2015 Workshop in Field-Based High Throughput Phenotyping

March 16 - 19, 2015

Maricopa Agricultural Center (MAC)

Link to MAC in Google Maps

To find directions on Google Map, please type in ‘University of Arizona Maricopa’.

Or, by typing the following coordinates into your GPS - Lat: 33° 4'21.72"N Long: 111°58'28.58"W

 

Videos

Videos of the lectures will be available soon. Please check this Website for more information.
 

Workshop Schedule

 

Lecturer

Topic

File Download

Mon

 

Workshop Welcome and Sensor Basics

 

07:30

 

Van departs from hotel area

 

08:15

 

Arrive at MAC, receive course material

 

08:30

Jeff Silvertooth (UofA)

Rick Ward (UofA)

Steve Naranjo (USDA)

Welcome, overview, participant introductions

 

09:00

Poland

Introduction to Field-Based High Throughput Phenotyping

Mon_0900_Introduction_JP

09:20

Thorp

Experimental design and field layout planning for phenomics

Mon_0920_Field Layout Planning_KT

09:40

French

Sensors 1: Thermal infrared

Mon_0940_ThermalSensorsAF2015

10:00

 

Break

 

10:30

 

Field Visit (Field 119)

 

11:00

White

Sensors 2: Ultrasonic proximity sensors

Mon_1100_Ultra_sonic_sensors_JW_MC

11:20

French

Sensors 3: LIDAR

Mon_1120_Sensors3_LIDAR_AF

11:30

Thorp

Sensors 4: Introduction to spectral reflectance (passive sensors)

Mon_1130_SpectralReflectance_PassiveSensors_KT

12:00

Andrade-Sanchez

Sensors 5: Introduction to spectral reflectance (active sensors)

Mon_1200_active-spectral-sensors

12:30

 

Lunch

 

13:30

Conley,White,French

 

Thorp, Andrade-Sanchez

Exercise A: Infrared thermometry & ultrasonic proximity

 

Exercise B: Reflectance sensors

Mon_1330_Ex_A_IRT_ultrasonic_sensors_MC_AF2_AT_JW

 

Mon_1330_Ex_B_ReflectanceSensors_KT_PA

14:30

(as above)

Exercise A&B Session II (groups swap on Exercises A & B)

 

 

15:30

 

Break

 

15:50

Andrade / Thorp

Exercise C (lab): Analysis and comparisons of reflectance data

Mon_1550_Ex_C_Reflectance_Data_KT_PA

Data Files-Exercise C

16:50

Andrade / Thorp

Review, Q&A for Exercises A, B & C

 

17:00

 

End of Monday’s activities

 

17:15

 

Transport back to hotel area

 
       

Tues

 

Vehicles and Sensor Integration

 

07:30

 

Van departs from hotel area

 

08:15

White / Poland

Recap of previous day and logistics

 

08:30

White / Andrade

Vehicle options: carts, tractors, gantry cranes, UAVs and more

Tue_0830_Vehicle options_JW_JP_PA

09:00

Andrade-Sanchez

GPS basics

Tue_0900_GPS-basics

09:40

Wang

Sensor electronics: power, grounding, signal types, etc.

Tue_0940_Sensor_Electronics_KW

10:00

 

Break

 

10:20

Andrade / White

Sensor deployment: height, field of view, refresh rates, etc.

Tue_1020_sensor-deployment

11:00

Wang / Conley

Data logging basics: Campbell and National Instruments options

Tue_1100_DataLogging_MC

11:30

Thorp / Wang

Georeferencing: geoprocessing

Tue_1130_Georeferencing by Geoprocessing within a GIS_KT

12:00

 

Lunch

 

13:00

 

Introduce afternoon activities (1h blocks with three groups)

 

13:05

(All instructors)

Exercise D: Sensor position (height, FOV, view angle)

 

 

Exercise E: Operation of Campbell CR-3000s

 

 

 

Exercise F: (to be determined based on interests)

Tues_1305_Ex_D_sensor_position_PA_JW_MC_AF

Data Files - Exercise D

 

Tues_1305_ExerciseE_CRBasicProgramming_KW_MC

Tues_1305_DataLoggerBasicsDemonstrationNotes

Data Files - Exercise E

 

Tues_1305_Ex_F1_scanning_seed_etc

 

Tues_1305_Ex_F1_soldering_continuity

15:00

 

Break: snacks and drinks available from 14:45 to 15:30

 

16:50

 

Review, Q&A for field exercises D, E & F

 

17:00

 

End of Tuesday’s activities

 

17:15

 

Transport back to hotel area

 
       

Wed

 

Data Processing and Analysis

 

07:30

 

Van departs from hotel area

 

08:15

White / Poland

Recap of previous day and logistics

 

08:30

Thorp / Wang

Exercise G (lab): Georeferencing sensor outputs

Wed_0830_Ex_G_Georeferencing_Sensor_Outputs_KT

Data Files - Exercise G

10:00

 

Break

 

10:30

Nan An / French

Imaging systems: camera basics

Wed_1030_CameraBasics_NA_AF

11:00

Wang

Imaging acquisition: georeferencing and camera control

Wed_1100_Image_acquisition_KW_JW

11:30

Welch / Nan An

Image analysis

Wed_1130_Image_Analysis_NA_SW

12:00

 

Lunch

 

13:00

JW, NA, AF, KW, SW

Exercise H (lab): Image analysis with ImageJ

Wed_1300_Ex_H_Intro_Image_Analysis_w_ImageJ

Data Files - Exercise H

14:40

White / Poland

The data analysis challenge: from raw data to phenotypes

Wed_1440_Data_analysis_overview_JW_JP

15:00

 

Break

 

15:20

White

Data analysis: responses at weekly and diurnal time scales

Wed_1520_Time_series_weekly_JW

15:40

Thorp / Welch

Model inversion

Wed_1550_Model Inversion_KT_SW

16:20

KT, SW, JW

Exercise I (lab): Inverse Modeling

Data Files - Exercise I

17:00

 

End of Wednesday’s activities

 

18:30

 

Evening picnic and social (Chandler)

 

20:30

 

Transport back to hotel area

 
       

Thur

 

Data Management and Workshop Review

 

07:30

 

Van departs from hotel area

 

08:15

White / Poland

Recap of previous day and logistics

 

08:25

Wang / Thorp

Overview of work flow

Thur_0825_Overview_of_work_flow_KW_KT

08:40

Thorp / Wang

Data management: From georeferencing to data storage & access

Thur_0840_Data_management_KW_KT

09:10

Poland / White

Course evaluation

Take the course evaluation

09:30

(all)

Open Discussion: Potential approaches and tools for data management

 

10:00

 

Break

 

10:20

Narro

iPlant Cyberinfrastructure and Phenomics

Thur_1020_iPlant_Field_Phenotyping_2015

11:00

Colgan

Industry perspective I - Blue River Technologies

Thur_1100_BlueRiver

11:20

Blonqusit

Industry perspective II - Apogee

Thur_1120_Apogee

11:40

Reidel

Industry perspective III - Lemnatec

Thur_1140_LemnaTec

12:00

Poland / White

Closing remarks and comments on course evaluations

 

12:15

 

Lunch

 

13:30

(all)

Small group/one-on-one meetings (Early departures)

 

15:00

 

Break

 

15:20

 

Continue small group meetings

 

16:00

Poland / White

Course closes

 

16:15

 

Transport back to hotel area