Larry M. York
@larrymyork.phenotyper.com
1.4K followers 710 following 110 posts
Scientist at Oak Ridge National Laboratory. Autonomous discovery, roots, plants, soil, and phenomics. My opinions. Life is a garden. www.phenotyper.com
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larrymyork.phenotyper.com
Get ready for MicrobeVision
A figure entitled MicrobeVision showing a pipeline with an imaging station for acquiring standardized images of a red fungal colony growing that is passed to the software showing a time-series plot of growth. The software has a logo with a blue circle filled with grey with three red overlapping circles representing a microbe colony on a petri dish.
larrymyork.phenotyper.com
I've been working on this then it hit me. Is this RhizoVision Tron?

With open hardware and software, we can accelerate root, soil, and microbiome research.

First, we have to solve the segmentation challenge of roots on soil so everyone can do it.

www.rhizovision.com
This is a aluminum profile structure with black plastic panels with a clear window on one side and a machine vision camera facing it from the other side about 60 cm away. On top of this, rhizotron is a computer laptop that shows a camera viewing software with a live feed depicting the current window which has a tool on it
larrymyork.phenotyper.com
Great idea! I'm in a different field but do image analysis. Zenodo.org is a good fit. Give every image a unique file name. Make a csv file where each row has the file name and columns for species, collection site, other info, then columns for the measurements. Separate file that defines columns.
larrymyork.phenotyper.com
I was asked to give that last minute. Thanks for staying!

www.rhizovision.com is still kicking, new version coming out soon.
RhizoVision Explorer
Get ready for RhizoVision - see roots like never before
www.rhizovision.com
Reposted by Larry M. York
plantphenomics.bsky.social
Studying root systems with germination papers offers high resolution but lacks natural conditions. Using FSPMs and RhizoVision, we analyzed Populus trichocarpa roots, finding thermal time correlation and varying 2D/3D accuracy.
Details: spj.science.org/doi/10.34133/p…
larrymyork.phenotyper.com
How did this go? We have a new Linux version of RhizoVision with a command line mode to call from Python scripts. Let me know if you think it'd be useful for your pipeline, hopefully we can share a beta version soon
Reposted by Larry M. York
botany.one
Advanced software, RhizoVision Explorer, analysed these images to extract detailed root architecture traits. The team also conducted genetic analysis using DarTSeq technology to identify DNA markers associated with root responses to phosphorus availability.
larrymyork.phenotyper.com
Do you have any information about the new model?

I share my protocols as PDFs on zenodo.org which provides a DOI and the ability to track views and downloads.

See phenotyper.com/datasets for examples
larrymyork.phenotyper.com
I upgraded to M365 Copilot which integrated some LLM with all my office apps. Kinda neat, has potential but needs work. On the other hand, when I right click words with red lines highlighting misspelling, there is no correction available!

UI: Get the basics right first!
larrymyork.phenotyper.com
I am concerned about that too.
larrymyork.phenotyper.com
Ha, well my memory is not as good. I've become really fascinated by agentic AI and how to use chatbots effectively. A single LLM is not enough but as we start bolting together many models, something profound is going to happen.

I miss the lack of discussion on human consciousness though.
larrymyork.phenotyper.com
Reminds me of the famous saying, "All art is plagiarism."

I sympathize but I also wonder what we really know about human creativity and thought. What exactly is different?
larrymyork.phenotyper.com
Worth sharing. Pay attention and remember drowning can be calm and quiet, watch out for kids. You know when they're quiet there might be trouble!
trishgreenhalgh.bsky.social
Thanks for the reminder @janemunday.bsky.social. Every summer, I repost this article DROWNING DOES NOT LOOK LIKE DROWNING. To date, I know of FOUR kids who were saved after someone who'd clicked on the link learnt how to spot actual drowning. Take time to read and pass on.

slate.com/technology/2...
Drowning Doesn’t Look Like Drowning
Drowning is not the violent, splashing call for help that most people expect.
slate.com
larrymyork.phenotyper.com
At the IPG Root Biology Symposium at the University of Missouri. ChatGPT helped summarize the abstract book in graphical form. Great speakers and familiar faces of root biologists. Thanks to the organizers for inviting me and looking forward to telling you all more about RhizoVision Transformer.
Man smiling and doing the peace sign in front of the life science building at University of Missouri Graphical output from chat GDP generated by asking the model to summarize the abstract book in a graphical form. It talks about advancing root biology, root architecture, multiomics and AI root microbe interactions abiotic stress, cross species and translational insights, genetic and molecular regulationary development and species and parole through imaging and modeling A beautiful sunset over the skyline of forest from downtown Columbia, Missouri Recognizing the sponsors. Thank you. Includes many departments within the University of Missouri companies like Bayer and cortava Danforth issr the ippn are gone and others
larrymyork.phenotyper.com
Who makes these UIs? I just want to copy and paste it.
screenshot of journal page where the 'cite' button brings up save and export options but not the actual citation.
larrymyork.phenotyper.com
Expanded the vegetable garden again this year - on the right side there. We enjoy planting and harvests throughout the year. Tennessee has a great climate for gardens but the clay soil needs work.

What about you? Anybody else garden?
Photo of fenced in vegetable garden with exposed soil and some plants in a yard with a wooden fence behind it and some visible houses and trees farther away
Reposted by Larry M. York
stephpau.bsky.social
How does #hyperspectral leaf reflectance vary with functional traits, site, and evolutionary lineage in #grasses? New paper, part of a special issue "Advancing Spectral Biology to Understand Plant Diversity Across Scales", check it out: esajournals.onlinelibrary.wiley.com/doi/10.1002/...
larrymyork.phenotyper.com
I remember seeing the terracotta soldiers there!
larrymyork.phenotyper.com
A boy and his drill press.

Drilling is an essential part of biology.
A man with black-framed glasses standing next to a drill press with his hand on the lever.
larrymyork.phenotyper.com
I'm still comprehending that our new 256 core, 1 TB RAM, 2x NVIDIA L40s analytics server is edge compute at a place like ORNL. AI-enabled image analysis is hungry. I'm fortunate to work with people who know what they are doing!
larrymyork.phenotyper.com
What, isn't it kinda weird you can't delete your last prompt and model output from context when it's not going well in ChatGPT? That seems like an obvious need after using it a few times.
larrymyork.phenotyper.com
Thanks Amit, interesting work
larrymyork.phenotyper.com
It's awesome! I've been watching your and other xray microscopy work for awhile but I wanted it for high throughout applications. Is it still a long scan time for something like root anatomy?
larrymyork.phenotyper.com
So for how many years did we miss updates on their incremental work?
larrymyork.phenotyper.com
Are the streaks of thin lines the hyphae?!