iiinova — where your digital self keeps evolving

Larry M. York @larrymyork.phenotyper.com · 29/06/2026

Meet Leafy 🌿 The newest member of the #GenesisMission. Built on Reachy Mini from Pollen Robotics and Hugging Face, Leafy is another step toward an experiment you can talk to. A physical avatar for a complete agentic stack for autonomous phenotyping. #Robotics

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International Society of Root Research @rootscientists.bsky.social · 17/06/2026

📅 SAVE THE DATE for the ISRR 13th International Symposium 12th - 17th September, 2027 In Beijing, China. Planning is underway and details will be shared when we have them.

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Larry M. York @larrymyork.phenotyper.com · 13/04/2026

Exploring a “Dark Knight Agent” built to observe ruthlessly, test competing hypotheses, and guide experiments under uncertainty. A superhero-inspired detective for science. And bats. From noisy data → to system insight. lmyork.github.io/MVBOT1-Status/ #GenesisMission #AI #AutonomousLabs

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Larry M. York @larrymyork.phenotyper.com · 27/03/2026

Do you know how to get your data AI-ready? Just upload to Zenodo.org with as good a description as you can muster and call it a day. Simply sharing has always been the most important part of open science. #GenesisMission #OpenScience

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Larry M. York @larrymyork.phenotyper.com · 25/03/2026

Spent the past year preparing for the DOE Genesis Mission—upskilling in robotics and AI. Programmed robots first. Now shifting to teaching them. From controlled automation to adaptable, dynamic lab systems. #GenesisMission #LabAutomation

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Larry M. York @larrymyork.phenotyper.com · 19/03/2026

A year ago I started with a cobot and block code. Now: a fully enclosed, safety-integrated, Python-driven autonomous lab system with imaging, custom hardware, and a full GUI. Next: streaming data, agents, and talking to the lab. The future of autonomous labs is open. #GenesisMission #OpenScience

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Larry M. York @larrymyork.phenotyper.com · 16/03/2026

Trying something new: moving from AI-assisted coding toward agentic engineering. Before writing code, we defined: • instructions • target architecture • phased development plan The idea: give AI a clear blueprint instead of a blank page. #AIforScience #ScientificComputing #GenesisMission

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Larry M. York @larrymyork.phenotyper.com · 25/02/2026

Ever dance with the devil in the pale moonlight? - The Joker Sometimes it's nice to just watch.

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Larry M. York @larrymyork.phenotyper.com · 23/02/2026

Forced a collision in our plate imaging robot to demonstrate something more important than automation: safe failure and deterministic recovery. Autonomy only works if safety is engineered first. Agentic layer coming up. #AutonomousLabs #GenesisMission

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Larry M. York @larrymyork.phenotyper.com · 21/02/2026

LLMs don’t actually use tools. They’re stateless: text in, text out. “Tool use” is orchestration — structured text that systems parse and execute in between. #AutonomousLabs #GenesisMission

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Larry M. York @larrymyork.phenotyper.com · 11/02/2026

Excited to share our first fully integrated prototype, safety-compliant robotic plate imaging workcell at ORNL—complete with enclosure, Banner SC10 controller, door interlocks, and protective stop with a uFactory xArm 5. #GenesisMission #AutonomousLabs #Robotics #OpenScience #LabAutomation

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Larry M. York @larrymyork.phenotyper.com · 10/02/2026

One year ago I led an effort to standardize microbial imaging at work, procuring a colony doc it imager. We've demonstrated high reliability measures of microbial responses to minerals and to other species. Now, I've created an open-source robotic workcell to do the same. More soon!

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Larry M. York @larrymyork.phenotyper.com · 09/02/2026

Excited to demo the first safety control system for our robotic workcell. As labs become more automated, it’s easy for safety to lag - getting it right early has been eye-opening. More to share soon as the COBOT Autonomous Lab continues to develop. #MachineSafety #AutonomousLabs #GenesisMission

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Larry M. York @larrymyork.phenotyper.com · 28/09/2025

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

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Plant Phenomics @plantphenomics.bsky.social · 04/03/2025

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…

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Botany One @botany.one · 20/09/2024

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.

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Larry M. York @larrymyork.phenotyper.com · 04/08/2025

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!

