Data: Tentacle prey capture in cuttlefish
Data files
Mar 18, 2026 version files 345.52 KB
-
Data_Analysis___Visualization.zip
334.10 KB
-
README.md
11.43 KB
Abstract
Cuttlefish extend soft tentacles to capture evasive prey. High-speed imaging of tentacle prey capture in two cuttlefish species reveals kinematically discrete, biphasic tentacle extension. A prolonged reach phase, often extending distances greater than their mantle length, is followed by a close-range, rapid attack phase. The reach phase duration is orders of magnitude longer and more variable than the attack phase duration. Attack phase speeds vary minimally, such that attack duration is determined by prey distance. Biphasic strikes integrate slow and stealthy prey tracking during the variable reach phase, followed by a less variable, close-range, fast attack phase. The attack phase is so brief that it is likely shorter than response latencies of many prey, but it is so brief that it may be limited to open-loop control. Comparisons among animals using soft, extensible predatory mechanisms reveal that cuttlefish biphasic tentacle strikes rival both distances and speeds of iconic vertebrate ballistic tongues.
Dataset DOI: 10.5061/dryad.gf1vhhn1t
Description of the data and file structure
This dataset supports a study of the prey capture of two species of cuttlefish (Cephalopoda: Coleoidea: Sepiidae), Ascarosepion bandense (Lupše et al., 2023; Rochebrune, 1884) (formerly Sepia bandensis, Adam, 1939) and Ascarosepion pfefferi (Lupše et al., 2023; Rochebrune, 1884) (formerly Metasepia pfefferi, Hoyle, 1885). Using high-speed video footage (1000–4000 fps), we recorded and analyzed tentacle extension during feeding events in small tanks. The dataset includes kinematic measurements (e.g., velocity, acceleration, and timing of prey capture phases), morphological measurements extracted from video (e.g., mantle and body length), and comparative data on soft-tissue prey capture kinematics from other taxa.
Experimental trials were conducted at Duke University. Cuttlefish were acclimated and filmed in tanks with a 1 mm grid. We tracked tentacle kinematics and morphological information using ImageJ. All data processing/analysis/visualization was completed using R.
In addition to species-specific kinematics, the dataset contains a curated comparative dataset from the literature, detailing strike velocities, accelerations, appendage extensions, and body lengths in other animals with soft, extensible prey-capture structures (e.g., frogs, salamanders, chameleons, cone snails, other cephalopods).
Files and variables
File: Data_Analysis___Visualization.zip
Description: This dataset includes high-speed prey capture kinematic data, processed and raw tracking files, metadata, statistical analysis scripts, and comparative data from other taxa. Files are organized into structured folders and clearly annotated data sheets.
Note: Throughout data analysis process, there was a shift in terminology regarding the phases reported in the manuscript but this change was not made in the raw data files.
Slow phase --> Reach phase
Fast phase --> Attack phase
Intermediate phase --> Prey capture phase
Recoil phase --> Retraction phase
📁 trials/
Description:
Contains positional tracking files (CSV format) exported from MTrackJ in ImageJ. Each file corresponds to a single prey capture event and includes tentacle ("lead") and body ("eye") tracking. "lead" is short form for leading tentacle or the tentacle closest to the prey item. "eye" was the feature tracked to assess full body movement of cuttlefish.
Key Variables:
track.id: Tracked point identity (lead,eye)raw.id: Tracked frame number output from ImageJpixels.x,pixels.y: X and Y coordinates (pixels)frame.id: True frame number from videophase: reflects the phase of tentacle movement
📁 mdfs/
Description:
Contains MTrackJ .mdf annotation files corresponding to each trial video. These files enable point-by-point verification of tracking data.
Note: .mdf files and original videos are not hosted on Dryad but are available upon request from S. Patek snp2@duke.edu.
📁 Supplemental Results/
Contents:
uncertaintyCoords.csv: Assesses pixel-level resolution and human digitization error.
📄 **velocity_acceleration_analysis.R **
- Computes displacement, velocity, and acceleration from tracked XY coordinates in
trials/. - Performs loess smoothing, peak extraction, and alignment to peak velocity.
- Produces downsampled and interpolated velocity/acceleration traces.
- Inputs:
cuttlefish_metasheet.csv
- Outputs:
cuttlefish_metasheet_final.csv(metadata with added columns of kinematic variables)
📄 visualization_and_stats.R
- Produces all figures and statistics from the manuscript.
- Inputs:
cuttlefish_metasheet.csvandcuttlefish_comparative_dataset.csv - Output visualizations:
- Reach vs. attack phase CVs
- Reach vs. attack duration
- Regression plots (attack distance vs. velocity, duration, extension)
- Comparative plots across taxa (velocity, acceleration, extension vs. body length)
📄 cuttlefish_metasheet.csv
Description:
Primary metadata sheet linking video trials to animal ID, species, experimental frame annotations, calculated durations, distances, and kinematic metrics.
