sleap-roots

Analysis tools for SLEAP-based plant root phenotyping.

📦 Installation

pip install sleap-roots

If you are using conda (recommended):

conda create -n sleap-roots python=3.11
conda activate sleap-roots
pip install sleap-roots

🌱 Usage

Trait pipelines supported:

• DicotPipeline – Primary + lateral roots (e.g. soy, canola)
• YoungerMonocotPipeline – Primary + crown roots (e.g. early rice)
• OlderMonocotPipeline – Crown roots only (e.g. later rice)
• PrimaryRootPipeline – Primary root only
• LateralRootPipeline – Lateral roots only
• MultipleDicotPipeline – Multi-plant dicot setup (batch from a single image)

🔁 Example: Dicot Pipeline

1. Compute traits for a single plant

import sleap_roots as sr

series = sr.Series.load(
    series_name="919QDUH",
    h5_path="tests/data/canola_7do/919QDUH.h5",
    primary_path="tests/data/canola_7do/919QDUH.primary.slp",
    lateral_path="tests/data/canola_7do/919QDUH.lateral.slp"
)

pipeline = sr.DicotPipeline()
traits = pipeline.compute_plant_traits(series, write_csv=True)

2. Compute traits for a batch

paths = sr.find_all_slp_paths("tests/data/soy_6do")
plants = sr.load_series_from_slps(paths, h5s=True)

pipeline = sr.DicotPipeline()
batch_df = pipeline.compute_batch_traits(plants, write_csv=True)

3. Use a single trait utility

from sleap_roots.lengths import get_root_lengths

pts = series.get_primary_points(frame_idx=0)
lengths = get_root_lengths(pts)

📓 Notebooks & Tutorials

Explore tutorials under notebooks/:

cd notebooks
jupyter lab

You can use the test data in tests/data or replace it with your own.

🧪 Development

1. Clone the repository:

git clone https://github.com/talmolab/sleap-roots && cd sleap-roots

2. Create the conda environment:

conda env create -f environment.yml
conda activate sleap-roots

This includes dev dependencies and installs the package in editable mode (--editable=.[dev]).

3. Run tests:

pytest tests

4. Remove the environment (optional):

conda env remove -n sleap-roots

📖 Trait Reference

See the latest trait documentation here:

👉 HackMD: sleap-roots Trait Docs

🤝 Acknowledgments

Created by the Talmo Lab and Busch Lab at the Salk Institute, as part of the Harnessing Plants Initiative.

Contributors

• Elizabeth Berrigan
• Lin Wang
• Andrew O'Connor
• Talmo Pereira

Citation

E.M. Berrigan et al., "Fast and Efficient Root Phenotyping via Pose Estimation", Plant Phenomics.
DOI: 10.34133/plantphenomics.0175