Populus Stomatal Images Datasets

This dataset is a detailed assembly of 11,000 annotated images for advanced analysis and machine learning applications in leaf stomatal research.

Dataset Details

Dataset Description

This dataset consists of around 11,000 unique images of hardwood leaf stomata collected from projects conducted between 2015 and 2022. Within the dataset, there are more than 7,000 images of 17 common hardwood species, such as oak, maple, ash, elm, and hickory. Additionally, the dataset contains over 3,000 images of 55 genotypes from seven Populus taxa. For each image, it is represented with image_id, species, scientific_name, image_path, image_magnification, width, height, and resolution and annotations. Within annotations, there are category id and information about the bounded box of the image.

Curated by: [Jiaxin Wang, Heidi J. Renninger and Qin Ma]
Language(s) (NLP): [English]
License: [http://creativecommons.org/licenses/by/4.0/]

Dataset Sources

Repository: [https://zenodo.org/records/8271253]
Paper: [https://www.nature.com/articles/s41597-023-02657-3]

Uses

(1) Employ state-of-the-art machine learning models to identify, count, and quantify leaf stomata; (2) Explore the diverse range of stomatal characteristics across different types of hardwood trees; (3) Develop new indices for measuring stomata.

Dataset Structure

{'image_id': 'STMHD0001',
 'species': 'Nuttall oak',
 'scientific_name': 'Quercus texana Buckley',
 'image': <PIL.JpegImagePlugin.JpegImageFile image mode=RGB size=1024x768>,
 'magnification': 100,
 'width': 1024,
 'height': 768,
 'resolution': 118,
 'annotations': {'category_id': [1,0,0,1,......,1,0,0],
                 'bounding_box': [{'x_center_rel': 0.25232601165771484,
    'y_center_rel': 0.014441000297665596,
    'width_rel': 0.022092999890446663,
    'height_rel': 0.02790999971330166},
    ......,
    {'x_center_rel': 0.9088180065155029,
    'y_center_rel': 0.9940109848976135,
    'width_rel': 0.06590700149536133,
    'height_rel': 0.010591999627649784}]
    }}

Dataset Field

"image_id"[string]: Unique identifier for each image, corresponding to the file name without the file extension.
"species"[string]: The common name of the tree’s species the stomata in the image belong to.
"scientific_name"[string]: The scientific or Latin name of the tree’s species.
"image"[PIL]: A PIL.Image.Image object containing the image.
"magnification"[integer]: The magnification level at which the image was captured, represented as an integer.
"width"[integer]: The width of the image.
"height"[integer]: The height of the image
"resolution"[integer]: The resolution of the image 
"annotation_coordinates"[dictionary]: A dictionary containing the category id, where inner_guard_cell_walls was labeled as “0”, whole_stomata (stomatal aperture and guard cells) was labeled as “1”. and bounding box coordinates for the annotated stomatal features, where the x_center and y_center are expressed as normalized coordinates that correspond to the center of the bounding box, while width and height are normalized values that represent the relative width and height of the box concerning the dimensions of the image

Curation Rationale

Machine learning (ML) algorithms have shown potential in automatically detecting and measuring stomata. However, ML algorithms require substantial data to efficiently train and optimize models, but their potential is restricted by the limited availability and quality of stomatal images. To overcome this obstacle, this dataset was established.

Source Data

The study utilized stomatal images from two datasets: Hardwood and Populus spp., acquired from 2015 to 2022. The Hardwood dataset contained 16 species, including American elm (Ulmus americana Planch), cherrybark oak (Quercus pagoda Raf.), Nuttall oak (Quercus texana Buckley), shagbark hickory (Carya ovata (Mill.) K. Koch), Shumard oak (Quercus shumardii Buckley), swamp chestnut oak (Quercus michauxii Nutt.), water oak (Quercus nigra L.), willow oak (Quercus phellos L.), ash (Fraxinus L.), black gum (Nyssa sylvatica Marshall), deerberry (Vaccinium stamineum Linneaus), leatherwood (Dirca palustris L.), red maple (Acer rubrum L.), post oak (Quercus stellata Wangenh.), willow (Salix spp.), and winged elm (Ulmus alata Michx.), with the age of seedlings ranging from 1–3 years for Nuttall oak, water oak, and Shumard oak, and 30–50 years for the rest. Using a compound light microscope (Olympus, Tokyo, Japan) equipped with a digital microscope camera (MU300, AmScope, USA) with a 5 mm lens and a fixed microscope adapter (FMA050, AmScope), over 10,000 stomatal images were captured. The Populus dataset consisted of over 3,000 images from 55 genotypes of seven taxa of hybrid poplar and eastern cottonwood (Populus deltoides), which were 4 to 5 years old.

Bias, Risks, and Limitations

This dataset includes only images of stomata from hardwood trees and Populus, limiting its applicability for studying stomata of other tree genera, though it may serve as reference data. This dataset is not divided into training and testing sets; users must divide it themselves when necessary.Despite following rigorous procedures in collecting leaves and micrographs, considering human and instrumental errors, there's a possibility of inaccuracies in the images and their associated information within the datasets. Even though the annotation process employed pre-trained model labeling methods, complemented by quick checks using LabelImg, potential model and computational errors could still lead to incorrect annotations.

Citation

Wang, J., Renninger, H.J. & Ma, Q. Labeled temperate hardwood tree stomatal image datasets from seven taxa of Populus and 17 hardwood species. Sci Data 11, 1 (2024). https://doi.org/10.1038/s41597-023-02657-3