metadata

license: cc0-1.0
task_categories:
  - image-classification
tags:
  - butterfly
  - heliconius erato
  - heliconius melpomene
  - full body
  - dorsal
  - RGB
  - bird view
  - butterfly view
  - bird acuity
  - butterfly acuity
  - imbalanced
  - mimicry
  - cv
pretty_name: Curated Gold Standard Cuthill Dataset
size_categories:
  - n<1K

Dataset Card for Curated Gold Standard Cuthill Dataset

Dataset Description

Dorsal full body images of subspecies of Heliconius Erato and Heliconius Melpomene (18 subspecies total). 960 images with 320 specimens, each photographed in RGB with bird and butterfly acuity included (3 images of each specimen). Subset of images processed from Cuthill, et. al. dataset available at doi:10.5061/dryad.2hp1978.

Note: dorsal_images_cuthill contains processed dorsal images from the original Cuthill dataset (all 1,234 specimens).

Homepage:
Repository: Butterfly-mimicry contains research done using this dataset.
Paper:
Leaderboard:
Point of Contact:

Dataset Summary

Supported Tasks and Leaderboards

[More Information Needed]

Languages

English

Dataset Structure

|-- dorsal_images_cuthill   
|		|    
|		|-- 10427965_D_lowres.tif    
|		|    
|		|-- 10427966_D_lowres.tif    
|		|    
|		|	...    
|    
|-- Acuities    
|		|    
|		|-- train_bird    
|		|		|    
|		|		|-- erato_cyrbia    
|		|		|    
|		|		|-- erato_etylus    
|		|		|    
|		|		|	...     
|		|    
|		|-- test_bird    
|		|		|    
|		|		|-- erato_cyrbia    
|		|		|    
|		|		|-- erato_etylus    
|		|		|    
|		|		|	...     
|		|    
|		|-- train_butterfly    
|		|		|    
|		|		|-- erato_cyrbia    
|		|		|    
|		|		|-- erato_etylus    
|		|		|    
|		|		|	...     
|		|    
|		|-- test_butterfly    
|				|    
|				|-- erato_cyrbia    
|				|    
|				|-- erato_etylus     
|				|    
|				|	...     
|    
|-- train    
|		|    
|		|-- erato_cyrbia    
|		|    
|		|-- erato_etylus    
|		|    
|		|	...     
|    
|-- test    
        |     
        |-- erato_cyrbia    
        |    
        |-- erato_etylus    
        |    
        |	...

Data Instances

Type: PNG
Size: 128px x 128px
Background: [210, 210, 210] (gray)
Fit in frame: Most padding is above and below the image, some on the left and right.
Ruler or Scale: None
Color (ColorChecker, white-balance, None): None

Data Fields

In Hoyal_Cuthill_GoldStandard_metadata_cleaned.csv:

NHM_Specimen: Natural History Museum Specimen number
Image_filename: filename of image of specimen
View: whether ventral or dorsal view of specimen (all dorsal)
Species: species of specimen (melpomene or erato)
Subspecies: subspecies of the specimen
Sex: sex of the specimen (male or female)
addit_taxa_info: additional taxonomic information (subspecies)
type_stat: [More Information Needed] 'ST', 'PT', or 'HT', but mostly null
hybrid_stat: hybrid status ('valid subspecies', 'subspecies synonym' or 'unknown' (only 1))
in_reduced: [More Information Needed] 0 or 1 to indicate yes or no
locality: where specimen was collected
lat: latitude where specimen was collected
lon: longitude where specimen was collected
speciesdesig: species designation, first initial of species '.' subspecies (eg., 'm. rosina')

Train_Test_Curated_GoldStandard_Hoyal_Cuthill.csv has three additional columns:

Image_filename_png: filename of (png) image of specimen, dorsal_images_cuthill/ + <Image_filename_png> is the filepath for the processed dorsal image
subset: whether this is part of the training or test set (train or test)
filepath: the filepath for the train or test image

Acuity_Curated_GoldStandard_Hoyal_Cuthill.csv also has Image_filename_png and subset, but subset references the bird and butterfly acuity training and test sets. Additionally, it has columns:

bird_filepath: the filepath for the bird acuity version of the image
butterfly_filepath: the filepath for the butterfly acuity version of the image

Data Splits

There are 250 images in each training set and 70 in each test set.

