annaviklund/massid45-specimens

MassID45 Individual Specimens

MassID45 is a multi-modal dataset comprised of DNA barcodes (COI) and images at two resolutions: of complete bulk insect samples and of the full set of individual specimens from those samples. In this repository, you will find images and metadata for 35,586 individual specimens.

The data for individual specimens is available on BOLD under recordset code DS-LPEPA22. This HuggingFace dataset makes images easier to access in bulk.

Further information about the MassID45 dataset is available in the pre-print A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level. Code for preprocessing and training/inference is available at GitHub.

Dataset structure

Images

The images directory contains specimen photographs organized in two resolutions. Images are further organized in sub folders based on bulk sample ids (see column fieldid in metadata/records.csv).

• images/originals: High-resolution images of individual specimens
• images/thumbnails: Lower-resolution thumbnail versions of the same specimens

File path format: images/[resolution]/[fieldid]/[processid].jpg

File path example: images/originals/G1P4N6/LPUAE001-22.jpg

Metadata

The metadata directory contains two CSV files with record and image information frmo BOLD. The metadata was collected using BOLD APIs and is unmodified.

• metadata/records.csv: Detailed metadata for individual specimens
• metadata/images.csv: Image-specific metadata for the same specimens

Dataset access

To clone this repository, use the following command:

git clone https://huggingface.co/datasets/annaviklund/massid45-specimens/

To exclude large files when cloning, use the following command:

GIT_LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/datasets/annaviklund/massid45-specimens/

Direct image access

File path format: https://huggingface.co/datasets/annaviklund/massid45-specimens/resolve/main/images/[resolution]/[fieldid]/[processid].jpg

File path example: https://huggingface.co/datasets/annaviklund/massid45-specimens/resolve/main/images/originals/G1P4N6/LPUAE001-22.jpg