Brightness cues affect gap negotiation behaviour in zebra finches

Borsier, Emma 1 ; Taylor, Graham1

Research facility: University of Oxford

Published Apr 09, 2024 on Dryad. https://doi.org/10.5061/dryad.t1g1jwt9c

Data files

Apr 09, 2024 version files 52.92 MB

cropped_frames_for_analysis.zip

52.88 MB
morphotype_classification_data.csv

33.65 KB
README.md

7.45 KB

Abstract

Flying animals have had to evolve robust and effective guidance strategies for dealing with habitat clutter. Birds and insects use optic flow cues to sense and avoid obstacles, but orchid bees have also been shown to use brightness cues during gap negotiation. Brightness cues might therefore be of general importance in structuring visually guided flight. To test the hypothesis that brightness cues affect gap negotiation behaviours in birds, we presented captive zebra finches Taeniopygia guttata with a symmetric or asymmetric background brightness distribution on the other side of a tunnel. The background brightness conditions influenced both the birds’ decision to enter the tunnel aperture, and their flight direction upon exit. Zebra finches were more likely to initiate flight through the tunnel if they could see a bright background through it; they were also more likely to fly to the bright side upon exiting. We found no evidence of the centring response that would be expected if optic flow cues were balanced bilaterally during gap negotiation. Instead, the birds entered the tunnel by targeting a clearance of approximately one wing length from its near edge. Brightness cues therefore affect how zebra finches structure their flight when negotiating gaps in enclosed environments.

This repository contains:

Rmarkdown.Rmd and Rmarkdown.html: R markdown containing the analysis (including the code, results and figures) of the tabular data obtained from the analysis of the flight video data (raw_data.csv is supplied in the Supplementary Material).
morphotype_classification_data.csv. CSV file compiling the results of the classification of the birds into 20 distinct morphotypes, which contains 6 columns and 422 rows (421 data rows + 1 header row). See below for an description of the rows and columns contents.
morphotype data visualisation.ipynb: Jupyter Notebook containing the data visualisations by morphotype (corresponds to Figures 3, S3 and S4).
barplots_CI_tables.xlsx: An Excel file containing two sheets to compute the Agresti-Coull confidence intervals for the proportions of left vs right sides of origins and arrivals which are used in Rmarkdown.Rmd to generate Figure 1C,D. See below for a description of contents.
Cropped frames for analysis.zip: Archive file containing all the cropped images (in JPEG format) from the video recording frames used as part of the data analysis (to measure the point of entry φ and assessing the birds' morphotypes). See below for a description of contents.

morphotype_classification_data.csv

Read below for a description of the contents of morphotype_classification_data.csv:

Rows

Each row corresponds to one instance of a bird flying through the tunnel from the interior aviary, as observed by the experimenter and recorded with 2 video cameras (ZCAM E2).
Only the instances which were included in the data analysis are included in this file. These can be found in Cropped frames for analysis.zip

Columns:

Filename (text): Name of the image file of the frame obtained from a recording of Camera 2 (placed below the tunnel) associated to a given flight which was analysed to assess the morphotype of the bird.
Datetime (numerical): the date and time of recording for each flight in the format YYYYMMDDHHMMSS
Session (numerical): number associated to the video camera's metadata and file naming (automatically incremented by the camera for each new recording).
Minute (numerical): time (in minutes passed since the start of recording) when a bird was observed crossing the tunnel by the experimenter.
**Category **(categorical): Category corresponding to the brightness condition as seen by looking through the tunnel, with letters as names so that the research technician who conducted the morphotype classification was blind to the conditions.
Can take four values:
- A for "Bright to the left": A blackout curtain is placed on the right, while the left side is bright.
- B for "Bright to the right": A blackout curtain is placed on the left, while the right side is bright.
- C for "Bright": There is no blackout curtain on either side. Both sides are bright.
- D for "Dark": A blackout curtain is placed on the right and on the left. Both sides are dark.
Morph (categorical): Category indicating the bird's morphotype as assessed using the video frames. Can take 20 values: 1, ...,19 for the 1st to 19th identified morphotypes, or undetermined for instances when the morphotype could not be visually determined.