Key Variables:
File_me: Trial/video filenameFail_success: prey capture success or failureView: Camera orientation with respect to cuttlefishSpecies: Species nameSex: If known is denoted, if blank animal was not sexedIndividual_id: Animal identifierprey.item: Food item placed in tanks for prey-capture trialsresolution: Camera resolutionshutter.speed: Camera shutter speedpix_per_mm: Pixel-to-mm conversion taken in ImageJpix_per_mm: Pixel-to-mm scalingFrames_per_second..HZ.: Frame rate of videobody_length_mm_from_video,mantle_length_mm_from_video: Measured from videoslow_phase_start_frame,fast_phase_start_frame,intermediate_phase_start_frame,recoil_phase_start_frame,recoil_phase_end_frame: Frame of video at onset or end of phase taken from ImageJpoint_on_prey_where_tentacle_hits: Location at which leading tentacle contacts preydistance_from_prey_slow_phase_mm,distance_from_prey_fast_phase_mm: Distance to prey at onset of reach phase and attack phaseslow_tentacle_extension_mm: Length of tentacle extension at onset of attack phase or end of reach phaseframe_full_extension: Frame in video in which cuttlefish reaches maximal tentacle extension taken in ImageJfull_tentacle_extension_mm: Length of maximum tentacle extensionaverage_body_length_mm,average_mantle_length_mm: Individual averagesmax_velocity_m.s,max_accel_m.s: Peak values computed from smoothed displacement fromvelocity_acceleration_analysis.Rcodeslow_phase_duration_s,fast_phase_duration_s,intermediate_phase_duration_s,recoil_phase_duration_s: Durations (s): Reach, attack, intermediate, recoil
📄 cuttlefish_comparative_dataset.csv
Description:
Literature-derived dataset of strike parameters in other taxa with soft, extensible appendages.
Key Variables:
Full citation: citation of publication containing informationPublication year: publication yearTopic: Organism categoryDOI: DOI of citationSpecies name listed in cited publication (not updated to current taxonomic uses)Frame Rate (Hz): frame rate of filming device used when collecting videosMax max speed (m/s): maximum of maximum recorded speeds in cited publicationAverage max speed (m/s): average of maximum recorded speeds in cited publicationFinal velocity data (m/s): data used in the figureMax or average velocity: states whether max or average velocity in "final velocity data" column was from average or maximum speedsMax max acceleration (m/^2): maximum of maximum recorded accelerations in citation publicationAverage max acceleration (m/s^2): average of max recorded accelerations in cited publicationFinal acceleration data (m/s^2): data used in figureMax or average acceleration: states whether max or average acceleration in "final acceleration data" column was from average or maximum accelerationsMax max appendage extension (mm): maximum of maximum recorded extension in citation publicationAverage max appendage extension (mm): average of max recorded extensions in cited publicationFinal appendage extension data (mm): data used in figureMax or average extension: states whether max or average extension in "final extension data" column was from average or maximum extensionsType of body measurement: where on the body the body measurement was taken: mantle, snout vent length (SVL), shell lengthMethod of SVL or BL average: how this length was calculatedSVL or BL average (mm): averageSVL or BL (mm) reported in paperSupplementary info: additional notes about previous columnsNotes: additional notes about previous columnsTaxon,Species: Animal group and speciesSVL.BL.average: Standard body length (mm)Final.velocity.data: Max or average velocity (m/s)Final.acceleration.data: Max or average acceleration (m/s2)Final.appendage.extension.data..mm.: Appendage extension (mm)Strike_Duration: Phase duration (s)Topic: Functional group (e.g., "cephalopod", "salamander")Max.or.average.velocity, etc.: Indicates whether values are maxima or averages
Notes on Missing Values
- Blank cells or
NAare used consistently across files to indicate missing measurements. - Reasons include tracking failure (e.g., occlusion or poor visibility) or inapplicability (e.g., certain metrics not recorded for some individuals).
Code/software
Software Required
All data processing and figure generation were performed using R (version 4.1.0 or higher), a free and open-source statistical computing language. To replicate the full workflow, users will need to install the following R packages:
Required R Packages
tidyversedplyrggplot2stringrviridislme4lmerTestggpubrmultcompcarMuMIntidyr
These packages are loaded within the scripts using library() and automatically installed if missing using install.packages().
File Relationships and Workflow
Step 1: Kinematic Extraction
Script: velocity_acceleration_analysis.R
Input:
trials/folder (raw tracked.csvfiles from MTrackJ)cuttlefish_metasheet.csv(metadata for each trial)
Output:
cuttlefish_metasheet_final.csv: Augmented metadata with max velocity and acceleration- Smoothed, body-corrected XY displacement data
- Aligned kinematic time series for velocity and acceleration
- Optional trial-level CSVs with aligned and interpolated data
Step 2: Figure Generation and Statistics
Script: visualization_and_stats.R
Input:
cuttlefish_metasheet.csvcuttlefish_comparative_dataset.csv
Output:
- All figures used in the publication (e.g., CV plots, reach vs. attack, inter-species comparisons)
- Summary statistics tables by individual and species
- Linear mixed model outputs for intra-species comparisons
- Wilcoxon tests for reach vs. attack variability
- Figures saved in
.pdfformat
Data Format Compatibility
- Tracking Data: All tracking files are in standard
.csvformat and readable by any spreadsheet or data analysis software. - Supplementary Files: The digitization precision file is in
.csvformat and readable by any spreadsheet or data analysis software. - Scripts: All R scripts are plain
.Rfiles and can be executed in any R console or IDE (e.g., RStudio).
Additional Notes
-
Video annotations used for generating tracking files were created with ImageJ (v1.54g) and the MTrackJ plugin (v1.5.1). While the
.mdftracking files are not hosted on Dryad, they are available upon request and can be viewed in ImageJ with MTrackJ. -
All scripts are thoroughly commented, and users are encouraged to contact Melody Young (mwy9@duke.edu) or S. Patek snp2@duke.edu with questions about code execution or data organization.