Update README.md

README.md

@@ -6,4 +6,68 @@ language:
 - en
 tags:
 - plant root phenotyping
----
+---
+
+# ChronoRoot nnUNet Dataset
+
+## Dataset Description
+
+### Dataset Summary
+This dataset contains 693 infrared images of Arabidopsis thaliana seedlings with expert annotations for six distinct structural classes, developed for training the ChronoRoot 2.0 segmentation model. The dataset includes raw infrared images and their corresponding multi-class segmentation masks, formatted according to nnUNet requirements.
+
+### Supported Tasks
+- Image Segmentation: Multi-class segmentation of plant structures
+- Plant Phenotyping: Analysis of root system architecture and plant development
+
+### Classes
+The dataset includes annotations for six distinct plant structures:
+1. Main Root (Primary root axis)
+2. Lateral Roots (Secondary root formations)
+3. Seed (Pre- and post-germination structures)
+4. Hypocotyl (Stem region between root-shoot junction and cotyledons)
+5. Leaves (Including both cotyledons and true leaves)
+6. Petiole (Leaf attachment structures)
+
+### Data Structure
+- Raw Images: 3280 x 2464 infrared images
+- Segmentation Masks: Multi-class masks in .png format
+- nnUNet Configuration: Standard nnUNet dataset organization
+
+### Source Data
+Images were captured using the ChronoRoot hardware system, featuring:
+- Raspberry Pi Camera v2
+- Infrared lighting (850nm)
+- Optional long pass IR filters (>830nm)
+- Controlled growth conditions
+
+### Data Split
+The dataset follows nnUNet's standard 5-fold cross-validation structure.
+
+## Dataset Creation
+
+### Annotations
+- Annotation Tool: ITK-SNAP
+- Annotators: Expert biologists
+- Verification: Multi-stage quality control process
+
+### Personal and Sensitive Information
+This dataset contains no personal or sensitive information.
+
+## Additional Information
+
+### Licensing Information
+The dataset is released under GNU GPL 3.0
+
+### Citation Information
+If you use this dataset, please cite:
+
+@article{gaggion2021chronoroot,
+  title={ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture},
+  author={Gaggion, Nicol{\'a}s and Ariel, Federico and Daric, Vladimir and Lambert, Eric and Legendre, Simon and Roul{\'e}, Thomas and Camoirano, Alejandra and Milone, Diego H and Crespi, Martin and Blein, Thomas and others},
+  journal={GigaScience},
+  volume={10},
+  number={7},
+  pages={giab052},
+  year={2021},
+  publisher={Oxford University Press}
+}