barplots_CI_tables.xlsx

barplots_CI_tables contains 2 Excel sheets:

The first sheet computes the lower and upper bounds of confidence intervals for the proportions of left vs right Arrivals for the four brightness conditions
The second sheet computes the lower and upper bounds of confidence intervals for the proportions of left vs right Origins for the four brightness conditions

For each of these, there are 13 columns:

Treatment: the four brightness conditions
Arrival/Origin: left or right
Sample size: all flights counted for the given brightness condition (sum of left, right, and ambiguous counts).
# successes: number of flights counted in the Arrival/Origin side
proportion: proportion of flights to/from the given side (= # successes/Sample size)
Frequency: proportion as a percentage (=proportion*100)
alpha: level of significance (set to 0.05)
zcrit: critical z-score (= NORM.S.INV(1–alpha))
p*: Using the Agresti-Coull method, p* is defined as:
$$ p* = frac{np + z_{crit}^2/2}{n+z_{crit}^2} $$
lower: lower bound of the 95% CI, defined as:
$$ p* - z_{crit} \sqrt{\frac{p*(1-p*)}{n+z_{crit}^2}} $$
upper: upper bound of the 95% CI, defined as:
$$ p* + z_{crit} \sqrt{\frac{p*(1-p*)}{n+z_{crit}^2}} $$
Freq_lower: lower as a percentage (=lower*100)
Freq_upper: upper as a percentage (=upper*100)

cropped frames for analysis.zip

Read below for a description of contents and the folder hierarchy of this archive file:

The archive file contains four subfolders, each corresponding to one of the background brightness conditions ("Bright to the left", "Bright to the right", "Bright", "Dark"). Each of these contain subfolders, one for each day of data collection (named in the date format YYYY_MM_DD), which themselves contain the cropped images from the corresponding date and background brightness condition.
- A for "Bright to the left" (a blackout curtain is placed on the right, while the left side is bright). Contains the following subfolders:
  - 2021_05_07: Contains 7 images.
  - 2021_05_10: Contains 3 images.
  - 2021_05_11: Contains 14 images.
  - 2021_05_13: Contains 8 images.
  - 2021_05_14: Contains 18 images.
  - 2021_05_17: Contains 45 images.
  - 2021_05_20: Contains 10 images.
- B for "Bright to the right" (a blackout curtain is placed on the left, while the right side is bright). Contains the following subfolders:
  - 2021_05_07: Contains 19 images.
  - 2021_05_10: Contains 8 images.
  - 2021_05_11: Contains 10 images.
  - 2021_05_13: Contains 30 images.
  - 2021_05_14: Contains 16 images.
  - 2021_05_17: Contains 15 images.
  - 2021_05_20: Contains 11 images.
- C for "Bright" (there is no blackout curtain on either side, both sides are bright). Contains the following subfolders:
  - 2021_05_12: Contains 67 images.
  - 2021_05_18: Contains 52 images.
- D for "Dark" (a blackout curtain is placed on the right and on the left, both sides are dark). Contains the following subfolders:
  - 2021_05_06: Contains 33 images.
  - 2021_05_07: Contains 13 images.
  - 2021_05_19: Contains 42 images.
Each .jpg image is named after the camera filenaming system, where for instance the image named B006C0002_20210507120753_0017_t1.214.Still005.jpg is from Camera B, Session006, Reel 0002, Recording Date 20210507(YYYYMMDD), Recording Start Time 12:07:53, Recording Minute 0017 , Timestamp t1 (for the 1st instance of a bird flying through the tunnel within this minute), Frame 214 (indicates the last frame before the bird's bill is obscured from view), Still 005 (this is arbitrary, refers to the image output by Adobe Premiere).