Credits

Robert Turnbull, Emily Fitzgerald, Karen Thompson, and Jo Birch from The University of Melbourne.

The paper describing the pipeline available in BioScience:

Turnbull, Robert, Emily Fitzgerald, Karen Thompson, and Joanne L. Birch. “Hespi: a Pipeline for Automatically Detecting Information from Herbarium Specimen Sheets.” BioScience (2025). DOI: 10.1093/biosci/biaf042.

You can also find the preprint of the paper on arXiv: arXiv:2410.08740.

Here is the BibTeX entry for the paper:

@article{hespi,
    title = {Hespi: a pipeline for automatically detecting information from herbarium specimen sheets},
    author = {Turnbull, Robert and Fitzgerald, Emily and Thompson, Karen and Birch, Joanne L.},
    year = {2025},
    journal = {BioScience},
    doi = {10.1093/biosci/biaf042}
}

This research was supported by The University of Melbourne’s Research Computing Services and the Petascale Campus Initiative. The authors thank collaborators Niels Klazenga, Heroen Verbruggen, Nunzio Knerr, Noel Faux, Simon Mutch, Babak Shaban, Andrew Drinnan, Michael Bayly and Hannah Turnbull.

Plant reference data obtained from the Australian National Species List (auNSL), as of March 2024, using the:

• Australian Plant Name Index (APNI)

• Australian Bryophyte Name Index (AusMoss)

• Australian Fungi Name Index (AFNI)

• Australian Lichen Name Index (ALNI)

• Australian Algae Name Index (AANI)

and the World Flora Online Taxonomic Backbone v.2023.12, accessed 13 June 2024.

This pipeline depends on YOLOv8, torchapp, Microsoft’s TrOCR.

Logo derived from artwork by ka reemov.

BibTeX

@article{hespi,
    title = {Hespi: a pipeline for automatically detecting information from herbarium specimen sheets},
    author = {Turnbull, Robert and Fitzgerald, Emily and Thompson, Karen and Birch, Joanne L.},
    year = {2025},
    journal = {BioScience},
    doi = {10.1093/biosci/biaf042}
}

@article{thompson2023_identification,
    author = {Thompson, Karen M. and Turnbull, Robert and Fitzgerald, Emily and Birch, Joanne L.},
    title = {{Identification of Herbarium Specimen Sheet Components From High-resolution Images using Deep Learning}},
    journal = {Ecology and Evolution},
    volume = {13},
    number = {8},
    pages = {e10395},
    doi = {https://doi.org/10.1002/ece3.10395},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.10395},
    note = {e10395 ECE-2023-05-00833.R1},
    year = {2023}
}

@misc{sheet_component_data,
    author = {Karen Thompson and Robert Turnbull and Emily Fitzgerald},
    title = {{Data available for `Identification of herbarium specimen sheet components from high-resolution images using deep learning': Annotations for selected MELU specimen sheet digital images}},
    year = {2023},
    month = {7},
    url = {https://melbourne.figshare.com/articles/dataset/_strong_Data_available_for_Identification_of_herbarium_specimen_sheet_components_from_high-resolution_images_using_deep_learning_Annotations_for_selected_MELU_specimen_sheet_digital_images_strong_/23597013},
    doi = {10.26188/23597013.v2}
}

This list of references is also available by using the following command:

hespi-tools bibtex