Software

SOFTWARE DEVELOPMENT TEAM:    SRUTI DAS CHOUDHURY, RUBI QUIÑONES, SRINIDHI BASHYAM, SRIKANTH MATURU

A. 2D Plant Phenotyping Tool
Windows x64 - Download here

Software to compute 2D plant phenotypes. 

Following 2D plant phenotypes will be computed for each plant in the input lemnatec dataset directory:

• Convex hull area of each side view of the plant.
• Plant pixel area of each side view of the plant.
• Ratio of plant pixel area and convex hull area of each side view of the plant.
• Bounding box height of side view 0 degrees of the plant.
• Top view enclosing circle diameter of the plant.
• Aspect ratio bounding box height/top view enclosing circle diameter.

If you use this software to generate results for your publication, please acknowledge software developers and cite our paper: 
S. D. Choudhury, V. Stoerger, A. Samal, J. C. Schnable, Z. Liang, J-G. Yu, Automated Vegetative Stage Phenotyping Analysis of Maize Plants using Visible Light Images, KDD workshop on Data Science for Food, Energy and Water (KDD -DSFEW), San Francisco, California, USA, 2016.

B. Leaf detection and component phenotype computation software

Download here  

If you use this software to generate results for your publication, please acknowledge software developers and cite our paper: 

S. D.  Choudhury, S. Bashyam, Y. Qui, A. Samal, T. Awada, “Holistic and Component Plant Phenotyping using Visible Light Image Sequence”, Plant Methods, 14:35, 2018.

C. HypeRpheno

HypeRpheno is a graphical user interface created in MATLAB 2019b. It analyzes hyperspectral images (high dimensional data) and performs spectral analysis, clustering analysis, and classification analysis using custom algorithms. A dataset sample is included in HypeRpheno.

To download HypeRpheno, click here.

If you use HypeRpheno, please cite the book chapter:

S. Gampa, R, Quiñones, "Data-Driven Techniques forPlant Phenotyping Using Hyperspectral Imagery", Intelligent Image Analysis for Plant Phenotyping, CRC Press, Taylor and Francis Group, First Edition, 2020.

D. iPlantSeg+: A Flexible Tool for Plant Segmentation

PlantSeg+, created in MATLAB 2022b, facilitate segmentation suitable for both researchers and practitioners of image-based phenotyping. The tool, currently under initial stage of development, is named as iPlantSeg+ and will have the following novel characteristics:

1. iPlantSeg+ provides a menu of both interactive and automated segmentation methods, thus allowing the users with the flexibility to select an algorithm best suited for a particular application.
2. Unlike the existing tools, which are designed for a specific plant species, the iPlantSeg+ tool will be applicable to a wide variety of plants and animals both in indoor greenhouse settings with uniform backgrounds as well as outdoor environments that have segmentation challenges due to illumination variation, presence of weeds and shadows.
3. It will perform accurate segmentation of plants with thin structures in the presence of cluttered background and illumination variation.
4. It will also facilitate the users to segment single or multiple non-overlapping objects (plants and animals) from their own image datasets.
5. It will segment plants in low-resolution images captured by cameras other than the traditional visible light, e.g., fluorescent, hyperspectral, near infrared, and infrared.
6. It will compute a set of common holistic phenotypes and stores them in a file/database.
7. A graphical user interface (GUI) will make the tool easy to use by non-experts.
8. It will include an option for batch processing of a set of plants with the option for storing intermediate images/results.

This work is supported by Agricultural Genome to Phenome Initiative (AG2PI) Seed Grant [grant no. 2021-70412-35233] from the USDA National Institute of Food and Agriculture.

To download iPlantSeg+, click here.

Contact person: Sruti Das Choudhury (s.d.choudhury@unl.edu)

Developers: Srinidhi Bashyam, Sruti Das Choudhury, Ashok Samal

© 2022 UNL Plantvision, University of Nebraska - Lincoln. All rights reserved.