RGB training images are in train folder and testing are in test.

For bird and butterfly acuities, their respective training and test images are in the train_bird (train_butterfly) and test_bird (test_butterfly) folders.

All of these folders are further subdivided by the subspecies. Filepaths to access these images are provided in Train_Test_Curated_GoldStandard_Hoyal_Cuthill.csv and Acuity_Curated_GoldStandard_Hoyal_Cuthill.csv, respectively.

Dataset Creation

Processing steps included:

Hybrid Separation
Label Correction
Removal of subspecies with no mimic pairs
Make background uniform across all images
Make image square via padding

Curation Rationale

This dataset was curated for training a model to classify different species of Heliconius Butterflies and to take into account mimicry between species and acuity of the observer (bird, butterfly, or human/other). The original data (Cuthill et al 2019) had misclassified species/subspecies and some locality/ collection sites were outside the known range of the butterflies. It also contained hybrid and aberrant samples, that had the potential to muddle classification results. To prevent this, the data was further refined by several Heliconius experts to remove hybrid and aberrant samples. Lastly, bird and butterfly acuities were added to provide another level of analysis.

Source Data

Cuthill, et. al. doi:10.5061/dryad.2hp1978.

Initial Data Collection and Normalization

[More Information Needed] Photographers: Robyn Crowther and Sophie Ledger, Natural History Museum, London.

Who are the source language producers?

[More Information Needed]

Annotations

Annotation process

The original data has some misclassified species/subspecies, and had multiple hybrid samples. These samples were removed by hand by OM, CL, JM, KK. Some localities were outside the known range of the butterflies, and were removed using QGIS and known sub species ranges.

Who are the annotators?

Christopher Lawrence Jim Mallet Owen McMilan Krystof Kozak

Personal and Sensitive Information

None

Considerations for Using the Data

Social Impact of Dataset

N/A

Discussion of Biases

Biased towards species and subspecies within Heliconius. Focused on Heliconius erato and Heliconius melpomene

Other Known Limitations

No genetic data available.
Non-uniform distribution of subspecies (imbalanced).

Additional Information

Dataset Curators

Krzysztof Kozak (University of California Berkeley) - ORCID: 0000-0001-8980-3173
Christopher Lawrence (Princeton University) - ORCID: 0000-0002-3846-5968
James Mallet (Harvard University) - ORCID: 0000-0002-3370-0367
Owen McMillan (Smithsonian Tropical Research Institute) - ORCID: 0000-0003-2805-2745
David Carlyn (The Ohio State University) - ORCID: 0000-0002-8323-0359
Mohannad Elhamod (Virginia Tech) - ORCID: 0000-0002-2383-947X

Licensing Information

[More Information Needed]

Citation Information

Krzysztof Kozak, Christopher Lawrence, James Mallet, Owen McMillan, David Carlyn, Mohannad Elhamod. (2023), "Curated_GoldStandard_Hoyal_Cuthill", https://huggingface.co/datasets/imageomics/Curated_GoldStandard_Hoyal_Cuthill.

Please also cite the original dataset from which this was adapted and its accompanying paper:

Hoyal Cuthill, Jennifer F. et al. (2019), Data from: Deep learning on butterfly phenotypes tests evolution’s oldest mathematical model, Dryad, Dataset, https://doi.org/10.5061/dryad.2hp1978.
Hoyal Cuthill, Jennifer F. et al. (2019), Deep learning on butterfly phenotypes tests evolution’s oldest mathematical model, Science Advances, Article-journal, https://doi.org/10.1126/sciadv.aaw4967

Contributions

The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) Institute program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning).