent non-breeding adults (n = 9) were between 11.96 and 14.92 m, while subadults (n = 28) were between 8.82 and 11.72 m long. Calves were between 5.15 and 7.53 m. Principal component analysis of the measurement data showed that widths (particularly at the positions of 30-80% along total body length) were most influential in PC1 (40.3% variance explained). Measurements of structural features (i.e. head and flukes) related more closely to PC2 (18.2% variance explained) and PC3 (14.8% variance explained). We, therefore, interpret PC2 and PC3 as representing structural size, while PC1 represents body condition. Subadults and non-breeding adults showed more variation in body condition than lactating females, highlighting the need for this demographic to maintain their body condition within a tighter range to meet the high nutritional demands of raising calves.
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Assessing the body condition of wild animals is necessary to monitor the health of the population and is critical to defining a framework for conservation actions. Body condition indices (BCIs) are a non-invasive and relatively simple means to assess the health of individual animals, useful for addressing a wide variety of ecological, behavioral, and management questions. The Antillean manatee ( Trichechus manatus manatus ) is an endangered subspecies of the West Indian manatee, facing a wide variety of threats from mostly human-related origins. Our objective was to define specific BCIs for the subspecies that, coupled with additional health, genetic and demographic information, can be valuable to guide management decisions. Biometric measurements of 380 wild Antillean manatees captured in seven different locations within their range of distribution were obtained. From this information, we developed three BCIs (BCI 1 = UG/SL, BCI 2 = W/SL ³ , BCI 3 = W/(SL*UG ² )). Linear models and two-way ANCOVA tests showed significant differences of the BCIs among sexes and locations. Although our three BCIs are suitable for Antillean manatees, BCI 1 is more practical as it does not require information about weight, which can be a metric logistically difficult to collect under particular circumstances. BCI 1 was significantly different among environments, revealing that the phenotypic plasticity of the subspecies have originated at least two ecotypes—coastal marine and riverine—of Antillean manatees.
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Monitoring the body condition of free-ranging marine mammals at different life-history stages is essential to understand their ecology as they must accumulate sufficient energy reserves for survival and reproduction. However, assessing body condition in free-ranging marine mammals is challenging. We cross-validated two independent approaches to estimate the body condition of humpback whales ( Megaptera novaeangliae ) at two feeding grounds in Canada and Norway: animal-borne tags ( n = 59) and aerial photogrammetry ( n = 55). Whales that had a large length-standardized projected area in overhead images (i.e. whales looked fatter) had lower estimated tissue body density (TBD) (greater lipid stores) from tag data. Linking both measurements in a Bayesian hierarchical model to estimate the true underlying (hidden) tissue body density (uTBD), we found uTBD was lower (−3.5 kg m ⁻³ ) in pregnant females compared to adult males and resting females, while in lactating females it was higher (+6.0 kg m ⁻³ ). Whales were more negatively buoyant (+5.0 kg m ⁻³ ) in Norway than Canada during the early feeding season, possibly owing to a longer migration from breeding areas. While uTBD decreased over the feeding season across life-history traits, whale tissues remained negatively buoyant (1035.3 ± 3.8 kg m ⁻³ ) in the late feeding season. This study adds confidence to the effectiveness of these independent methods to estimate the body condition of free-ranging whales.
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The eastern North Pacific gray whale Eschrichtius robustus experienced an unusual mortality event (UME) in 2019-2020, with 384 whales found dead along the Pacific coasts of Mexico, USA and Canada. A similar UME in 1999-2000 was speculated to have been caused by starvation, but body condition data were not available to test this hypothesis. Between 2017 and 2019, we used unmanned aerial vehicles (drones) and photogrammetry methods to measure the body condition of gray whales in San Ignacio Lagoon, Baja California Sur, Mexico. Body condition was calculated from the residual of the relationship between body volume and length. The body condition of gray whales was significantly lower in 2018 (-11.1%, SE = 1.74, n = 531) and 2019 (-9.7%, SE = 1.76, n = 628) compared to 2017 (n = 59) for all reproductive classes (calves, juveniles, adults and lactating females). Overall, lactating females were in good body condition. The reduction in body condition of whales in 2018-2019 is unlikely to have affected their survival, but could have reduced their reproductive rate by prolonging the post-weaning recovery time. This could explain the low number of mother-calf pairs observed in the San Ignacio Lagoon in 2018 and 2019. For juveniles and adults that arrived in the lagoons with less energy reserves, their reduced body condition may have been close to their survival threshold. This could explain the high proportion of juveniles and adults among the stranded dead whales in 2019-2020. Although the underlying cause of the reduction in gray whale body condition is unknown, starvation likely contributed to the 2019-2020 UME.
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Creating accurate 3D models of marine mammals is valuable for assessment of body condition, computational fluids dynamics models of locomotion, and for education. However, the methods for creating 3D models are not well-developed. We used photography and video to create 3D photogramme-try models of harbor porpoises (Phocoena phocoena). We accessed one live adult female (155.5 cm total length), and two dead animals, one juvenile (110 cm total length) and one calf (88 cm total length). We accessed the two dead individuals through a stranding network in Germany, and the live individual through the Fjord and Baelt research center in Den-mark. For all porpoises, we used still photographs from hand-held cameras, drone video, and synchronized GoPro videos to create 3D photogrammetric models. We used Blender software , and other 3D reconstruction software, to recreate the 3D body meshes, and confirmed the accuracy of each of the 3D body meshes by comparing digital measures on the 3D models to original measures taken on the specimens. We also provide a colored, animated version of the live harbor porpoise for educational purposes. These open-access 3D models can be used to develop methods to study body morphomet-rics and condition, and to study bioenergetics and locomotion costs.
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The use of drones to study marine animals shows promise for the examination of numerous aspects of their ecology, behaviour, health and movement patterns. However, the responses of some marine phyla to the presence of drones varies broadly, as do the general operational protocols used to study them. Inconsistent methodological approaches could lead to difficulties comparing studies and can call into question the repeatability of research. This review draws on current literature and researchers with a wealth of practical experience to outline the idiosyncrasies of studying various marine taxa with drones. We also outline current best practice for drone operation in marine environments based on the literature and our practical experience in the field. The protocols outlined herein will be of use to researchers interested in incorporating drones as a tool into their research on marine animals and will help form consistent approaches for drone-based studies in the future.
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Conservation efforts of the beluga whale (Delphinapterus leucas) of the St. Lawrence estuary include a mortality surveillance program which has the objective of documenting the causes of mortality. The evaluation of the animal's body condition is a key component in the diagnostic process. There is currently no consensual method to measure or calculate body condition indices in beluga whales. Morphological measurements recorded during necropsy were used to design a scaled mass body condition index that was compared to currently used visual evaluation, and to alternative morphological indices. Beluga whales were separated into two size-based groups. The scaled mass index was well correlated with analog-visual-scale derived scores in beluga whale >290 cm, but not in animals <290 cm. Both methods showed almost perfect agreement regarding the categorization of carcasses belonging to the first quartiles. The alternative indices that were best correlated with the scaled mass index were those calculated using the sacral circumference and the ventral adipose thickness in animals <290 cm and the epaxial muscle mass and maximum circumference in beluga whales >290 cm. These scaled indices could provide objective tools to evaluate body condition of stranded beluga whales.