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Static site files for brachypodium.org


MedPlant RNAseq Database Website
PlantCV image analysis scripts used in Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, et al. A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria. Mol Plant. 2015;8: 1520–1535.
PlantCV website repository


LemnaTec front end.

Jupyter Notebook

PlantCV Workshops
The following are scripts and instruction necessary to set up 4 Raspberry Pi Powered Imaging Platforms
PlantCV image analysis scripts used in the PlantCV v2.0 paper
Repository for Outreach Activities
Phenome 2020 Digital Phenotyping workshop materials
A repository for interactive PlantCV documentation using Binder


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Code and notebooks for camelina projects
PlantCV workflows for the Brachypodium ENCODE project
PlantCV scripts for analyzing data from the TERRA-REF project


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National Science Foundation Research Experience for Undergraduates internship bioinformatics and phenotyping workshop materials


The Donald Danforth Plant Science Center Bioinformatics Core Facility public repository




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Plant image analysis using OpenCV
Seed phenotyping with PlantCV
A collection of scripts for building and running HTCondor jobs and workflows
Data Science Tools
Services for managing phenotyping data sources
Development image analysis scripts
Hyperspectral analysis tools in PlantCV
Falcon2Fastg is a tool for converting a FALCON assembly to FASTG format to visualize with Bandage
Suite for phased clusters discovery, comparison, annotation and to identify miRNA triggers - uses MapReduce model [In review]
Persistent homology
PlantCV parallel processing add-on package


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R Package that handles and maintains a connection to GWAS database.
Gehan Lab Shiny App to Explore Quinoa Phenotype Data
Gehan Lab shiny app to graph JTK Cycle Output


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Shiny App for Public Data by Gehan Lab