smartr t - uliege.be · quick root tracing overview. 9 quick root tracing overview. 10 tracing...
TRANSCRIPT
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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
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What we do in our lab
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What is SmartRoot?
• Semi-automated
• Root tracing software
• Morphology, topology
• Wide range of image
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Why semi-automated?
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Heterogenous image
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Heterogenous image
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Local information
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Local information
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Root system as a population
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Root system as a population
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Why semi-automated?
• Local information is needed
• Sample the root system
• Sample the image
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How does it work?
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Quick root tracing overview
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Quick root tracing overview
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Tracing algorithm - 1
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
mouse click
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Tracing algorithm - 1
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
mouse click
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Tracing algorithm - 1
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
mouse click
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Tracing algorithm - 1
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
mouse click
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Tracing algorithm - 1
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
mouse click
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Tracing algorithm - 2mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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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
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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
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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
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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
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Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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12
Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 3mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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13
Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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13
Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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13
Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 4mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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Tracing algorithm - 5mouse click
node creation
search path
node creation
diameter check
append node
node centering
node centering
local threshold
local threshold
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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]
![Page 55: SmartR T - uliege.be · Quick root tracing overview. 9 Quick root tracing overview. 10 Tracing algorithm - 1 node creation search path node creation diameter check append node node](https://reader034.vdocuments.us/reader034/viewer/2022042811/5fa478307e21943f5b381d9e/html5/thumbnails/55.jpg)
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Vector based
Coordinates in the pixel space
Vector coordinates
[x, y]
[root, pos]
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Working withreal images?
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Real life examplesLupin proteoid root
Potato root growth
Maize root architecture
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Lupin proteoid rootsaeroponic, time lapse
[contrast + , resolution + ]
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![Page 59: SmartR T - uliege.be · Quick root tracing overview. 9 Quick root tracing overview. 10 Tracing algorithm - 1 node creation search path node creation diameter check append node node](https://reader034.vdocuments.us/reader034/viewer/2022042811/5fa478307e21943f5b381d9e/html5/thumbnails/59.jpg)
Lupin proteoid rootsaeroponic, time lapse
[contrast + , resolution + ]
19
![Page 60: SmartR T - uliege.be · Quick root tracing overview. 9 Quick root tracing overview. 10 Tracing algorithm - 1 node creation search path node creation diameter check append node node](https://reader034.vdocuments.us/reader034/viewer/2022042811/5fa478307e21943f5b381d9e/html5/thumbnails/60.jpg)
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 + ]
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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 + ]
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Maize root architectureaeroponic
[contrast - , resolution - ]
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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 [ ]
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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
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Acknowledgments
- Tristan Lavigne- Geoffrey Berguet- Hélène Cordonnier- Chantal Lemarié
Beta testers
Funding
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