Objective: Find a tool to determine relative ground cover of living plants, plant residues, and bare soil by batch processing digital images.
- Ground cover by crops can be an important tool for quantifying plant vigor in genotypic trials. Ground cover by crops or crop residues is an important modifier of the soil surface environment and affects germination and establishment of weeds.
- The accessibility of digital photography and computing power makes analysis of images an attractive tool for determining ground cover in field experiments.
- Preliminary analysis (see next page) showed that low red:green color ratio was generally diagnostic of green tissue, and that high intensity was typical of residue. The commercial (proprietary) image analysis software tools we examined did not support the use of color ratios or the use of multiple thresholds.
- Free and Open Source Software (FOSS) includes several useful programs that together can provide a flexible set of tools for analyzing images. These tools may require customization to maximize their usefulness to particular applications.
- ImageJ: a free image analysis tool from the US National Institutes of Health. We use ImageJ mostly for pixel sampling, but it is a powerful tool, with many available plugins.
- R: An open-source, free statistical analysis environment. We use R here for graphic analysis of pixel colors to find thresholds. R is widely used for all kinds of analytical projects.
- CIMG: a free library for C++ that allows images to be manipulated as 3 matrices of color values - one each for red, green, and blue.
Spotlight
Study shows ‘steep, cheap and deep’ roots help corn plants deal with drought
Jagdeep Sidhu and Sam Walker win awards at 2022 CSA (Crop Science, Soil Science, Agronomy Societies) meetings
Jonathan Lynch recognized as highly cited researcher in 2022 by Clarivate
Jonathan Lynch recognized as highly cited researcher in 2021 by Clarivate
Publication receives award from Crop Science Society of America
Tools for breeding cowpea with better roots highlighted in CSA news article
Breeding Beans for Better Roots
Professor Kathleen Brown retires after 41 years
Amelia Henry receives humanitarian award
Jagdeep Sidhu receives research award
Roots lab research focus of podcast from West German Public Radio
Newly discovered trait helps plants grow deeper roots in dry, compacted soils | Penn State University
CSA news article on Roots Lab work with bean breeding
Jagdeep Sidhu Receives College Research Funding
Jonathan Lynch recognized as Highly Cited Researcher by Clarivate
Graduate student receives special award for early career contributions to ASPB
LAT root image wins photo competition of Egyptian Academy of Scientific Research
Graduate student awarded Outstanding Agricultural Graduate Student Award from AASIO
News story on bean root architecture reaches 6 million people, worth $240,000
Bean root architecture results highlighted in CSSA News
Field work proceeds with physical distancing, safety precautions
Spotlight
Study shows ‘steep, cheap and deep’ roots help corn plants deal with drought
Jagdeep Sidhu and Sam Walker win awards at 2022 CSA (Crop Science, Soil Science, Agronomy Societies) meetings
Jonathan Lynch recognized as highly cited researcher in 2022 by Clarivate
Jonathan Lynch recognized as highly cited researcher in 2021 by Clarivate
Publication receives award from Crop Science Society of America
Tools for breeding cowpea with better roots highlighted in CSA news article
Breeding Beans for Better Roots
Professor Kathleen Brown retires after 41 years
Amelia Henry receives humanitarian award
Jagdeep Sidhu receives research award
Roots lab research focus of podcast from West German Public Radio
Newly discovered trait helps plants grow deeper roots in dry, compacted soils | Penn State University
CSA news article on Roots Lab work with bean breeding
Jagdeep Sidhu Receives College Research Funding
Jonathan Lynch recognized as Highly Cited Researcher by Clarivate
Graduate student receives special award for early career contributions to ASPB
LAT root image wins photo competition of Egyptian Academy of Scientific Research
Graduate student awarded Outstanding Agricultural Graduate Student Award from AASIO
News story on bean root architecture reaches 6 million people, worth $240,000
Bean root architecture results highlighted in CSSA News
Field work proceeds with physical distancing, safety precautions