This repository contains the data and Python script used in the study: Attard et al. (In review) Feasibility of using very high-resolution satellite imagery to monitor Tristan albatrosses Diomedea dabbenena on Gough Island. Endangered Species Research.
The study evaluates the detectability of Tristan Albatrosses in high-resolution WorldView-4 satellite imagery (31 cm resolution) over Gough Island, Tristan da Cunha. The goal is to determine whether satellite imagery can facilitate population monitoring of this critically endangered species during the breeding season.
- Introduction
- Script Overview and Workflow
- Installation
- Usage
- Structure
- Results
- Reusing or Adapting the script
- Acknowledgements
- License
- Funding
The Tristan albatross Diomedea dabbenena is critically endangered, facing threats such as bycatch and predation. Monitoring this species is challenging due to financial constraints and logistical difficulties. Satellite imagery offers a potential solution for cost-effective population monitoring.
This repository includes a Python script that automates the analysis of satellite imagery data to assess the detectability of Tristan albatrosses. It also generates the figures and tables required for the study.
The Python script processes the data and performs the necessary analysis to determine the visibility and detectability of Tristan albatrosses in satellite imagery. It uses the input data from the various folders and generates output plots and tables for further analysis.
Script workflow:
- Loads the necessary data (csv, xlsx, or jpeg files from the data folder).
- Processes the satellite imagery data and field survey nest GPS coordinates.
- Conducts an analysis to assess albatross detectability based on various predictors.
- Generates output plots (figures) and tables, which are saved in the output folder.
To set up the project:
git clone https://github.com/mariergattard/tristan-albatross.git
cd project-namepython -m venv venvpip install -r requirements.txtIf requirements.txt is unavailable, manually install dependencies.
The script is designed to be run in a Jupyter Notebook environment. Follow these steps:
pip install jupyterlabjupyter notebookOpen Tristan_albatross_satellite_image_detection.ipynb in the python_script folder. Ensure all input data is correctly placed in the data folder. Run the cells sequentially to execute the analysis.
The project is designed as follows:
Tristan Albatross Satellite Detection Analysis
│
├── Data
│ │ Input files for the python script.
│ │ Contains satellite image data, nest GPS coordinates, reference and observer annotations.
│ │
│ ├──Gough_island_landscape_features
│ │ Shapefiles for Gough Island coastline, ocean, contours, and mountain peaks.
│ │ Source: Extracted from Digital Terrain Model (DTM) with <10 m resolution.
│ │
│ ├──nest_boundaries
│ │ Shapefiles of Tristan albatross nest boundaries on Gough Island provided by RSPB.
│ │
│ ├──nest_GPS_coordinates
│ │ GPS coordinates of Tristan albatross nests in cloud-free regions of the satellite image.
│ │ Source: RSPB for the 2017/18 breeding season. Hand-held GPS accurate to 10 m.
│ │
│ ├──nesting_bird_information:
│ │ ├──Tristan_albatross_age_sex_data.csv: Minimum age and sex of each nesting bird.
│ │ ├──Tristan_albatross_nest_colony_information.csv:
│ │ Nest ID of active nests in 31 cm orthorectified satellite image from RSPB.
│ │ └──Tristan_albatross_nest_location_data.csv
│ │ Slope (degrees) and aspect data of nests extracted from DTM in ArcGIS Pro.
│ │
│ ├──observer_annotations
│ │ CSV files with raw annotations from 9 observers using VGG Image Annotator (VIA).
│ │
│ ├──reference_annotations
│ │ CSV files & point shapefiles of reference 1 (MRGA) and 2 (PC) annotations.
│ │
│ ├──tile_coordinates_georeference
│ │ CSV file with latitude and longitude of the top-left corner of each tile raster.
│ │ Used to convert tile x, y pixel coordinates into geographical coordinates.
│ │
│ ├──tile_fishnet_grid
│ │ A 100m x 100m fishnet grid and FID to create tiles in ArcGIS Pro.
│ │
│ └──tiles
│ Non-georeferenced satellite image tiles (n=30) in jpeg format. Each measuring 100m x 100m.
│ 30 tiles randomly selected to complete observer annotations.
│ The number at the end of the filename is the FID from tile_fishnet_grid.
│
├── Output
│ │ Collection of files exported using the python script.
│ │
│ └──tile_images
│ This contains two subfolders:
│ 1. tiles_with_raw_observer_labels_not_georeferenced:
│ Tile jpeg images with raw non-georeferenced observer annotations.
│ Symbols: coloured circles represent each unique observer ID.
│ 2. tile_with_observer_nest_labels_georeferenced:
│ Tile jpeg images containing georeferenced observer labels and nest GPS coordinates.
│ Symbols: square = observers; white circle = nest GPS coordinates.
│
├── python_script
│ Processes annotations and assesses detectability of Tristan albatrosses in satellite imagery.
│ Input data from 'data' folder and generates all output files.
│
└── README
Description of github files, acknowledgements, licencing of script and tiles, funding source.
The analysis generates key outputs such as:
Generalised linear model (GLM) results for the influence of minimum age on the detectability of nesting albatrosses. Estimates represent the change in log-odds of detection, with corresponding standard errors, z-values, p-values, and odds ratios (OR) provided for each predictor. Confidence intervals are in square brackets. The odds ratio indicates the change in odds of detection per unit increase in minimum age. Males and Females analysed separately.
