Image Analysis Workflow
Figure 3. Pixel Classification Scheme
Box Plot
Hairy Vetch
Browning of the roots; Roots smell differently
Comparison of Healthy vs. Nitrogen deficient plants

Shoot / root ratio is altered; Left full Epstein nutrient solution - Right Epstein's without N

Comparison of Healthy vs. Phosphorus deficient plants

Shoot / root ratio is altered; Left full Epstein nutrient solution - Right Epstein's without P

Figure 1
Figure 2
Figure 8
Figure 9
Screen image of Roots
Poor Threshold Value
Proper Threshold value
R graph example
Plants grown in PVC cylinders
Wooden Base
Plastic Sleeve
Protecting cylinders from excess sunlight
Pulling sleeve out of PVC Cylinder
Measuring roots
Washing Roots
Harvested Roots
Measuring roots
Root storage
Root washing
Excavated Root crown
Selecting sample plants
Monitoring root development
Car jack used to pull out soil corer
Soil Core cleaning equipment
Shaking Core out of Sleeve
Pushing Core out of Sleeve
Washing Core
Washing Roots
Digging crown
Digging larger plant crown
Soaking the crown
Washing and scoring root crowns
Picture board
Picture board - good nodules
Crown phenotyping
Deep Roots
Shallow roots
Digging up crowns
Washing crowns
Hose washing root crowns
Scoring root crowns
Image Representation of traits
Hose washing root crowns
Driving in cylinder for core
Removing core from cylinder
Too much coring
Nutrient Budget Model
Modeling with SimRoot
SimRoot example
Schematic overview of SimRoot
SimRoot overview
SimRoot overview
Barbara Cushman Model
BCM results
SimRoot demo
Roothair Density
Roothair length
Field Phenotyping
Score board
Analyzing Data
Jonathan Lynch
Roots Lab Fall 2011
Root Box Bank

bank of maize seedlings for high throughput phenotyping

7 day old maize seedling

7 day old maize seedling grown in root box

Kineroot screenshot
Jonathan Roots Talk

root length photos

RootSlice Aerenchyma Development
RootSlice Aerenchyma Variation
Claire 2012 ASA meeting
Harini 2012 ASA meeting
Eric present Joseph's 2012 ASA meeting
Larry 2012 ASA meeting
Kutu Jim Khwan Larry 2012 ASA meeting
Lab with Epstein 2012 meeting
Labmates in Cinci bridge
Nan 2012 ASA meeting
Matthias khwan nan
khwan in japan shovelomics
research group in japan
Edward shovelomics
Example OneNote Lab Notebook
Willcox Sign 600
North Pivot Sampling 600
North pivot and blue skies
Rows of mesocosms in the greenhouse

Mesocosms allow root systems to grow to their full size

Root Washer

The root washer allows multiple soil samples to be washed simultaneously while roots contained in the samples are collected on screens.

P32 analysis

P32 is a radioactive form of phosphorus that can be used to measure P uptake


WinRhizo is used to scan washed roots and to analyze length and morphological measurements.


The spectrophotometer is used for colormetric assays for plant tissue and soil nutrient content.

Laser Ablation Facility

This laser cuts the surface of the root and allows high-throughput imaging.

Gas chromotagraphy

Gas chromotagraphy can be used to quantify the levels of many compounds. We have used it for ethylene.

Tyson Greenhouses and Mt. Nittany
Minirhizotrons being used at the rainout shelters
Rainout shelter with tracks and motor house
Using isotope tracers for understanding uptake
Low nitrogen maize in field versus high
Planting by hand in low N maize fields
Two maize experiments in different fields
Interns at URBC installing TDRs
Larry with high and low N maize
Interns phenotyping root crowns at URBC
Student field trip to URBC 2012
The plant nutrition lab at URBC
U of Limpopo students group photo
Stan explaining P field
Tsitso explaining maize RSA
Tino explaining the SPAD meter
Chris explaining ECHO's work
Larry waving his arms about the lab's work
Apache site photo test
ARBC Apache photos

Apache first site photos - 2013

online lab repository
BREAD Figures
2013 Magalhaes prize
Fall 2013 Lab Members
SEB Oct 2013 short article

in News 2013

CRIB photos

photos in CRIB Home directory

Fall 2014 Lab members
11329805_10206162866168075_8402251383375989510_n (1).jpg
10424269_10206162866288078_5719928298733933977_n (1).jpg
sean and christian washing roots P7210006.jpg
Using the Li-3000 leaf area meter P7200256.jpg
10919405_10206375480803308_5336046993141338546_o (1).jpg
Discussing root sampling for anatomical samples

Stephanie Klein explains to members of the visiting Nobel Foundation about her research and root sampling methods.

lab photo 2016
Group photo
bean recipe

Bean recipe research in Mozambique

kitchen women

Bean recipe research in Mozambique

corn shucking

Bean recipe research in Mozambique

Bean root anatomy
Bean root anatomy 2
Crops in silico FFAR logo
IPG travel award Shirley Nichols
IPG travel award Mina Rostamza
Hannah Schneider headshot
Roots lab, December 2017
Graduation Jimmy

Jimmy Burridge (right) discussing his research

Graduation Molly Kathy Hannah
Graduation all with K and J
Rainout shelter with maize
Rainout shelter control plot with maize
Laser Hannah user

JPEG image, 371.6 KB

Laser maize root on stage

JPEG image, 295.4 KB

High and Low RCA
Khwan award_flowers
Khwan award_certificate
Hannah at old laser setup
OpenSimRoot-Rice poster from Ishan
SimRoot rice root system
2018 Khwan receives award
2018 Rice vs maize by Mohamed
2018 Tania conference poster
January 2019 photo
2019 Ishan Poster for Newton Fund meeting in Thailand.png
2019 Rice digital staining.png
2019_Jenna_poster_Plant Vascular Biology_2019_final.png
2019 Steph PVB_Poster_spoonflower copy.jpg
2019 group photo at SEB Seville meeting.png
Group photo
LAT2 housing whole setup
LAT2 internal setup
LAT2 root cassette

Root cassette made from 3d printed PLA and stainless-steel capillary tubes.

bean 5gal.png
bean 10L.png
washing rice roots from mesocosm.JPG
Pouring roots.jpg
Root teasing.jpg
Spanish Whorls.jpg
pot bound roots.jpg
Several Mesocosms.jpg
2018 Curtis Frederick.jpg
Khwan award_receiving flower bouquet from Faculty of Science.jpg