Schürholz, Daniel; Chennu, Arjun (2022): Dense and taxonomically detailed habitat maps of coral reef benthos machine-generated from underwater hyperspectral transects in Curaçao [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.946315
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Abstract:
This dataset contains 248 benthic habitat maps, that were created from 31 underwater hyperspectral images captured with the HyperDiver device in 8 reef sites across the western coastline of Curacao (see https://doi.org/10.3390/data5010019 for information on the acquisition of the transects). The maps were produced by 8 combinations of two semantic labelspaces (detailed and reefgroups), two machine learning classifiers (patched and segmented), and two spectral signals (radiance and reflectance). Maps in the detailed labelspace have each pixel assigned to one of 43 labels, which are taxonomic labels at family, genus and species levels for biotic components of the reef (corals, sponges, macroalgae, etc.), as well as substrate labels (sediment, cyanobacterial mats, turf algae) and survey material labels (transect tape, reference board, etc.). The set of maps in the reefgroups labelspace cluster the labels in the detailed labelspace into 11 classes that describe reef functional groups (i.e. corals, sponges, algae, etc.). All habitat maps were produced with high accuracy (Fbeta 87%), by two different machine learning methods: a random forest ensemble classifier (segmented method) and a deep learning neural network classifier (patched method). The maps are further divided by the signal type from the hyperspectral image that was used, either radiance or reflectance (the latter was calculated with a reference board located at the beginning and end of each transect). These benthic habitat maps can be used to obtain accurate descriptions of the benthic community and habitat structure of coral reef sites in Curacao. The dataset also contains: an assessment of the accuracy and data efficiency of the machine learning methods, a consistency assessment of the mapped regions, a comparison of habitat metrics (class coverage, biodiversity indices, composition and configuration) between habitat maps produced by each method, and an effort-vs-error analysis of sparse sampling techniques on the densely classified maps.
Keyword(s):
Supplement to:
Schürholz, Daniel; Chennu, Arjun (2022): Digitizing the coral reef: Machine learning of underwater spectral images enables dense taxonomic mapping of benthic habitats. Methods in Ecology and Evolution, 2041-210X.14029, https://doi.org/10.1111/2041-210X.14029
Related to:
Chennu, Arjun; Färber, Paul; De'ath, Glenn; de Beer, Dirk; Fabricius, Katharina Elisabeth (2017): A diver-operated hyperspectral imaging and topographic surveying system for automated mapping of benthic habitats. Scientific Reports, 7(1), 19, https://doi.org/10.1038/s41598-017-07337-y
Chennu, Arjun; Rashid, Ahmad Rafiuddin; den Haan, Joost; de Beer, Dirk (2020): Taxonomically annotated underwater hyperspectral and color images of coral reef transects from Curaçao. PANGAEA, https://doi.org/10.1594/PANGAEA.911300
Rashid, Ahmad Rafiuddin; Chennu, Arjun (2020): A Trillion Coral Reef Colors: Deeply Annotated Underwater Hyperspectral Images for Automated Classification and Habitat Mapping. Data, 5(1), 19, https://doi.org/10.3390/data5010019
Project(s):
Funding:
Coverage:
Median Latitude: 12.147903 * Median Longitude: -68.964690 * South-bound Latitude: 12.042249 * West-bound Longitude: -69.158931 * North-bound Latitude: 12.375344 * East-bound Longitude: -68.745104
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Comment:
The files for the habitat maps are in the form: habitat_maps_dataset/habitat_maps/transects/transect_<num>/habitat_map_<labelspace>_<spectrum>_<method>.<ext>
where the parameters can have the following values:
num: 005, 006, 019, 024, 026, 028, 031, 043, 044, 046, 054, 080, 081, 082, 084, 085, 086, 090, 091, 095, 097, 102, 107, 114, 118, 125, 129, 130, 132, 134, 141
labelspace: detailed, reefgroups
spectrum: radiance, reflectance
method: patched, segmented
ext: nc or jpg
For each transect, the following files are available:
habitat_map_<labelspace>_<spectrum>_<method>.nc in netCDF4 format: contains the habitat map data for the given combination of semantic labelspace, signal type (or spectrum) and machine learning method used. The map data contains a 2D (Y, X) dataarray classmap which has an integer in each position. The integers are a code for each class. To decode the class integers into the class labels, a lookup table for each labelspace is provided in the attributes 'label' and 'label_id' of the data array for each class map.
habitat_map_<labelspace>_<spectrum>_<method>.jpg: an image file that visualizes the habitat map with a corresponding color for each class.
Parameter(s):
# | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
---|---|---|---|---|---|---|
1 | Binary Object | Binary | Schürholz, Daniel | |||
2 | Binary Object (Media Type) | Binary (Type) | Schürholz, Daniel | |||
3 | Binary Object (File Size) | Binary (Size) | Bytes | Schürholz, Daniel | ||
4 | File content | Content | Schürholz, Daniel |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
12 data points