Male nesting albatross
Estimate SE z p OR estimate OR SE OR z OR p
----------------------------------------------------------------------------------------------
(Intercept) -1.50 1.21 -1.24 0.22 0.22 0.27 -2.87 0.00
[-3.88, 0.88] [0.02, 2.41]
Minimum age 0.03 0.06 0.42 0.68 0.99 0.07 0.41 0.68
[-0.10, 0.15] [-0.91, 0.16]
----------------------------------------------------------------------------------------------
Female nesting albatross
Estimate SE z p OR estimate OR SE OR z OR p
----------------------------------------------------------------------------------------------
(Intercept) 0.79 1.08 0.73 0.46 2.21 2.40 0.51 0.61
[-1.33, 2.92] [0.26, 18.51]
Minimum age -0.06 0.07 -0.86 0.39 0.94 0.07 -0.89 0.37
[-0.20, 0.08] [0.82, 1.08]
----------------------------------------------------------------------------------------------
Generalised linear models (GLM) testing the effects of incubating parent (sex, minimum age) and nest characteristics (slope and aspect) on detectability of Tristan albatrosses in a 31 cm resolution satellite image (n=52).
Top-ranked GLM models (δAICc ≤ 2)
-------------------------------------------------------------------------------------
Equation AICc δAICc R2 LogLik Weight
Nest visibility ~ Aspect 71.06 0.00 0.00 -33.53 1.00
Nest visibility ~ Minimum age 70.66 0.00 0.01 -33.33 1.00
Nest visibility ~ Sex 67.98 0.00 0.05 -31.99 1.00
Nest visibility ~ Slope 71.08 0.03 0.00 -33.54 0.99
Nest visibility ~ Minimum age + Sex 69.82 1.84 0.05 -31.91 0.40
Nest visibility ~ Aspect + Sex 69.95 1.97 0.05 -31.97 0.37
Nest visibility ~ Slope + Sex 69.95 1.97 0.05 -31.97 0.37
-------------------------------------------------------------------------------------
Conditionally averaged results from top-ranked GLM models (δAICc ≤ 2)
----------------------------------------------------------------------------------------------
Predictor Model-averaged coef SE 95% CI (Lower) 95% CI (Upper) p-value
Interval -0.79 1.03 -2.80 1.22 0.44
Aspect 0.00 0.00 -0.01 0.01 0.86
Slope -0.05 0.62 -1.27 1.16 0.93
Minimum age -0.02 0.05 -0.11 0.07 0.60
Sex (Male:Female) 1.04 0.61 -0.15 2.24 0.09
----------------------------------------------------------------------------------------------
Summary of detection metrics (F-score, precision and recall values) for presumed albatrosses annotated by nine observers relative to (A) gold standard and (B) active nests.
Summary of detection metrics (F-score, precision and recall values) for presumed albatrosses annotated by references and gold standard in orthorectified and non-orthorectified satellite image relative to active nests. The number of nests matched and reference annotations that did not match a nest are included.
----------------------------------------------------------------------------------------------
Image Annotator Precision Recall F1 score GPS nests Nest matched No match Total ref
Ortho ref 1 0.92 0.54 0.68 152 82 7 89
ref 2 0.89 0.70 0.79 152 107 13 120
Gold standard 0.89 0.68 0.77 152 103 13 116
Non-ortho ref 1 0.82 0.55 0.66 152 84 19 103
ref 2 0.82 0.67 0.74 152 102 22 124
gold standard 0.81 0.60 0.69 152 91 22 113
----------------------------------------------------------------------------------------------
Hierarchical clustering of raw observer annotations to create the clustered dataset.
Example of a tile with nests shown in white circles and observer annotations shown in coloured squares. Satellite imagery © 2024 Maxar Technologies.
Example of a tile with spatially clustered data, with the number of observers in agreement stated inside each square. Satellite imagery © 2024 Maxar Technologies.
If you reuse or adapt this script, please cite the associated manuscript:
Marie R. G. Attard, Richard A. Phillips, Steffen Oppel, Ellen Bowler and Peter T. Fretwell (In Review) Feasibility of using very high-resolution satellite imagery to monitor Tristan albatrosses Diomedea dabbenena on Gough Island. Endangered Species Research.
This study is a contribution to the Ecosystems and Wildlife from Space programmes within the British Antarctic Survey’s Polar Science for Planet Earth initiative, funded by the Natural Environment Research Programme. MRGA is funded by Darwin Plus (DPLUS132). We are grateful to the Tristan da Cunha Conservation Department and Island Administrators for granting permission to conduct this research.
We acknowledge the Conservation Data Management Unit at RSPB, particularly Alex Whittle and Antje Steinfurth, for providing digital elevation models and geographic information, as well as RSPB for supplying breeding boundary data for Tristan albatrosses at Gough Island. Special thanks go to the Gough Island field team—Roelf Daling, Vonica Perold, Kim Stevens, Jaimie Cleeland, Kate Lawrence, and Fabrice LeBouard—for their dedication in collecting and sharing the ground count data that informed this study.
We sincerely thank Penny Clarke for her invaluable assistance as a reference annotator, and Cath Attard, Connor Bamford, Marcia Blyth, Hannah Cubaynes, Hana Merchant, Elizabeth Pearmain, Norman Ratcliffe, and Sally Thorpe for their efforts in completing observer annotations. Finally, we thank Maxar technologies for granting permission to publish satellite image tiles and associated annotations derived from their imagery.
The code in this repository is licensed under an open-source license. The satellite images and annotations are subject to the Maxar Satellite Imagery License Agreement: https://www.maxar.com/legal/internal-use-license
Funding was provided by the Darwin Plus (grant ID: DPR9S2\1032). For more details, visit the Darwin Initiative project website: https://www.darwininitiative.org.uk/project/DPLUS132