Jeff Neyhart's Projects
Poster for 2023 Tri-Societies Meeting presenting research on stagewise analysis of perennial breeding trials
AgML is a comprehensive library for agricultural machine learning. Currently, AgML provides access to a wealth of public agricultural datasets for common agricultural deep learning tasks.
The following are scripts and instruction necessary to set up 4 Raspberry Pi Powered Imaging Platforms
An R package to run phenotypic data processing, optimized for the UMN Barley Breeding Group
A pipeline for measuring quality traits on cranberries using images of berries in a lightbox
Code for capturing and analyzing thermal images of berries in a heat chamber
Script to perform various bioinformatics operations
Simple repository of links to tools for plant breeding and genetics
Repository for documenting cranberry exploration and collection trips
GBS Pipeline for SNP calling in historically genotyped cranberry populations
Pipeline to select environmental covariates for use in plant breeding analysis and prediction
Functions to analyze experimental data from the Android Field Book App
Repository of template scripts for implementing fully convolutional neural networks for image segmentation
Field Book
Function to create a formatted excel file based on a plot design function
PyTorch implementation of the paper "Finding Berries: Segmentation and Counting of Cranberries using Point Supervision and Shape Priors". Peri Akiva, Kristin Dana, Peter Oudemans, Michael Mars. CVPRW2020.
An R package for imputing data from genotyping-by-sequencing experiments in bi-parental populations of finite generations of selfing
A pipeline for handling genotyping-by-sequencing data and calling variants
Demo showcasing crown and stem rust detection on perennial ryegrass leaves
A web-app for exploring genomic predictions
A R package for genomic or genomewide selection
Heritability in plant breeding
Poster on cranberry environmental association for the 2021 International Vaccinium Symposium
Recent finds in journals covering genetics, genomics, and evolutionary biology.
Examples of using mixed models for plant breeding applications
Repository supporting the genetic analysis of cranberry interspecific "F2" population
Poster on optimizing regional plant breeding nurseries for the 2022 NABRW/BIC meeting