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Protocols

phytoMorph specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Edgar P. Spalding

Publication for phytoMorph

phytoMorph citations

 (8)
call_split

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

2017
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 http://github.com/joegage/TIPS.git and a set of 200 sample images can be found at http://phytomorph.wisc.edu/download/TIPS. […]

library_books

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

2015
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 http://phytomorph.wisc.edu/download/HeckwolfPlantMethods2015/ along with a composite test image representing a variety of transection phenotypes so that the performance of future tools for studying stalk ana […]

library_books

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

2014
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: http://www.doane.edu/doane-phytomorph 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 […]

library_books

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

2013
Genetics
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 http://phytomorph.wisc.edu/hardware/fixed-cameras.php. 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 […]

library_books

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

2013
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 […]

library_books

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

2013
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 http://phytomorph.wisc.edu/G3. Also presented there for download are all the raw images and the comma separated value files containing the filtered results obtained from each image. […]

Citations

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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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