DOI: 10.5061/dryad.000000087
title: Nesting chinstrap penguins accrue large quantities of sleep through seconds-long microsleeps

description: Microsleeps, the seconds-long interruptions of wakefulness by eye closure
 and sleep-related brain activity, are dangerous when driving and might be
 too short to provide the restorative functions of sleep. If microsleeps
 fulfill sleep functions, then animals faced with a continuous need for
 vigilance might resort to this sleep strategy. We investigated
 electroencephalographically-defined sleep in wild chinstrap penguins at
 sea and while nesting in Antarctica constantly exposed to an egg predator
 and aggression from other penguins. The penguins nodded off &gt;10,000
 times per day, engaging in bouts of bihemispheric and unihemispheric
 slow-wave sleep lasting on average only 4 s, but resulting in the
 accumulation of over 11 h of sleep for each hemisphere. The investment in
 microsleeps by successfully breeding penguins suggests that the benefits
 of sleep can accrue incrementally. This repository contains raw
 electrophysiological data (Electroencephalography and electromygraphy)
 with identified accelerometry, ambiant temperature and depth. We also add
 the different ethograms and Slow waves sleep episod detected for each
 cerebral hemisphere.
description: See the associated code repository and manuscript for additional
 information on the methods for data collection and processing.
description: The electrophysiology data could be opened on any scientific
 software that could opened interlaced 16bits binary data.
 The video could be run with any videoplayer.
 the CSV and xls file could be opened with adapted
 software our .exp file could be opened with a text
 editor like notepad++ The sleep event are provided in a
 mat file which could be opened in matlab (Mathworks) 
 The analysis pipeline was writen in matlab R2020 (associated with
 signal processing and image processing toolbox and chronux, http://chronux.org/).
 Our scripts are provided with our exptoolbox build to read and process
 easily our data.
description: Nesting chinstrap penguins accrue large quantities of sleep via
 seconds-long microsleeps This dataset containts all the
 electrophysiological data (4 EEG, 1 EMG) with accelerometry, video,
 behavioral scoring, GPS, depth, weather data and any metadata related to
 the experiment. The dataset was collected in December 2019 on Barton
 Peninsula (62°14.30 S, 58°46.50 W), King George Island, Antarctica on
 Chinstrap penguins (Pygoscelis antarctica). We investigated
 electroencephalographically-defined sleep in wild chinstrap penguins at
 sea and while nesting in Antarctica constantly exposed to an egg predator
 and aggression from other penguins. The data show that the penguins nodded
 off &gt;10,000 times per day, engaging in bouts of bihemispheric and
 unihemispheric slow-wave sleep lasting on average only 4 s, but resulting
 in the accumulation of over 11 h of sleep for each hemisphere. The
 investment in microsleeps by successfully breeding penguins, suggests that
 the benefits of sleep can accrue incrementally. This repository contains
 the data and code for our paper: Libourel P.-A.; Lee W. Y.; Achin I.;
 Chung H.; Kim J.; Massot B.; Rattenborg N.C., Nesting chinstrap penguins
 accrue large quantities of sleep throught seconds-long microsleeps.
 Methods description and detailled results are available in the article
 supplementary materials. To run the script the filename file and folder
 organisation should be keep as it. Description of the data and file
 structure ## Additional Information (folder) ### nest_distance (foder) the
 csv table with GPS data for each individual (W#) are stored in the
 W#_gps.csv Column descriptions: Date_Time - Date & time (format:
 'YYYY-MM-DD HH:MM:SS') UTC for penguin GPS location
 Decimal_Longitude - Decimal degree for longitude of penguin GPS point
 Decimal_Latitude -Decimal degree for latitude of penguin GPS point POINT_X
 - X coordinate value for penguin GPS point in Antarctic Polar
 Stereographic projection EPSG:3031 POINT_Y - X coordinate value for
 penguin GPS point in Antarctic Polar Stereographic projection EPSG:3031
 distance_from_nest - Shortest distance from nest to penguin GPS point
 inferred from Haversine formula Script to use : ImportLocationTimesXls.m
 ### individual information chinstrap sleep project All Data.xlsx this file
 contains all individual information collected for experimental and control
 birds Empty cell mean that no data are available for that particular
 condition (animal not recaptured, not weigthed, information not collected
 ...) Column descriptions: id - Animal number W# for xperimental birds and
 C# for control birds capture time - date and Time in local time (UTC-3),
 format dd/mm/yyy hh:mm:ss for a single event, yyyy/mm/dd hh:mm:ss AM/PM -
 hh:mm:ss AM/PM for long event (start - end time) sex - sex weight at
 capture (kg) - weight at capture in kg release time - release date and
 time format: dd/mm/yyyy hh:mm:ss (UTC-3) recapture time - recapture date
 and time format: dd/mm/yyyy hh:mm:ss (UTC-3) weight at recapture (kg) -
 weight at recapture in kg recapture site - recapture site , could be :
 coast / nest during incubation / standing next to the nest distance from
 the colony boundary (m) - nest distance from the colony boundary (m) bill
 length (mm) - bill length (mm) bill depth (mm) - bill depth (mm) RFID
 number - RFID number breeding success (no. of chicks) - breeding success
 (nb. of chicks) Nest Hill position - Nest position related to the hill.
