smartr t - uliege.be · quick root tracing overview. 9 quick root tracing overview. 10 tracing...

SmartR T

UCL

Guillaume Lobet, Loïc Pagès and Xavier Draye

A novel image analysis toolbox enabling quantitative analysis

of root system architecture

6th of September 2012

1

What we do in our lab

2

What is SmartRoot?

• Semi-automated

• Root tracing software

• Morphology, topology

• Wide range of image

3

Why semi-automated?

4

Heterogenous image

5

Local information

6

Root system as a population

7

Why semi-automated?

• Local information is needed

• Sample the root system

• Sample the image

8

How does it work?

9

Quick root tracing overview

10

Tracing algorithm - 1

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

mouse click

10


node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

path

pixel valuepath

local threshold

local threshold

mouse click

10


node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

path

pixel value

local threshold

local threshold

mouse click

10


node creation

search path

node creation

diameter check

append node

node centering

node centering

path

local threshold

local threshold

path

pixel value

local threshold

mouse click

11

Tracing algorithm - 2mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

11


Region of Interest

mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

11


pixel value

freq

uenc

y

MIN MAX

Region of Interest

mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

11


pixel value

freq

uenc

y

MIN MAX

Region of Interest

p

mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

11


pixel value

freq

uenc

y

MIN MAX

Region of Interest

THRESHOLD

p

T = p + MIN

2 + MAX

2

mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12


node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13


node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

14


node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

14


node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

Diameter freeze

15

Object oriented

Nodes as individual objects

Root as individual object

15

Object oriented

Nodes as individual objects


Individual actions[move, crop, append]

15

Object oriented

Nodes as individual objects Topology


Individual actions[move, crop, append]

16

Vector based

16

Vector based

Coordinates in the pixel space

[x, y]

16

Vector based

Coordinates in the pixel space

Vector coordinates

[x, y]

[root, pos]

17

Working withreal images?

18

Real life examplesLupin proteoid root

Potato root growth

Maize root architecture

Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

19



primary root tracing

19




identify proteoid LR of interest across images

19





annotate cluster position

19





annotate cluster position

spatial and temporal root development dynamics[ ]

19

Root growth in rhizotronsrhizotron, apex tracking

[contrast - , resolution + ]

20


root tracing


20


root tracing

mark positioning


20

Root growth in rhizotrons

[growth = f(type, age, position)]

rhizotron, apex tracking

root tracing

mark positioning


20

Maize root architectureaeroponic

[contrast - , resolution - ]

21



trace the primary

21



trace the primary

automatic lateral tracing

21



trace the primary

automatic lateral tracing

diameters, root length interbranch, angles [ ]

21

Take home message- Morphology, topology

- Wide range of: • image quality• plant species• biological questions

- Vector based and object-oriented

- Annotation tool

- User interface, data export, ....

22www.uclouvain.be/smartroot

http://www.uclouvain.be/smartroot

http://www.uclouvain.be/smartroot

Acknowledgments

- Tristan Lavigne- Geoffrey Berguet- Hélène Cordonnier- Chantal Lemarié

Beta testers

Funding

23

smartr t - uliege.be · quick root tracing overview. 9 quick root tracing overview. 10 tracing...

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