README.md

metadata

language:
  - en
pretty_name: Beetlepalooza Dataset
task_categories:
  - image-classification
  - image-segmentation
tags:
  - biology
  - image
  - animals
  - CV
  - beetles
  - elytra
  - elytra width
  - elytra length
  - size
size_categories:
  - n<1K
  - 10K<n<100K
configs:
  - config_name: group_images
    data_files:
      - BeetleMeasurements.csv
      - group_images/*.jpg
  - config_name: individual_images
    data_files:
      - individual_metadata.csv
      - individual_images/*.jpg

Dataset Card for Beetlepalooza Dataset

Dataset Details

Dataset Description

• Curated by: list curators (authors for data citation, moved up)
• Homepage:
• Repository: [related project repo]
• Paper:

[More Information Needed]

Supported Tasks and Leaderboards

[More Information Needed]

Dataset Structure

In group_images we have 577 images of multiple beetles in a reasonably regular pattern (see sample image below). Each of these images contains a centimeter-based scalebar and a barcode representing the sample (collection of beetles in the image). Each row in BeetleMeasurements.csv corresponds to a measurement of the elytra (length or width) of an individual beetle.

The individual_images directory contains images of each individual segmented from the group images. These connect back to their group image based on the individualID.

/dataset/
    group_images/
        <pictureID 1>.jpg
        <pictureID 2>.jpg
        ...
        <pictureID 577>.pg
    individual_images/
        <individualID 1>.jpg
        <individualID 2>.jpg
        ...
        <individualID n>.jpg
    BeetleMeasurements.csv
    individual_metadata.csv

Data Instances

[More Information Needed]

Data Fields

[More Information Needed]

BeetleMeasurements.csv:

• PictureID: Name of the image (<sample-barcode>.jpg, though sometimes it's <NEON_sampleID_>.jpg). Unique identifier for the 577 group images, not for dataset. There are 11,104 individual beetles?
• scalebar: Pixel coordinates of the ruler/scalebar in the image.
• scale_dist_pix: Integer. The length in pixels of the scalebar.
• individual: Integer. The beetle in the image to whom the measurements refer. Awaiting confirmation of how they are counted.
• structure: Whether the measurement applies to the length or width of the elytra (ElytraLength or ElytraWidth, respectively).
• lyingstraight: Whether or not the beetle is "straight" in the image (Yes or No). Further guidance on this term's meaning would be helpful.
• coords_pix: Pixel coordinates of the line marking the length or width of the elytra (green or purple --confirm which is which). Note that the lines are more than one pixel wide, which is why these coordinates form a rectangle.
• dist_pix: Float. The length or width of the elytra (indicated by structure) as measured in pixels.
• dist_cm: Float. The length or width of the elytra (indicated by structure) as measured in centimeters using the scalebar (the red line in the reference image denotes the pixel count for 1cm).
• scientificName: Scientific name of the specimen (<Genus> <species>). There are 85 different species among 36 genera. The 17 individuals in PictureID MOAB_001.S.20180724.jpg are missing the scientific name label.
• NEON_sampleID_ : NEON identifier for the sample (576 unique IDs), prefixed by the plotID.
• siteID: String. Identifier for the site from which the specimens were collected. There 30 different site IDs.
• field_site_name: Name of site from which the specimens were collected. There are 43 different field site names. -- These lack consistency, and will be updated using the site codes.
• plotID: Identifier for the plot from which the specimens were collected (<siteID>_<plot number>). There are 144 different plots from which specimens were collected.
• user_name: Name of person inputting the information? (<first><Last>) or just their username in the system? Only 3 of them. --looks like username
• workflow_id: Integer identifier for the workflow used...?? There are 5.
• genus: Genus of the individual (generated by taking the first word in the scientificName).
• individualID: Unique identifier for the beetles (based on the assumed uniqueness of the PictureID), generated from PictureID (minus the .jpg) plus _<individual>. There are 11,104 individuals photographed and annotated.
• file_name: Relative path to image from the root of the directory (<group_images>/<pictureID>.jpg); allows for image to be displayed in the dataset viewer alongside its associated metadata.

*TODO: Make metadata file for viewer once we have segmented images too: individual_metadata.csv:

• individualID: ID of beetle in the individual image (matches individualID in BeetleMeasurements.csv). This is a unique identifier for this CSV.
• pictureID: Name of the group image (<sample-barcode>.jpg, though sometimes it's <NEON_sampleID_>.jpg). Unique identifier for the 577 group images, not for dataset. (Matches pictureID in BeetleMeasurements.csv.)
• scientificName: Scientific name of the specimen (<Genus> <species>). There are 85 different species among 36 genera.
• elytraLength: Length of the elytra in centimeters. Indicated by the green line in the image below.
• elytraWidth: Width of the elytra in centimeters. Indicated by the purple line in the image below.
• file_name: Relative path to image from the root of the directory (<individual_images>/<individualID>.jpg); allows for image to be displayed in the dataset viewer alongside its associated metadata.

Figure #. Sample image of beetles with green and purple lines to indicate the measurement used for the elytra length and width, respectively.

Data Splits

[More Information Needed]

Dataset Creation

Curation Rationale

[More Information Needed]

This dataset was curated for use at BeetlePalooza 2024 to help drive scientific discovery through machine learning and computer vision.

Source Data

The specimens come from NEON sites, as indicated in the BeetleMeasurements CSV. They were identified by domain scientists (beetle experts) based on physical examination. Each sample consists of a single species. For more information about general NEON data, please see their Ground beetles sampled from pitfall traps page.

Isa Fluck photographed the beetles in each sample in 2022, using <fill in camera info>.

Data Collection and Processing

[More Information Needed]

Who are the source data producers?

[More Information Needed]

Annotations

Annotations (elytra length and width) were completed in Zooniverse by Isa Fluck and two summer REU students (Riley Wolcheski and Isha Chinniah); annotator is indicated by their NEON system usernames in the BeetleMeasurements CSV. The annotations were repeated for a subset of the images to measure observation error introduced in the annotation process. Taxonomic labels were provided by NEON with the samples.

Annotation process

[More Information Needed]

Who are the annotators?

[More Information Needed]

Personal and Sensitive Information

[More Information Needed]

Considerations for Using the Data

[More Information Needed]

Bias, Risks, and Limitations

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Recommendations

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Licensing Information

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Citation

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BibTeX:

Acknowledgements

The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle. This material uses specimens and/or samples collected as part of the NEON Program. Additionally, this material is based upon work supported by the National Science Foundation under Award No. 2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning), and under Award Numbers 2301322 and 2242803 and the USDA National Institute of Food and Agriculture, Hatch Project Number ME0-22425 through the Maine Agricultural and Forest Experiment Station. 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.

Glossary

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Dataset Card Authors

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Dataset Card Contact

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