PowerPoint Presentation

Image-based Phenotyping:Capturing and quantifying the world in pixels

Digital images are comprised of pixels

image tutorialBit is binary 1 or 0

Image is 10 pix across x 11 tall pix = 110 pixels

If it were 10 across x 11 tall then = 1 DPI

One byte in an 8-bit image has 8 slots or 28 = 256 combinations of 1/0Bit #7 1/0 Bit #6 1/0Bit #5 1/0Bit #4 1/0Bit #3 1/0Bit #2 1/0Bit #1 1/0Bit #0 1/0

8-bit 16-bit 64-bitThese can be expressed as shades of gray or colors

One byte in a 32-bit image 232 = 4.29 x 109 combinations of 1/0One byte in a 16-bit image has 216 = 65,536 combinations of 1/0information content aka increasingly realistic representation of reality

The living world is dynamic

So how do we define phenotype?

Phenomics has a modest goal: to understand the entirety of phenotype at multiple scales across the breadth of genetic variation

Mapping genotype to phenotype:But what is phenotype?Does phenotype simply correlate to genotype?

Chitwood and Topp COPB 2015

Mapping genotype to phenotype:

Actually Phenotype space is enormous= Genotype (all gene interactions)

Mapping genotype to phenotype:Phenotype is at least Genotype x Environment

B73 maize grown in 3 environments

Mapping genotype to phenotype:Phenotype space is enormous= Genotype (all gene interactions) x Environment

Varieties of the phenotypic experience: small scale

Atomic force microscopyHigh content cell screening

2D gel electrophoresisarstechnica.com

Varieties of the phenotypic experience: Field Scale

Field phenotyping with hyperspectral imaging

Mapping genotype to phenotype:

Phenotype space is enormous= Genotype (all gene interactions) x EnvironmentxScale (from submolecular to ecological scales)

Varieties of the phenotypic experience

Mapping genotype to phenotype:

Phenotype space is enormous= Genotype (all gene interactions) x EnvironmentxScale (from submolecular to ecological scales and those interactions) x Time (dynamics)

allele Aallele B

a simple example of a multivariate traitCheng-Ruei Lee

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allele Aallele B

no difference in allele effects on one univariate axisWidthCheng-Ruei Lee

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allele Aallele B

no difference in allele effects on one axis or the otherDepthCheng-Ruei Lee

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WidthDepth

allele Aallele B

e.g. Multivariate Trait= 2*Depth - 3*Width

a new multivariate axis separates allele effectsCheng-Ruei Lee

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Mapping genotype to phenotype:

Phenotype space is enormous= Genotype (all gene interactions) x EnvironmentxScale (from submolecular to ecological scales and those interactions) x Time (dynamics) xThe way in which we study it (phenotyping approach)

Video informatics uses imaging and computational methods to quantify complex and dynamic phenotypesSportsvision

Video informatics uses imaging and computational methods to quantify complex and dynamic phenotypes

Latent (hidden) phenotypes can be identified through multivariate measurements and analysis

Latent (hidden) phenotypes can be identified through multivariate measurements and analysis

Latent (hidden) phenotypes can be identified through multivariate measurements and analysismultivariate QTL identified

We can leverage advances in robotics, computer vision/AI, and engineering systems for science!

FIJI: Fiji Is Just ImageJ

IMAGING TECHNOLOGY

RAW DATA ACQUISITION computer cannot distinguish object of interest from background

IMAGE PROCESSING computer can now distinguish object of interest from background

IMAGE ANALYSIS Feature Extraction: object of interest measured in different ways

Fahlgren, Feldman, Gehan et al. Plant Phys. In pressImage analysis pipeline