DOI: 10.5061/dryad.z34tmpgb7
title: Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

description: In fishes, swimming performance is considered an important metric to
 measure fitness, dispersal, and migratory abilities. Swimming performance
 of individual larval fishes is often integrated into models to make
 inferences on how environmental parameters affect population-level
 dynamics (e.g., connectivity). However, little information exists
 regarding how experimental protocols affect the swimming performance of
 marine fish larvae. In addition, the technical setups used to measure
 larval fish swimming performance often lack automation and accurate
 control of water quality parameters and flow velocity. In this study, we
 automated the control of multi-lane swimming chambers for small fishes by
 developing an open-source algorithm. This automation allowed us to execute
 repeatable flow scenarios and reduce operator interference and
 inaccuracies in flow velocity typically associated with manual control.
 Furthermore, we made structural modifications to a prior design to reduce
 areas of lower flow velocity. We then validated the flow dynamics of the
 new chambers using computational fluid dynamics and particle tracking
 software. The algorithm provided accurate alignment between set and
 measured flow velocities and we used it to test whether faster critical
 swimming speed (Ucrit) protocols (i.e., shorter time intervals and higher
 velocity increments) would increase Ucrit of early life stages of two
 tropical fish species (4-10 mm standard length). The Ucrit of barramundi
 (Lates calcarifer) and cinnamon anemonefish (Amphiprion melanopus)
 increased linearly with fish length, but in cinnamon anemonefish, Ucrit
 started to decrease upon metamorphosis. Swimming protocols using longer
 time intervals (&gt;2.5 times increase) negatively affected Ucrit in
 cinnamon anemonefish but not in barramundi. These species-specific
 differences in swimming performance highlight the importance of testing
 suitable Ucrit protocols prior to experimentation. Automated control of
 flow velocity will create more accurate and repeatable data on swimming
 performance of larval fishes. Integrating refined measurements into
 individual-based models will support future research on the effects of
 environmental change.
description: Please refer to the original manuscript for details on how the
 data were collected. Regarding the swimming protocol
 data, the ISI Web of Knowledge was searched (Clarivate Analytics, Core
 collection search on 19.02.2019) using the term: ((swim* OR sust* OR
 prolong* OR burst*OR cruis* OR routin* OR Ucrit OR endur*) AND (early life
 stage* OR larv*) AND (marin* OR sea* OR brack*) AND (fish* OR teleost*))).
 The results were manually checked and 36 papers were identified were fish
 were swum in multi-lane swimming chambers. The video
 files show recordings of fluorescent green polyethylene buoyant particles
 (850-1000 µm) inside the multi-lane swimming chambers at 10 and 40 cm
 s<sup>-1</sup>, respectively. The original recordings were
 processed using a Flowtrace algorithm (see original manuscript for further
 details) and inverted using Sony Vegas Pro 13.0 (VEGAS Creative Software).
 A still of the multi-lane swimming chamber, added to the background of the
 videos, allowed the evaluation and tracking of individual particles in
 each raceway. The video of the lower velocity (10 cm
 s<sup>-1</sup>) is provided at the original speed, whereas the
 video of the higher velocity (40 cm s<sup>-1</sup>) is slowed
 down to 0.25x speed.
description: In the Excel file, several sheets present the data that were used
 for the analyses in our study. The sheet
 'Modelled flow velocity' presents the modeled velocities,
 obtained through a computational fluid dynamics software, in the column
 'velocity_modeled', all set velocity values (10 or 40 cm
 s<sup>-1</sup>) in the column 'velocity_set_cm_s'.
 The data are separated by chamber design ('chamb_design') and
 the section at which the velocity was modeled
 ('chamb_section'). In the sheet 'Flow
 control', we present results from testing the alignment of set
 ('FLOWSV.ValueY') versus actually measured (processed)
 velocities ('FLOWPV.ValueY'). The 'Interval' column
 represents the time interval the algorithm waited before the velocity
 increment was increased (by 2 cm s<sup>-1</sup>).
 'Deviation' is the difference between 'FLOWSV.ValueY'
 and 'FLOWPV.ValueY', and represents how well the set and
 measured velocities aligned. 'FLOWSV.Time' and
 'Time_s' stand for the duration of these tests.
 The sheet 'Particle tracking' holds data from the
 experiments where we tracked fluorescent beads. 'Set_Speed_cm_s'
 indicates at what set velocity the flow was measured, 'Lane'
 represents the raceway in which the particles were tracked,
 'Measurement' gives the number of the measured particle (10 per
 raceway), 'Nr_frames' indicates how many frames were used for
 tracking a particle, 'Frame_rate_frames_s' represents the frame
 rate used in the video recording, 'Time_s' is the time that a
 particle took to travel a certain distance ('Distance_cm'),
 'Velocity_cm_s' is the speed of the particle, and
 'Actual_Speed_cm_s' is the speed that the flow meter measured as
 actual speed (see ''FLOWPV.ValueY' above).
 'Actual_Speed_SD' is the standard deviation of the set
 speed's velocity during the measurement. The
 sheet 'Swimming protocols' holds data on critical swimming speed
 (<em>U</em><sub>crit</sub>) protocols that were
 gained through a literature search (see Methods). 'Study_ID'
 refers to the study that was investigated,
 'Speed_Increment_cm_s' is the velocity increase or step height
 measured in cm s<sup>-1</sup>,  sometimes reported as
 'Speed_Increment_BL_s', where BL abbreviates body length.
 'Time_Interval_min' is the step length or duration of each
 measurement in the <em>U</em><sub>crit</sub>
 protocol. '. 'Climatic_region' represents the tested
 fish's regional Fishbase classification, and 'Reference'
 refers to the study's authors. Please note, that many studies did not
 presented speed increments in both cm s<sup>-1</sup> and BL
 s<sup>-1</sup>. In the sheet
 'Swimming trials', we present data collected during experimental
 trials with two tropical fish species, Cinnamon anemonefish
 (<em>Amphiprion melanopus</em>) and barramundi
 (<em>Lates calcarifer</em>). 'ID', 'Date',
 and 'Spec' refer to the individually tested fish, the date of
 the trial and the tested species. 'Age_dph' is the age in days
 post hatch, while 'Increment_cm_s' and 'Interval_min'
 abbreviate the step height and length used in the
 <em>U</em><sub>crit</sub> trial.
 'SL_mm_mean' is the standard length in mm, measured right after
 the swimming trial. 'Time_start', 'Time_stop', and
 'Total_Time' indicate at what time and for how long a fish was
 sum. 'Intervals_passed' is the number of time intervals a fish
 managed to swim at (required for calculating
 <em>U</em><sub>crit</sub>).
 'U_Last_Int_cm_s' and 'Time_Last_Int_s' are the final
 velocity a fish reached during the trial, and the time it spent swimming
 at this last velocity, respectively. These variables were used to
 calculate the critical swimming speed 'Ucrit_cm_s'. The column
 'Notes' holds information of unusual behaviour or other
 occurrences.