Image analysis workflow
- Images grouped into batches by cropping system and date to maximize uniformity.
- When multiple images available, images selected for uniformity of exposure and color
- Occasional images possessed atypical color - in these cases, color balance was adjusted on a copy of the image, and both the original and copy were analyzed. (After review of false color images, the adjusted copy was retained only if classification was improved.) Note: We have fewer instances of this since we began using a DSLR camera in 2009 .
- Pixels sampled using a custom macro in ImageJ.
- Thresholds determined graphically for each batch of images (using R ). We used several custom functions in R to facilitate threshold determination.
- Images were batch processed using a shell script that called the C++ image analysis program and compiled the output.
- False color images reviewed to assure correct classification. Thresholds adjusted and batch processing repeated if needed.
Original Image
In this image, the soil has a reddish color not present in the other images in this group.
Color Adjusted Image
Here we have adjusted the color in the image to reduce the red color in the soil. We used GIMP (www.GIMP.org) but any good image editor should work.
Original Image - Evaluation
Leaves 13%; Residue 26%; Bare Soil 57%; Ambiguous 4%
Color Adjusted Image - Evaluation
Leaves 25%; Residue 25%; Bare Soil 47%; Ambiguous 2%
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