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phytoMorph specifications


Unique identifier OMICS_34347
Name phytoMorph
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Edgar P. Spalding

Publication for phytoMorph

phytoMorph citations


TIPS: a system for automated image based phenotyping of maize tassels

Plant Methods
PMCID: 5374692
PMID: 28373892
DOI: 10.1186/s13007-017-0172-8
call_split See protocol

[…] downstream analysis of results was performed in R [].Scripts for image and analysis can be found on Github at and a set of 200 sample images can be found at […]


Image analysis of anatomical traits in stalk transections of maize and other grasses

Plant Methods
PMCID: 4404653
PMID: 25901177
DOI: 10.1186/s13007-015-0070-x

[…] cal solutions produced an effective tool for high-throughput quantification of anatomical features in grass stalks. The tool, written in the Matlab computer language, is staged for download at along with a composite test image representing a variety of transection phenotypes so that the performance of future tools for studying stalk ana […]


Using Flatbed Scanners to Collect High resolution Time lapsed Images of the Arabidopsis Root Gravitropic Response

PMCID: 4091038
PMID: 24513680
DOI: 10.3791/50878

[…] ng 10 ml of transparent medium and 9 seeds planted across the middle of each plate were used. Procedures for plate labeling, media preparation and planting can be found at: Retrieve the first agar plate and absorb collected condensation on the lid and rim of the lid of the agar plate with a Kimwipe.Apply Triton X-100 (a detergent) to lid with a Kimwipe -- be g […]


High Throughput Computer Vision Introduces the Time Axis to a Quantitative Trait Map of a Plant Growth Response

PMCID: 3813838
PMID: 23979570
DOI: 10.1534/genetics.113.153346

[…] as many Petri plates, each backlit with 880 nm radiation in a room maintained at ∼22°, essentially as previously described (; ). Instructions on how to create a similar apparatus are posted at To initiate the experiment, each Petri dish was held in a custom plate holder in front of a camera and rotated by 90°. Framing, focusing, and starting i […]


The RootScope: a simple high throughput screening system for quantitating gene expression dynamics in plant roots

BMC Plant Biol
PMCID: 3852858
PMID: 24119322
DOI: 10.1186/1471-2229-13-158

[…] ractice. In this paper we report using the RootScope as a fluorescence microscope for quantifying a GFP based transcriptional reporter. Similar to existing non-fluorescent phenotyping systems such as Phytomorph, the microscope is flexible and could also be used to generate high resolution incident light images to characterize growth dynamics in multiple plants simultaneously [,]. Because the optic […]


Mapping Quantitative Trait Loci Affecting Arabidopsis thaliana Seed Morphology Features Extracted Computationally From Images

PMCID: 3538336
PMID: 23316443
DOI: 10.1534/g3.112.003806

[…] ter filtering to remove nonseeds were the traits subjected to statistical genetic analyses.The algorithm, written in the Matlab language and operating instructions is presented for download at Also presented there for download are all the raw images and the comma separated value files containing the filtered results obtained from each image. […]


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phytoMorph institution(s)
Department of Botany, University of Wisconsin-Madison, Madison, WI, USA; Department of Agronomy, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, Madison, WI, USA
phytoMorph funding source(s)
Supported by National Science Foundation grant IOS -1444456 and USDA Hatch grant WIS01639.

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