 Could be: Shore/ Up to the hill / down to the hill EEG Reference - EEG
 reference position and whether or not the screw was going through the
 skull, on the cranial suture or not. The cell precide the localisation of
 the reference electrodes EMG - EMG type, could wires cut at the tip or
 wires with 1mm of the wire exposed. On one animal there is a doubt if the
 electrodes are in the muscles (writen muscle ??) EEG Signal Quality - EEG
 Signal Quality based on visual observations EMG Signal Quality - EMG
 Signal Quality based on visual observations sleep logger recording start
 date - Sleep Logger starting date and time in local time (UTC -3)
 Theorical recording end date - Sleep Logger theorical ending date and time
 in local time (UTC -3) recording end date - Real end recording date and
 time in local time (UTC -3) Nb Bin Files - Number of 24 hour files
 recorded by the sleep logger EEG Signal Quality - Global visual
 appreciation of the EEG signal quality EMG Signal Quality - Global visual
 appreciation of the EMG signal quality Script to use :
 ImportCaptureAndReleaseTimeXls.m ### Temperature depth recording Offset
 and drift correction Chinstrap_tdr_offset_ephy.xlsx this file contains
 time events from referenced from the electrophysiological data and the
 corresponding event (offset in sec) from the tdr file this is used to
 evaluate the drift and offset between electrophysiological data and
 temperature depth recording recording (TDR). Each line is an event found
 in both files type. Column descriptions Animal - Animal number W# Time
 (min) - Time elasped in min from the first sample recorded corresponding
 to the event offset (s) - offset in sec on the TDR file for the same event
 Script to use: ImportTDRCsv.m ### Behavioral and video information model
 chinstrap location.xlsx : This file contains date and time for direct
 behavioral observations and video recordings Empty cell mean that no data
 are available for that particular condition (no video for that particular
 time) Column descriptions. Animal ID - Animal number W# date - date and
 Time in local time (UTC-3), format dd/mm/yyyy hh:mm:ss for a single event,
 yyyy/mm/dd hh:mm:ss AM/PM - hh:mm:ss AM/PM for long event (start - end
 time) State - direct observation : 0 = not seen at the nest, 1 =
 incubating, 2 = standing near the nest, 3 = observed near the shore, 4 =
 start to dive into the sea, 5 = arrive at the seashore Video - 1 if a
 video is available at that time Script to use: ImportLocationTimesXls.m
 ### Weather information The wind speed and ambiant temperature in the
 colony during the experiment could be obtain here:
 https://kpdc.kopri.re.kr/live-data/weather ## Raw Data all individual raw
 data are stored in a folder named with the animal ID W#, which contains
 one folder tdr containing temperatiure depth recording data and on data
 folder with video and electrophysiology data - ### temperature depth
 recording (tdr) this folder contains a CSV file tabuated file with the
 temperature (°C), and depth (m), recorded from a logger fixed at the leg
 of the birds. W#_TD.csv Empty cell mean that no data are available for
 that particular condition (Temperatures are often missing because the
 sampling rates are different between temperature and depth) Column
 descriptions. Date_Time - date and Time in (local time UTC -3), format
 yyyy-mm-dd hh:mm:ss Temperature - ambiant temperatue at the leg level in
 °C recorded every minutes Depth - Depth recorded in meters from the
 surface recorded every second Depth_Filt - Depth recording filtered in
 meters Script to use: ImportTDRCsv.m ### ***data*** this folder contains:
 * Header files ('.exp' files which are xml coded: `W#.exp` &
 `W5_Activity-Inactivity.Exp`) * raw electrophysiological data (`bin`
 folder) * land/sea scoring (folder `Hypno_W#`) * behavioral activity
 scoring (folder `Hypno_W#_Activity-Inactivity`) * Video (`video` folder) *
 Sleep events (`W#_SWS_Events 2-12.mat`) #### ***Header files*** the two
 exp files W#.exp & W#_Activity-Inactivity.expare xml files. they
 contain the following information fields descriptions Animal/Name Animal
 ID W# Animal/Acquisition/SamplingRate : the acquisition sampling rate in
 Hz for all the bin files Animal/Acquisition/NbChan : number of channel in
 the bin files Animal/Acquisition/AcquisitionType : type of encoding
 Animal/Acquisition/HeaderOffset : number of bytes before in the header
 before the data (ususally 0) Animal/Acquisition/Files/File/FileName : list
 of the bin files related to the each indivual recording
 Animal/Acquisition/Files/File/TStart : absolute time start format:
 yyyy-mm-ddThh:mm:ss:fff (fff are the 3 digit of the milliseconds)
 Animal/Acquisition/Files/File/Duration : file duration in seconds
 Animal/Acquisition/Channels/Channel/Id : channel number
 Animal/Acquisition/Channels/Channel/Name : channel name, AL: EEG
 Hyperpallium anterior Left; AR: EEG Hyperpallium anterior right: PL: EEG
 Hyperpallium posterior left; PR: EEG Hyperpallium posterior right
 Animal/Acquisition/Channels/Channel/Offset : channel offset in the unit of
 the channel Animal/Acquisition/Channels/Channel/Gain : channel Gain
 Animal/Acquisition/Channels/Channel/AcquisitionRangeMax : channel range in
