PhenomeForce
Resources
- Welcome to PhenomeForce
- Fridays Hands-On: A Workshop Series in Data+Plant Sciences
- YouTube Tutorial
- Slack Channel
- Contact
Welcome to PhenomeForce
During the last decade, plant phenomics has grown enormously as a research field in agriculture. With incredible technological advancements in computer vision tools, plant phenomics has found many applications, including, for instance, plant species recognition, plant stress quantification, and crop yield prediction. These various applications of plant phenomics have evolved into multiple specialized niches involving national, international, and multi-disciplinary experts (e.g., plant physiologist, breeders, engineers, informatics, etc.). In the meantime, plant phenomics is increasingly accessible to a larger number of researchers worldwide thanks to the introduction of new, cost-effective setups, adaptable phenotyping platforms, and the emergence of open-source image processing software.
With the growing interest in plant phenomics, a unique platform where experts and novices can easily connect and exchange knowledge and resources are a priority. Fostering communication and cooperation among different stakeholders as well as promoting the interdisciplinary training required for effective plant phenotyping research are among the main purposes of our group.
This group is a platform imagined as an interactive “ metabolic network ”, where the nodes represent the different areas of plant phenomics applications, along with their sub-communities of experts. The main purpose is to provide all the knowledge essential to plan and start your own project of plant phenomics, making phenomics easy for everybody.
This platform will contribute to the goals of Digital Agriculture:
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Bringing together a broad network of experts to share information on data and data science-related projects, collaborations, tools, practices, and discoveries.
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Building partnerships and resources that address emerging issues and discuss challenges and opportunities in agriculture using novel approaches from diverse disciplines.
2021 Fridays Hands-On Workshop Series: “Principles, Protocols, and Pipelines for Drone Phenotyping”
This fall, we will have the 3rd season of the Fridays Hands-On Workshop Series, which will partner with Drone2Phenome (D2P), a new multi-institutional group focused on empowering researchers who use UAVs in plant and animal agricultural research. D2P wants to understand how people use UAVs in their research to identify patterns and principles that can provide a foundation for shared protocols and pipelines. With this in mind, this year’s workshop series will focus primarily on drone image acquisition and analysis. D2P will be using this as an opportunity to curate and share protocols. Usually, the workshop lasts about 2 hours and includes a hands-on section and it is broadcasted live on our Phenome-Force YouTube Channel.
Registration: https://forms.gle/SAmPXZXP8BfYW6gDA
| Speakers | Date | Workshop |
|---|---|---|
| Atena Haghighattalab | 29/Oct | Implementation of high throughput phenotyping pipelines on large plant breeding programs |
| Chongyuan Zhang | 5/Nov | Crop trait phenotyping in plant breeding programs using UAS and feature extraction pipeline |
| Zhou Zhang | 12/Nov | Alfalfa yield and quality prediction using UAV-based hyperspectral imagery |
| Jinha Jung | 19/Nov | How to share UAS data using public clouds |
| Margaret Kruase | 03/Dec | Predicting grain yield with aerial hyperspectral reflectance data |
| Ce Yang & Tyler Nigon | 10/Dec | An automated approach for spatial cropping and plot identification of hyperspectral aerial imagery used in small-plot and on-farm research |
| Alper Adak | 17/Dec | UAV pipeline for image and data analysis using R tools |
Preparing for the next workshop:
Workshop-07: UAV pipeline for image and data analysis using R tools
Speaker: Alper Adak
- GitHub links: https://github.com/alperadak/PhenomeForce
YouTube
Fridays Hands-On Workshop Series 0.3
1) Implementation of high throughput phenotyping pipelines on large plant breeding programs
2) Crop trait phenotyping in plant breeding programs using UAS and feature extraction pipeline
3) Alfalfa yield and quality prediction using UAV-based hyperspectral imagery
5) Predicting grain yield with aerial hyperspectral reflectance data
Fridays Hands-On Workshop Series 0.2
2) Using TERRA REF high throughput, sensor-collected plant data with R
3) RGB-Depth plant phenotyping from top view: system and image analysis
4) Measurement of plant phenotypes with low-cost Raspberry Pi computers and cameras
7) Scalable, cost-effective phenotyping solutions to facilitate quantitative genetics in potato
8) PhytoOracle: A scalable, modular data processing pipeline for phenomic data
9) Use of an Arduino platform for obtaining long term pH readings in plant tissue
10) The basics of drone flights and data extraction for small plot research
Fridays Hands-On Workshop Series 0.1
1) FIELDimageR pipeline: Image analyses applied to plant breeding
2) Quantizing and Quantifying Fruit and Leaf Shape in the Latent Space Using R
4) Mr.Bean: An R-Shiny Web Application for the Analysis of Plant Breeding Experiments
5) Getting Started with WebODM: An Open-Source Solution to Your Mapping Problems
8) Leaf-level hyperspectral reflectance to rapidly estimate plant chemical traits
9) Getting started with ImageBreed: Managing and storing drone imagery
10) Root scanning and image analysis using RhizoVision Explorer
Slack Channel
PhenomeForce Slack Channel is a single place for our community to share messages, tools, pipelines, and files. All main areas of plant phenotyping are being covered by specialists enthusiastic to share their knowledge. If you are interested to be part of this group, please send a message to phenomeforce@gmail.com.
Contact
- Annarita Marrano (annarita.marrano@umb.edu)
- Filipe Matias (fmatias@wisc.edu)
- Noah Fahlgren (nfahlgren@danforthcenter.org)
- GitHub