2014 Workshop in Field-Based High Throughput Phenotyping

 

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

 

Workshop Schedule

April 7-10, 2014

 

Lecturer

Topic

Mon

 

Workshop Welcome and Sensor Basics

07:30

 

Van departs from hotel area

08:15

 

Arrive at MAC, receive course material

08:30

P Andrade/J Poland/J White

Welcome, overview, participant introductions

09:00

J Poland

Introduction to Field-Based High Throughput Phenotyping

09:20

J Poland/K Thorp

Experimental design and field layout planning for phenomics

09:40

A French

Sensors 1: Thermal infrared

10:10

 

Break

10:30

J White

Sensors 2: Ultrasonic proximity sensors

11:00

M Conley/J White/A French

Exercise A (field): Infrared thermometry & ultrasonic proximity

12:20

 

Return to MAC

12:30

 

Lunch

13:30

MC, JW, AF

Q&A for field exercise A

13:40

K Thorp

Sensors 3: Introduction to spectral reflectance (passive sensors)

14:10

P Andrade

Sensors 4: Introduction to spectral reflectance (active sensors)

14:30

KT, PA

Exercise B (lab): Demonstration of reflectance sensors

15:00

 

Break

15:20

P Andrade/R Strand,/J White

Exercise C (field): Reflectance sensors: tractor and cart

16:45

PA, RS, JW

Q&A for field exercises 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

J White/J Poland

Recap of previous day and logistics

08:30

J White/J Poland

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

09:00

P Andrade

GPS basics

09:40

R Strand

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

10:00

 

Break

10:20

P Andrade

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

10:40

P Andrade/J White

Exercise D (lab & field): Sensor positioning (height, field of view, view angle)

12:30

 

Lunch

13:30

K Wang/M Conley

Data logging basics and Campbell loggers

14:00

R Strand

LabView and National Instruments options

14:15

KW, MC, RS

Lab exercise E1[1]: Operation of Campbell CR-3000s

14:15

JP, JW, AF, KT

Lab exercise E2: (to be determined based on interests)

15:00

 

Break

15:20

 

(Continue lab exercises)

16:45

(various)

Review of exercises D & E

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

J White/J Poland

Recap of previous day and logistics

08:30

K Thorp

Georeferencing: geoprocessing within a GIS

09:00

K Wang

Georeferencing: post-processing sensor outputs

09:20

K Thorp/K Wang

Exercise F (lab): Georeferencing sensor outputs

10:00

 

Break

10:15

 

(continue Exercise F)

11:15

J White/J Poland

The data analysis challenge: from raw data to phenotypes

12:00

 

Lunch

13:00

J White

Data analysis: responses at weekly time scales

13:30

A French

Data analysis: diurnal responses

13:50

K Thorp/S Welch

Inverse modeling

14:30

JW, AF, KT, SW

Exercise G (lab): Analyzing time series—weekly and daily data

15:00

 

Break

15:15

 

(continue Exercise G)

16:00

R Walls

iPlant Cyberinfrastructure and Phenomics

16:45

 

Recap of workshop activities

17:00

 

End of Wednesday’s activities

17:30

 

Western barbecue (Chandler)

19:30

 

Transport back to hotel area

     

Thurs

 

Data Management and Workshop Review

07:30

 

Van departs from hotel area

08:15

J White/J Poland

Recap of previous day and logistics

08:30

J White

Metadata for describing field experiments and phenotyping

09:00

J Poland/K Wang

Overview of work flow

09:20

K Wang

Data management: from georeferencing to data storage and access

   

Break

9:30

S Welch/Nan An/J White

Imaging and image analysis: the next frontier

10:20

S Welch/E Reidel/J Poland

Round-table: Second and third generation field phenomics

11:20

J Poland

Course evaluation

11:50

 

Group photo

12:00

 

Lunch

13:00

Nan An

Lab Exercise - Image Analysis

14:00

(all)

Continue small group or one-on-one meetings

15:00

 

Break

15:30

J Poland/J White

Closing remarks and comments on course evaluations

17:00

 

Course closes

17:15

 

Transport back to hotel area

 


[1] Participants who are already familiar with data loggers or who have access to data logging expertise will be polled for other exercises or discussion options.

