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Rosette Tracker: an open source image analysis tool for automatic quantification of genotype effects Jonas De Vylder Filip Vandenbussche Yuming Hu Wilfried Philips Dominique Van Der Straeten

Rosette Tracker

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Outline 1. 2. 3. 4. 5.

Why? How? What? Is it usable? Conclusion

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Outline 1. Why? 2. 3. 4. 5.

How? What? Is it usable? Conclusion

Rosette Tracker

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Plant monitoring

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Plant monitoring

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Constraints

Generic

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Outline 1. Why?

2. How? 3. What? 4. Is it usable? 5. Conclusion Rosette Tracker

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Workflow 30000 30000

00

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Colour calibration

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A) Input

B) Hue

Restricted to VIS? C) Histogram

300 00

0

300 00

D) Model

0

E) segmentation

F) Connected components

G) Rosette detection

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To easy?

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Registration

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Corrections

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Outline 1. Why? 2. How?

3. What? 4. Is it usable? 5. Conclusion

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Size measurements

RGR=ln( Area1/Area2)/t

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Scaling calibration

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Shape measurements

stockiness  4

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Area perimeter ²

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Intensity Measurements

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Outline 1. Why? 2. How? 3. What?

4. Is it usable? 5. Conclusion

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Example 1: Col-0 size measurements

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Example 2: Time lapse analysis

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Easy to use

Demo.wmf

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Outline 1. 2. 3. 4.

Why? How? What? Is it usable?

5. Conclusion Rosette Tracker

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Conclusion •Digital phenotyping tool •Plug in for imageJ •http://telin.ugent.be/~jdvylder/RosetteTracker

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Rosette Tracker - an open source image analysis tool for quantification of genotype effects  

PDF of the talk at the PhenoDays 2012 in Wageningen, NL

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