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Larry M. York @larrymyork.phenotyper.com · 28/06/2025

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!

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Larry M. York @larrymyork.phenotyper.com · 22/05/2025

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

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Larry M. York @larrymyork.phenotyper.com · 06/05/2025

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.

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Larry M. York @larrymyork.phenotyper.com · 04/05/2025

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

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Stephanie Pau @stephpau.bsky.social · 01/05/2025

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/...

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Larry M. York @larrymyork.phenotyper.com · 17/04/2025

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.

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Larry M. York @larrymyork.phenotyper.com · 22/03/2025

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!

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Larry M. York @larrymyork.phenotyper.com · 18/03/2025

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.

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Larry M. York @larrymyork.phenotyper.com · 19/01/2025

What is publication post-super intelligent AI? Is writing the same background over and over that important when a chatbot can summarize your field in 3 seconds? It's more clear than ever that we are stewards of reliable experiments including data collection, analysis, and depositing.

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Borjana Arsova @borjana-a.bsky.social · 15/01/2025

Dear 🧪PIs, I'm curious: do u have a #strategy for finishing projects in situations when the hired 🧑‍🔬 changes jobs while the project is still running? *we r a few months b4 project end & there is a 2nd unfin. project (from before my time as #PI). A 🪙 for your thoughts! #PlantScience #GroupLeader

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Tom Buckley @tombuckleylab.bsky.social · 14/01/2025

Anyone out there dealt with the issue of your uni's postdoc salary scale being higher than what a grant provides? (NSF postdoc in this case.)

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Larry M. York @larrymyork.phenotyper.com · 11/01/2025

The snow lay as a cold blanket. Today in Oak Ridge, Tennessee, USA - a beautiful place to live and work. Looking north to my roots in Kentucky.

A snowy view towards mountains in the distance and down on a neighborhood with several snow covered houses and trees. White clouds and a peak of blue sky

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Larry M. York @larrymyork.phenotyper.com · 08/01/2025

Not long ago we dreamed up this fungal imaging experiment comparing two species growing on 3 levels of nitrogen in glucose minimal media. 5 reps. I did the best I could to get clear, daily images for 12 days. Big kudos to @lagergren.bsky.social and Anand for doing initial analysis in 1! day.

360 images of fungi growing on petri dishes arranged by two species Fusarium and Linemannia, 3 nitrogen levels, and 12 days. Fusarium looks red and linemannia white. You can see they grow over time but reduced nitrate reduces their growth.

A graph depicting time series area with the two strains colored by green and red, and the 3 nitrogen levels depicted by shapes and line type. Can see FG in red grows faster and for both species growth rate only a little affected from 100% to 10% N, but greatly from 10% to 1%.

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Rachel Mitchell @funeco.bsky.social · 06/01/2025

Peer-Review PSA: 1) review the paper you have, not an imaginary paper. Telling someone they could have done a different experiment is not helpful! 2) If you say someone missed sources or observations or whatever, provide citations! Support the author, don't pretend it's a citation easter egg hunt!

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Larry M. York @larrymyork.phenotyper.com · 06/01/2025

Do you want to study roots? We released RhizoVision Explorer 3 years ago and now have 12,500+ downloads. RVE is free, open-source software for analyzing root images. The website covers common reproducible imaging approaches. Feel free to ask any questions! Version 2 coming! www.rhizovision.com

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Larry M. York @larrymyork.phenotyper.com · 05/01/2025

I'm really into humanoid robots. You know, the ones that can walk on two legs, have arms, all that. In the past year there has been an explosion of these robots, at least 10 advanced varieties. For me, the possibilities are exciting. Check out my YouTube list and... youtube.com/playlist?lis...

youtube.com

Humanoid robots - YouTube

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Larry M. York @larrymyork.phenotyper.com · 31/12/2024

So fungal people. Is this a thing? Measuring respiration of fungus growing on agar in petri dish? Well if not, it is now. 🥸

In lab. Imager, stack of petri dishes, clear enclosure with dish attached to infrared gas analyzer, barcode scanner, and laptop logging increase in CO2.

Overhead shot of petri dish with white and red fusarium fungus inside clear enclosure with tubing ports attached for gas flux analysis.