 

 

 

LECTURE NOTES

 

DAY 1 - Monday, April 7, 2014

Introduction to Field-Based High Throughput Phenotyping

Lecture notes - Introduction to Field-Based High Throughput Phenotyping

Presentation - Introduction

Experimental Design and Field Layout Planning for Phenomics

Lecture notes - Experimental design and field layout planning for phenomics

Presentation - Experimental design

Sensors 1: Thermal Infrared

Lecture notes - Sensors 1: Thermal infrared

Presentation - Thermal Infrared

Sensors 2: Ultrasonic

Lecture notes - Sensors 2: Ultrasonic proximity sensors

Presentation - Ultrasonic

Sensors 3: Introduction to Spectral Reflectance - Passive Sensors

Sensors 3: Introduction to spectral reflectance (passive sensors)

Presentation - Passive Sensors

Sensors 4: Introduction to Spectral Reflectance - Passive Sensors

Sensors 4: Introduction to spectral reflectance (active sensors)

Presentation - Active Sensors

 

 

DAY 2 - Tuesday, April 8, 2014

Vehicle options: Carts, Tractors, Gantry Cranes, UAVs and more

Lecture Notes - Vehicle options

Presentation - Vehicle options

GPS Basics

Lecture Notes - GPS basics

Presentation - GPS basics

Sensor Electronics: Power, Grounding, Signal Types, etc.

Lecture Notes - Sensor electronics

Presentation - Sensor electronics

Sensor Deployment: Height, Field of View, Refresh Rates, etc.

Lecture Notes - Sensor deployment

Presentation - Sensor deployment

Data Logging Basics

Lecture Notes - Data logging basics and Campbell loggers

Presentation - Data Logging / Campbell Loggers

 

Lecture Notes - LabView and National Instruments options

Presentation - LabView and National Instruments

 

 

DAY 3 - Wednesday, April 9, 2014

Georeferencing: Geoprocessing within a GIS

Lecture Notes - Georeferencing: geoprocessing within a GIS

Presentation - Georeferencing with GIS

Georeferencing: Post-processing sensor outputs

Lecture Notes - Georeferencing: post-processing sensor outputs

Presentation - Georeferencing Post-processing

Data Analysis Challenge

Lecture Notes - The data analysis challenge: from raw data to phenotypes

Presentation - Data Analysis Challenge

Data Analysis: Weekly Time Scale

Lecture Notes - Data analysis: responses at weekly time scales

Presentation - Data analysis: responses at weekly time scales

Data Analysis: Diurnal Responses

Lecture Notes - Data analysis: diurnal responses

Presentation - Data analysis: diurnal responses

Inverse Modeling

Lecture Notes - Inverse modeling

Presentation - Inverse modeling

iPlant Cyberinfrastructure and Phenomics

Lecture Notes - iPlant Cyberinfrastructure and Phenomics

Presentation - iPlant

iPlant supplemental documents

 

 

DAY 4 - Thursday, April 10, 2014

 

Metadata for Field Phenomics

Lecture Notes - Metadata for describing field experiments and phenotyping

Presentation - Metadata

Workflow

Lecture Notes - Overview of work flow

Presentation - Workflow

Data Management

Lecture Notes - Data management: from georeferencing to data storage and access

Presentation - Data Management

Imaging and Image Analysis

Lecture Notes - Imaging and image analysis: the next frontier

Presentation - Image Analysis

 

EXERCISE FILES

 

Exercise A

1. Exercise A: IRT and ultrasonic sensors

 

Exercise B

1. Exercise B: Demonstration of reflectance sensors

 

Exercise C

1. Exercise C: Analysis and comparisons of reflectance data

2. Spectra.csv

3. ACS-430_height-test.txt

4. ACS-430_grass-conditions.txt

 

Exercise E1

1. Exercise E1: Operation of Campbell CR3000

2. Ultrasonic sensor test program (FB-HTP_Training.txt)

3. GPS test program (Logging_GPS_Training.txt)

4. Campbell Scientific CR3000 Datalogger Operator's Manual

 

Exercise F

1. Exercise F: Georeferencing sensor outputs

2. plotnodes.csv

3. crop circle instructions.csv

4. F1119_2012_DOY201_1pm_CC.csv

5. IRT instructions.csv

6. F1119_2012_DOY201_1pm_IRT.csv

Files for Mac OSX

2b. plotnodes_mac.csv

3b. crop_circle_instructions_mac.csv

4b. F119_2012_DOY201_1pm_CC_mac.csv

5b. IRT_instructions_mac.csv

6b. F119_2012_DOY201_1pm_IRT_mac.csv

 

Image Analysis

FB-HTP_FieldPlotStitched.jpg

Fiii Download

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