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

4

Heterogenous image

5

Local information

5

Local information

6

Root system as a population

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

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

Tracing algorithm - 1

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

mouse click

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

Tracing algorithm - 1

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

mouse click

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

Tracing algorithm - 1

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

Tracing algorithm - 1

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

Tracing algorithm - 1

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

Tracing algorithm - 1

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

Tracing algorithm - 1

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

Tracing algorithm - 1

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

Tracing algorithm - 1

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

10

Tracing algorithm - 1

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

10

Tracing algorithm - 1

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

Tracing algorithm - 2

Region of Interest

mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

11

Tracing algorithm - 2

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

Tracing algorithm - 2

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

Tracing algorithm - 2

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

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

12

Tracing algorithm - 3mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

13

Tracing algorithm - 4mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

14

Tracing algorithm - 5mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

14

Tracing algorithm - 5mouse click

node creation

search path

node creation

diameter check

append node

node centering

node centering

local threshold

local threshold

Diameter freeze

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Object oriented

Nodes as individual objects

Root as individual object

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Object oriented

Nodes as individual objects

Root as individual object

Individual actions[move, crop, append]

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Object oriented

Nodes as individual objects Topology

Root as individual object

Individual actions[move, crop, append]

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Vector based

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Vector based

Coordinates in the pixel space

[x, y]

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Vector based

Coordinates in the pixel space

Vector coordinates

[x, y]

[root, pos]

17

Working withreal images?

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Real life examplesLupin proteoid root

Potato root growth

Maize root architecture

Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

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Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

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Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

primary root tracing

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Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

primary root tracing

identify proteoid LR of interest across images

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Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

primary root tracing

identify proteoid LR of interest across images

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Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

primary root tracing

identify proteoid LR of interest across images

annotate cluster position

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Lupin proteoid rootsaeroponic, time lapse

[contrast + , resolution + ]

primary root tracing

identify proteoid LR of interest across images

annotate cluster position

spatial and temporal root development dynamics[ ]

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Root growth in rhizotronsrhizotron, apex tracking

[contrast - , resolution + ]

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Root growth in rhizotronsrhizotron, apex tracking

[contrast - , resolution + ]

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Root growth in rhizotronsrhizotron, apex tracking

root tracing

[contrast - , resolution + ]

20

Root growth in rhizotronsrhizotron, apex tracking

root tracing

mark positioning

[contrast - , resolution + ]

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Root growth in rhizotrons

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

rhizotron, apex tracking

root tracing

mark positioning

[contrast - , resolution + ]

20

Maize root architectureaeroponic

[contrast - , resolution - ]

21

Maize root architectureaeroponic

[contrast - , resolution - ]

trace the primary

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Maize root architectureaeroponic

[contrast - , resolution - ]

trace the primary

automatic lateral tracing

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Maize root architectureaeroponic

[contrast - , resolution - ]

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

Acknowledgments

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

Beta testers

Funding

23