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Root Phenomics Team

@rootphenomics

We advance root phenotyping that links form to function from basic to applied science focusing on carbon. @LarryMattYork leads @ORNL. Member opinions only

 Oak Ridge, TN
rootbiologist.com
Joined July 2016
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The lab is fully-vaccinated! We had our first in-person social event, an outside BBQ, since December, 2019. We enjoyed great company and great food. Still cautious in general, but was great to see everyone together. @ASeethepalli @haichao_guo @soilnwater @LarryMattYork
Image from Root Phenomics Team (@rootphenomics)
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Did you ever wish there was a public image set based on scans of physical objects with known length, diameter, and volume for validating image analysis algorithms? Granted! This set was used to validate @RhizoVision Explorer and includes ground truth data doi.org/10.5281/zenodo.46775…
An example image from the linked public image set showing a greyscale scan of 12 copper wires with varying diameter and approximately equal lengths.

ALT An example image from the linked public image set showing a greyscale scan of 12 copper wires with varying diameter and approximately equal lengths.

Tabular data with 5 columns and 28 data rows, 1 row for each image of one or more wires. The column names are file name, average diameter, total length, total surface area, total projected area, and total volume. CSV file of this data available in the linked public repository.

ALT Tabular data with 5 columns and 28 data rows, 1 row for each image of one or more wires. The column names are file name, average diameter, total length, total surface area, total projected area, and total volume. CSV file of this data available in the linked public repository.

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An illustrated protocol, example R code, and example data output have been released detailing how to use @LICOR_ENV 850 gas analyzers (roughly $6,000) for high-throughput measures of root respiration and to process directories of output. #gasflux zenodo.org/record/4247873
Photo of three gas analyzers and bead bath described in the illustrated protocol included in the link.

ALT Photo of three gas analyzers and bead bath described in the illustrated protocol included in the link.

Page describing title, authors, and parts needed in the illustrated protocol. Full text included as PDF in the link.

ALT Page describing title, authors, and parts needed in the illustrated protocol. Full text included as PDF in the link.

Page describing methods and root chamber in the illustrated protocol. Full text included as PDF in the link.

ALT Page describing methods and root chamber in the illustrated protocol. Full text included as PDF in the link.

Page describing use of the gas analyzer software in the illustrated protocol. Full text included as PDF in the link.

ALT Page describing use of the gas analyzer software in the illustrated protocol. Full text included as PDF in the link.

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Happy birthday to Yaxin! We surprised our lab manager, Dr. Ge, with flowers and muffins! She's been with us for almost one year and keeps the lab running and always improving.
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The interactive version of RhizoVision Analyzer is on the way. Built for scanned disconnected roots or whole roots such as root crowns or seedling root systems. You choose. See how thresholding changes your results, add diameter classes, batch mode. Free. Open source.
Image from Root Phenomics Team (@rootphenomics)
Image from Root Phenomics Team (@rootphenomics)
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Our lab including three summer interns who are finishing up their projects soon. Lab meetings are a lot more fun with such a diverse and talented group.
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We welcome Kundan Dhakal @soilnwater to the @rootphenomics lab. Kundan brings experience working with cropping systems simulations and will focus on using APSIM and OpenSimRoot to better under the roles root traits play in determining yield in variable environments.
Image from Root Phenomics Team (@rootphenomics)
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We are a lab that uses a lot of pipe. Some suspect we are a band of plumbers.
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We are recruiting a postdoctoral fellow to work on a Noble-funded project "Virtual plants for real progress in optimizing cropping systems." We need somebody with plant simulation experience who can integrate into a phenomics group. Contact me for details careers-noble.icims.com/jobs…
Image from Root Phenomics Team (@rootphenomics)
Image from Root Phenomics Team (@rootphenomics)
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We welcome our first lab manager, Dr. Yaxin Ge. Yaxin has a lot of experience managing labs and in just a couple weeks has gotten the place decluttered, organized, secured more storage space, secured instruments from departing labs, and made contributions to several experiments.
Image from Root Phenomics Team (@rootphenomics)
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