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Larry M. York @larrymyork.phenotyper.com · 25/12/2024

OK well here's one way to get a lot of images making use of barcodes for sample IDs and staying focused to acquire two different light source images per petri dish by manually flipping the switches. About a minute a dish. Sped up 10x. Merry Christmas and Happy Solstice.

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Larry M. York @larrymyork.phenotyper.com · 25/12/2024

Cultured fungi can be really beautiful and interesting to look at. We should take more pictures.

A round petri dish with a red fungal plug in the center and white hyphae spreading away radially across the entire plate.

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Larry M. York @larrymyork.phenotyper.com · 16/12/2024

My colleague @lagergren.bsky.social leading a hackathon to teach two interns, Jack and Janou, and our software developer, Anand, how to build a convolutional neural network for image analysis from scratch on their journey to be leaders in AI for research!

Image of man standing in front of 3 other men sitting around a table with laptops. The standing man is pointing to a large screen with computer code as the others look on.

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Dr. Katrin Fleischer @kaaze7.bsky.social · 13/12/2024

Could not make it to #BES2024 or to the cross-biome tree root trait and function session @moniqueweemstra.bsky.social and I organized? No worries, I will summarize it here.

A large podium with 6 people sitting in front of an audience with one person
chairing the discussion. In the back is a green screen titled “thematic session - tree root traits and functions: A balanced cross-biome perspective”

View from behind a desk onto a large audience.

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José Dinneny @josedinneny.bsky.social · 09/12/2024

Proud to share our new @plantphys.bsky.social review exploring the anatomical and molecular basis for root adaptations to the environment. Prashanth Ramachandran and Andrea Ramirez detail cell types and pathways that help plants stay resilient in a changing world. academic.oup.com/plphys/advan...

academic.oup.com

Rooting for survival: how plants tackle a challenging environment through a diversity of root forms and functions

Abstract. The current climate crisis has global impacts and will affect the physiology of plants across every continent. Ensuring resilience of our agricul

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Jeff Dukes @dukesjeff.bsky.social · 03/12/2024

Interested in how and where trees move water? I'm hiring a plant ecophys postdoc to study hydraulic redistribution in Indiana forests. If you'll be at AGU and want to discuss, please reach out! jobs.carnegiescience.edu/jobs/postdoc...

jobs.carnegiescience.edu

Job: Postdoctoral Opportunity: Hydraulic redistribution in forests | Carnegie Science Careers

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Larry M. York @larrymyork.phenotyper.com · 04/12/2024

I enjoy writing reviews. I learn a lot reading the literature and organizing thought in the field. Attempting to synthesize ideas and proposing conceptual advancements is how we move a field forward. It is a great chance for early career researchers to plant a flag. Here's a review of my reviews 👇

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Bluesky @bsky.app · 03/12/2024

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

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Sophien Kamoun @kamounlab.bsky.social · 02/12/2024

My talk "How to science (and how not to science)" presented at the Swedish University of Agricultural Sciences; course "How to pick a scientific problem" organized by Shamik Mazumdar and Simon Stael. November 18, 2024. doi.org/10.5281/zeno...

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Larry M. York @larrymyork.phenotyper.com · 30/11/2024

I wasn't very sure why the handles on Bluesky were so long. Turns out that is a method for identity verification by which you can attach your own custom domain. I've had a website for a long time and was able to combine a couple steps to get LarryMYork.phenotyper.com as my handle. Want your own? 👇

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Dan Udwary @danudwary.secondarymetabolism.com · 25/11/2024

OK, I've adjusted the Secondary Metabolism feed to no longer catch the words "natural products", since it was getting way too much non-scientific stuff. So, it's on all of us now to tag cool natural products content with #secmet or #natprod !

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Wolfgang Busch @rootstrapping.bsky.social · 23/11/2024

Great opportunity for postdocs including 🌱! Join Salk’s Rising Stars Symposium, May 13–14. Present your research, engage with leading scientists & explore pathways at Salk. Apply by January 10, 2025! salk.edu/about/our-co... #PlantBiology #RisingStars #SalkInstitute

salk.edu

Rising Stars Symposium - Salk Institute for Biological Studies

We are pleased to announce the second annual Rising Stars Symposium at the Salk Institute for Biological Studies. This symposium is intended to recognize the accomplishments of outstanding postdoctora...

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