Plant Image Analysis tools. Current trends and limitations

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P L A N T I M A G E

A N A L Y S I S TO O L S :

C U R R E N T T R E N D S

A N D L I M I TAT I O N S

F U T U R E C H A L L E N G E S

P L A N T I M A G E

A N A L Y S I S TO O L S :

C U R R E N T T R E N D S

A N D L I M I TAT I O N S

G U I L L A U M E L O B E T , X A V I E R D R A Y E & C L A I R E P É R I L L E U X P L A N T I M A G E A N A L Y S I S A N D S O L U T I O N S 1 5 T H O F A P R I L 2 0 1 5 , M A D I S O N Plant Physiology ULg 1 guillaume.lobet@ulg.ac.be @guillaumelobet

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2

C U R R E N T T R E N D S

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T H E P H E N O T Y P I N G C H A L L E N G E

3 / 26

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G E N E T I C VA R I AT I O N P H E N O T Y P I C VA R I AT I O N N E X T G E N E R AT I O N S E Q U E N C I N G P H E N O T Y P I N G P L AT F O R M S

Image

analysis

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P L A N T - I M A G E - A N A L Y S I S . O R G

Lobet et al. 2014 Plant Methods

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I N C R E A S I N G N U M B E R O F P U B L I S H E D TO O L S

time [year] n umber of tools [ − ] 1995 2000 2005 2010 2015 5 10 15 20 5 / 26 Average citations / year 5,6 [Scopus]

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n umber of tools [ − ] 0 5 10 15 journals

L A R G E I N T E R E S T B Y T H E P L A N T C O M M U N I T Y

Plant Physiology Plant Journal Plant Cell New Phytologist Generalist plant journals 6 / 26

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Freeware [82] Commercial D I S T R I B U T I O N O F P L A N T I M A G E A N A L Y S I S TO O L S All [114] Cross-platform [53] Windows Shoot

[14] Root [16] Cell [8] Others [15]

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D E G R E E O F A U TO M AT I O N D E P E N D S O N T H E O R G A N 0 25 50 75 100

shoot_automated root _{semi-automated}cell other_manual

8

Shoot Root Cell Others

images tend to be more

complex/noisy

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B E N C H M A R K D ATA S E T S

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Photo credit: ©John Carey

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shoot root cell general other

M E A S U R E M E N T O V E R L A P B E T W E E N TO O L S

measur ement types root length rosette area # tools measurement type

How can we choose

between them?

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N E E D O F B E N C H M A R K D ATA S E T S

Online repository - ClearedLeafDB Simulated images - ElonSim - ground truth Benoit et al, 2014 Das et al, 2014 11 / 26

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C O N S I S T E N C Y B E T W E E N D ATA S E T S

Nodal root ? Crown root ? Principal root ? Primary root ? - Plant Ontology [www.plantontology.org] - Trait Ontology [www.gramene.org] 12 Depth? Height? m? cm? mm? / 26

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C O M M O N F O R M A L I S M S

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- Multi Tree Graph [MTG]

[openalea.gforge.inria.fr]

[Godin and Caralagio, 1998]

- Root System Markup  

Language [RSML]

[rootsystemml.github.io] 

[Lobet, Pound, Diener, Pradal et al, 2015]

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14 R O O T N AV S M A R T R O O T R S A A N A L Y S E R R O O T R A K R H I Z O S C A N

“One

language

to bring them all

and in your

pipeline

bind them”

E Z R H I Z O 2 R I M A G E J P Y T H O N E X C E L A R C H I D A R T R - S W M S R O O T B O X A R C H I S I M P L E RSML I M A G E A N A L Y S I S A N A L Y S I SD ATA M O D E L I N G

Lobet, Pound, Diener, Pradal et al, 2015, Plant Physiology

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G E T T I N G M O R E O U T O F P L A N T I M A G E S

15 / 26

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M O V I N G AWAY F R O M S E E D L I N G S

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In-depth analysis of

complex root systems

is still missing…

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M U L T I - D I M E N S I O N A L I M A G I N G

17 Chaerle et al. 2000 - Multi-spectral imaging - infra-red - thermography - … - 3D imaging - reconstruction - segmentation - …

- Combining multiple scales

- cell

- organ - …

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M O V I N G TO T H E F I E L D

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D ATA S TO R A G E A N D B A C K U P S

/ 26 - Aeroponics robot in LLN - 250 000 images - 4000 x 15000 px

- 2Mb / images (in jpeg) - 500Gb / experiment

Need for specific storage

and backup solution

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L I M I TAT I O N S O F A C A D E M I C TO O L S

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"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com

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L O N G T E R M M A I N T E N A N C E I S N O T E N S U R E D

tool development

funding for an in-house

image analysis specialist

W E S H O U L D D E V E L O P A N I M A G E A N A L Y S I S TO O L ! manual publication use _????

Maintaining academic

tools is not profitable on

the short term

21 / 26 W E T R Y W H AT ’ S O U T T H E R E A N D I T D O E S N ’ T W O R K …

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W R I T I N G A L G O R I T H M

≠

D E V E L O P I N G TO O L S

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User interface is of important for

dissemination in the plant scientific community

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S O U R C E C O D E I S N O T A L WAY S AVA I L A B L E

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Making the source available is a way to ensure durability

- version control - DOI

- …

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W R A P P I N G U P

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TA K E H O M E M E S S A G E .

- many tools available [www.plant-image-analysis.org] - ranging from cell to canopies

- fair proportion of free, automated, cross-platform solutions

Current trends

- need for benchmark image datasets - getting more out complex images

- increase automation for complex problems - moving out of the lab

- ensuring long-term maintenance of useful tools

Future challenges

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UPCOMING EVENTS:

Emerging technologies for root system scale imaging and phenotyping

Roundtable at Rhizosphere 4 Meeting - 21-25 June 2015 www.rhizo4.org

Insights into plant biological processes through phenotyping

Ghent, Belgium - 13-19 Sept 2015

http://events.embo.org/15-plant-phenotyping/

Workshop on Image Analysis Methods for the Plant Sciences

Louvain-la-Neuve, Belgium - 21-22 Sept 2015 http://www.phytosystems.ulg.ac.be/iamps15/

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Thank you for

your attention.

Any questions?

Presentation available on figshare

bit.ly/plantimage-lobet

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