This contains the entire list of all datasets I care about RE [[[230529-1413 Plants datasets taxonomy]]] for 230507-2308 230507-1623 Plants paper notes

• GBIF

  • Search
  • Seems to be a central place for all similar and not-similar datasets with a centralized API

• Pl@ntNet

  • FULL dataset: Pl@ntNet observations
    • 
    • https://www.gbif.org/occurrence/search?dataset_key=7a3679ef-5582-4aaa-81f0-8c2545cafc81
    • Contains num of species and yet another exploring thing:World flora: Species - Pl@ntNet identify
  • datamanager @ data
    • Not sure what this is but sounds interesting, maybe connected to downloading their stuff
    • 
  • OpenReview review of their paper: Pl@ntNet-300K: a plant image dataset with high label ambiguity and a long-tailed distribution | OpenReview

• https://flora-on.pt/

  • portuguese-only?

  • Flora-On: Flora de Portugal Interactiva. (2023). Sociedade Portuguesa de Botânica. www.flora-on.pt. Consulta efectuada em 29-5-2023.

  • Used in <@herediaLargeScalePlantClassification2017 (2017) z/d>

• iNaturalist-xxx

  • Has 2017-2018-… variants
    • iNaturalist 2018 Benchmark (Image Classification) | Papers With Code
  • train/val plants numbers in the paper, test sets unclear and needs to be downloaded to calculate
    • consensus (kaggle, paperswithcode etc.) seems to be train/val use for all of them
  • Competitions
    • All: visipedia/inat_comp: iNaturalist competition details
    • 2017:
      • (seems to be the coolest/most_used dataset)
      • Plantae, Insecta,Aves,Reptilia,Mammalia,Fungi,Amphibia,Mollusca,Animalia,Arachnida,Actinopterygii,Chromista
        • rows: supercategory (animalia, etc.), per-image attribution and license, GBIF (id, link, ..), others
        • Sample rows from dataset: iNat competition GBIF info - Google Sheets
      • <@vanhornINaturalistSpeciesClassification2018 (2018) z/d>
    • Added the rest to the spreadsheet, 2019 is the only one with missing per-category things

• INaturalist

  • Website is mirrored in GBIF
  • You can filter stuff in the website and get numbers, GBIF has a viewer that also can do things but not list of species
  • ‘research grade’ are the good observations: Help · iNaturalist
  • SPECIES!=IDENTIFIER! The latter seems to contain also families etc.
  • “iNaturalist Research-grade Observations”
    • On GBIF is the entire dataset: Occurrence search
      • This is the filter they used on iNaturalist: Observations · iNaturalist
    • Plants-only GBIF: Occurrence search
      • GBIF file with ‘species lst’: Download
        • It contains 129k records, but they aren’t just species, also families etc.
      • Corresponding iNat filter: Observations · iNaturalist
  • Plant seedlings dataset
    • https://github.com/TheSaintIndiano/Plant-Seedlings-Classification/blob/master/Seedlings.ipynb
    • num of images based on that doc: 390+ 611+ 231+ 496+ 221+ 475+ 287+ 385+ 221+ 654+ 516+ 263

• Flora Incognita

  • A lot of conflicting info!
    • Main site: Flora Incognita | EN – The Flora Incognita app – Interactive plant species identification
      • 16k+ plant types
  • 2020 Paper giving some numbers about the dataset Multi-view classification with convolutional neural networks | PLOS ONE
    • 
    • 775 classes
  • 2021 paper about app with some details about the num of plants and comparison to other datasets: The Flora Incognita app – Interactive plant species identification - Mäder - 2021 - Methods in Ecology and Evolution - Wiley Online Library
    • 4851 classes in table 1
  • Flora Capture: a citizen science application for collecting structured plant observations - PMC
  • Flowers, leaves or both? How to obtain suitable images for automated plant identification - PubMed is about the number of images for classification, and

    we curated a partly crowd-sourced image dataset, comprising 50,500 images of 101 species.

  • Paper using FI app, not FI dataset itself! Plant image identification application demonstrates high accuracy in Northern Europe | AoB PLANTS | Oxford Academic

    2494 observations with 3199 images from 588 species, 365 genera and 89 families

• PlantCLEF

  • PlantCLEF2021
    • PlantCLEF 2021 | ImageCLEF / LifeCLEF - Multimedia Retrieval in CLEF
    • 
    • TRAIN: 321270 herb sheets, 6316 field photos, 354 observations of both herbarium+field; TEST SET: “3,186 photos in the field related to 638 plant observations (about 5 pictures per plants on average).”
    • Dataset here: https://zenodo.org/record/3658343#.ZDe9x1qxVhE

REALLY NICE OVERVIEW PAPER with really good overview of the existing datasets! Frontiers | Plant recognition by AI: Deep neural nets, transformers, and kNN in deep embeddings

• Flavia

• Datasets | The Leaf Genie has list of leaf datasets! TODO

• Herbarium 2021

  • Huge ds and paper linking to smaller ones - preliminarily added them to the spreadsheet
  • [[2105.13808] The Herbarium 2021 Half-Earth Challenge Dataset](https://arxiv.org/abs/2105.13808
  • <@delutioHerbarium2021HalfEarth2021 (2021) z/d>)

Next steps

Spreadsheet

• Update it for all the sub-datasets if practical - e.g. web and friends if needed
• Done

Datasets

• Nice picture of who stole from whom
• Done