imageomics/STRI-Samples

Dataset Card for Smithsonian Tropical Research Institute (STRI) Samples

Dataset Summary

Dorsal images of butterfly wings collected by Owen McMillan and members of his lab at the Smithsonian Tropical Research Institute.

Full dataset will be 24,119 RGB images: Dorsal and Ventral images of separated wings. This sample contains 207 dorsal butterfly images used as part of the training data for Imageomics/butterfly_detection_yolo.

Supported Tasks and Leaderboards

Note that this is just a subset of a larger dataset that has yet to be curated. It was used in combination with images from other sources to train the Imageomics/butterfly_detection_yolo model, and is not large or representative enough for use in training on its own yet.

Dataset Structure

/dataset/
    <images>/
        <img_name_no_ext 1>.JPG
        <img_name_no_ext 2>.JPG
        ...
        <img_name_no_ext 207>.JPG
    metadata.csv

Data Instances

• Type: JPG
• Background (color or none): Sometimes gray sometimes white
• Fit in frame: tight
• Ruler or Scale: No
• Color: 5x6 Color checker

Potential for future addition of genetic sequencing data.

There are 11 species represented in this sample of 207. They are primarily from the genus Heliconius, but the following genera are also represented: Junonia, Eueides, Neruda, and Dryas.

The CSV also includes labels regarding the quality of the specimen: damaged, dorsal, or incomplete, which were used for the segmentation model. Below is a species distribution chart for this data colored by quality label.

Data Fields

metadata.csv: minimal data record for the images; this is a subset of all the information potentially available for each image since curation of this dataset is still ongoing. This also means that there are some duplicative columns (e.g., there are multiple NCSU and STRI IDs).

• label: indicates quality of specimen, either damaged, dorsal, or incomplete.
• img_name_no_ext: FileName without the type extension.
• source_url: not actually a URL, but a box location, with the folder.
• source_dataset: All STRI, holdover from combination into larger dataset.
• FileName: filename given to image (with extension, e.g., ".JPG"). Often <NCSU_id>_D.JPG.
• Folder: folder in which images or a record is kept, seems to be date followed by number; part of the "source_url".
• Box: Box in which specimen was kept ("Box 11" or "Box 10").
• Genus: genus of the specimen; primarily "Heliconius", but also "Junonia", "Eueides", "Neruda", or "Dryas". Labeled for all images.
• species: species of the specimen; 11 unique species, but mostly "erato" and "melpomene". Labeled for all but six of the images.
• subspecies: subspecies of the specimen if provided, or parent subspecies if hybrid. Labeled for 168 images.
• subspecies II: second parent subspecies of the specimen if it is a hybrid (there are 16 with the label "hybrid"). Labeled for 70 images.
• Subfamily: subfamily of the specimen (only labeled for 18 images, all "Heliconiinae").
• id uncertain: indicates uncertainty in the taxonomic identity of the specimen? -- 11 images, but there is another image with a question mark in the subspecies name.
• sex: sex of the specimen ("male" or "female", one instance of "?", most labeled).

Columns maintained for future clean-up and recombination

• MULTIPLE IDS -- keep for alignment and standardization later

• NCSU_id, ID from NCSU? Did all values have this or is it just NCSU prefix?

• NCSU_num (previously NCSU #) --relation to NCSU ID and STRI ID?

• stri_id, --relation to NCSU id?

• STRI ID, -- relation to other versions above?

• Other ID,-- relation to other versions above?

• Date Collected: date specimen was collected? Seem to be mostly DD-MM-YY, but not consistent.

• Collector: person who collected the specimen?

• Taxonomic ID: --- only labeled for 18 images, what is this? Seems to be scientific name: "Genus species (ssp x ssp II)" or "Genus species (hybrid)". Remove or do same for the remaining images?

• Sample type: "Wild" or "Stocks", only labeled for 18 images.

• Owner of Sample: -- only labeled for 18 images, mostly "BLUM - STRI", but also two "MCMILLAN - STRI", corresponds to Collector for BLUM, but not for MCMILLAN.

Data Splits

All of these sample images were used in training the Imageomics/butterfly_detection_yolo model.

Dataset Creation

Curation Rationale

These images were selected and labeled to use in training the Imageomics/butterfly_detection_yolo model. The larger dataset is still undergoing curation.

Source Data

Images are of specimens collected by the Smithsonian Tropical Research Institute and photographs of this subset were taken by Daniel Romero, Carlos Arias, and other members of the Owen McMillan Lab at the Smithsonian Tropical Research Institute Gamboa Station.

Data Collection and Processing

[More Information Needed]

Photographs of the wings were taken using an Olympus OM-D EM-1 digital camera with an Olympus Zuiko Digital ED 60 mm f/2.8 macro lens.

Who are the source data producers?

The dataset is a collection of images taken of the McMillan Lab's collection of butterfly samples obtained from field collection surveys and several raised in captivity for genetic and other studies.

Annotations

There are several annotations in this data that are not standard and are very specific. Further annotation is needed. In general, taxonomic information down to the species and subspecies name is provided but is not always correct and needs double checking at this moment.

Annotation process

Damage annotations were completed by Michelle Ramirez for training the Imageomics/butterfly_detection_yolo model she created.

Who are the annotators?

Annotation data (other than the damage labels) was provided by the McMillan Lab.

Personal and Sensitive Information

[More Information Needed]

Considerations for Using the Data

Bias, Risks, and Limitations

This is a small sample of minimally curated butterfly images intended only for wing segmentation and damage detection. It is not intended for species classification.

Recommendations

This is not a complete dataset, nor is it curated for greater use. The purpose of this dataset is to provide the 207 image sample used as part of a larger training set for the Imageomics/butterfly_detection_yolo model. More information on the full project can be found in the GitHub repository.

Recommended use is only for segmentation.

Additional Information

Dataset Curators

• Christopher Lawrence (Princeton University) - ORCID: 0000-0002-3846-5968
• Owen McMillan (Smithsonian Tropical Research Institute) - ORCID: 0000-0003-2805-2745
• Daniel Romero (Smithsonian Tropical Research Institute)
• Carlos Arias (Smithsonian Tropical Research Institute) - ORCID: 0000-0002-1546-5156

Licensing Information

CC BY

Citation Information

Christopher Lawrence, Owen McMillan, Daniel Romero, Carlos Arias. (2024). Smithsonian Tropical Research Institute (STRI) Samples. Hugging Face. https://huggingface.co/datasets/imageomics/STRI-Samples.

Acknowledgements

This work was supported by US National Science Foundation (NSF) grant IOS 2110532, with additional support from the Imageomics Institute, which is funded by the NSF's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.