 the unit of the channel Animal/Videos/Video/Files/File/FileName : list of
 the video files related to the each indivual recording
 Animal/Videos/Video/Files/File/TStart : absolute time start format:
 yyyy-mm-ddThh:mm:ss:fff (fff are the 3 digit of the milliseconds)
 Animal/Videos/Video/Files/File/Duration : video file duration in seconds
 Animal/Videos/Video/Files/File/SamplingRate : video sampling rate (frames
 per second) Animal/Hypnogram/Files/File/FileName : file name of the .H
 file which contains scorig states, the file a coded in uint16 sampled at
 1Hz Animal/Hypnogram/Files/File/TStart :absolute time start format:
 yyyy-mm-ddThh:mm:ss:fff (fff are the 3 digit of the milliseconds)
 Animal/Hypnogram/Files/File/Duration : file duration in seconds
 Animal/Hypnogram/SamplingRate duration : of each epoch scored, this is not
 realted to the sampling in the file which is always 1 Hz
 Animal/Hypnogram/Statuses : States definition of .H files
 Animal/Hypnogram/Statuses/Status/Level : value coded in the H file
 Animal/Hypnogram/Statuses/Status/Label : Label of the corresponding state
 Animal/Hypnogram/Statuses/Status/Key : Key used to score
 Animal/Hypnogram/Statuses/Status/Color : Color used for the corresponding
 state, coded in decimale see function dec2ARGB.m Script to use: loadEXP.m
 this script can open the '.exp' file into matlab #### ***bin***
 Bin File description This folder contain all the binary files
 ('.bin') corresponding to each individual recording They contain
 the EEG, EMG, and accelerometry data the files are named with their
 starting date time coded as follow: PREFIX_yyyy-mm-dd_hh-mm-ss-fff.bin the
 binary file are interlaced 16 bit files, they could be uint16 or int16 see
 corresponding exp file. the number of channels is also indicated in th
 eexp file. Each sample is coded on 16bits and the absolute value could be
 obtain with the gain, offset and range specified in the exp file the
 function ADC2Real.m script could be used to convert them. Script to use:
 ReadChanBinFile.m / ADC2Real.m #### ***Hypno_W#*** Folder description This
 folder contain one .H file per electrophysiological binary file. We coded
 whether the animal is on land or at sea based. these files where used as a
 reference to later score automatically the activity and inactivity state
 they are nammed with their respective absolute starting time the H file
 are uint16 coded with one channel sampled at 1Hz. the H file contained
 three state code 0 for undeterminded, 15 when the animal is on land, 75
 when the animal is at sea. #### ***Hypno_W#_Activity-Inactivity*** H file
 description This folder contain one .H file per electrophysiological
 binary file. they are nammed with their respective absolute starting time
 the H file are uint16 coded with one channel sampled at 1Hz. These files
 contain the animal location and behavior. This ethogram was obtained from
 accelerometry data and depth recording. They contain the following states:
 0 for undeterminded, 10 On land Active Lying Down 15 On land Inactive
 Lying Down 40 On land Active Standing 45 On land Inactive Standing 70 At
 Sea Active at the surface 71 At sea Active UnderWater 75 At sea Inactive
 at the surface 76 At sea Inactive UnderWater #### ***video*** folder
 description This folder contain all the Videos related to an individual
 recording they are encoded in MPEG4 with the avi container #### ***Sleep
 events*** the matlab file `W#_SWS_Events 2-12.mat` contain the sleep event
 detected from the clustering algorythm presented in our related article.
 these event were detected from the instant power inthe 2-12 Hz spectral
 band, in the left and right hemisphere File description BandLimDen - 1x2
 double matrix containing the limit of the denominator used for the sleep
 event detection could be empty if no deniminator was used BandLimNum - 1x2
 double matrix containing the limit of the numerator used for the sleep
 event detection usually [2 12], which correspond to the 2-12Hz frequency
 band used for sleep detection in our article. Data - Sleep event
 Settings.Chan 1x2 double matrix containing the channels number (from the
 exp file) used for the left and right hemispheres is the value, there is
 two value if a differential measurement is used (this is not the case in
 this dataset) Event.Deb 1xn double matrix with the begining of all events
 coded in seconds since the first sample of the first binary file listed in
 the exp file recorded. Event.End 1xn double matrix with the ending of all
 events coded in seconds since the first sample of the first binary file
 listed in the exp file recorded. Event.Type 1xn double matrix containing
 the hemisphere in which the event was detected 0 left hemisphere, 1 right
 hemisphere Sharing Information This is a section for linking to other ways
 to access the data, and for linking to sources the data is derived from,
 if any. Links to other publicly accessible locations of the data:
 Code/Software The analysis pipeline was writen in matlab R2020 (associated
 with signal processing and image processing toolbox and chronux,
 http://chronux.org/)). Our scripts are provided with our exptoolbox build
 to read and process easily our data.