Larry M. York
@larrymyork.phenotyper.com
Scientist at Oak Ridge National Laboratory. Autonomous discovery, roots, plants, soil, and phenomics. My opinions. Life is a garden.
www.phenotyper.com
www.phenotyper.com
Pinned
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
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
September 28, 2025 at 6:36 PM
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
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
Reposted by Larry M. York
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…
Details: spj.science.org/doi/10.34133/p…
March 4, 2025 at 11:41 AM
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…
Details: spj.science.org/doi/10.34133/p…
Reposted by Larry M. York
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.
September 20, 2024 at 11:30 AM
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.
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!
UI: Get the basics right first!
August 4, 2025 at 9:20 PM
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!
UI: Get the basics right first!
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!
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...
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
June 28, 2025 at 3:34 PM
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!
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.
May 22, 2025 at 3:54 AM
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.
Who makes these UIs? I just want to copy and paste it.
May 6, 2025 at 9:30 PM
Who makes these UIs? I just want to copy and paste it.
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?
What about you? Anybody else garden?
May 4, 2025 at 6:29 PM
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?
What about you? Anybody else garden?
Reposted by Larry M. York
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/...
May 1, 2025 at 10:23 PM
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/...
A boy and his drill press.
Drilling is an essential part of biology.
Drilling is an essential part of biology.
April 17, 2025 at 5:13 PM
A boy and his drill press.
Drilling is an essential part of biology.
Drilling is an essential part of biology.
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!
March 22, 2025 at 1:48 AM
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!
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.
March 18, 2025 at 1:23 AM
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.
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.
January 19, 2025 at 7:49 PM
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.
Reposted by Larry M. York
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
*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
January 15, 2025 at 10:27 AM
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
*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
Reposted by Larry M. York
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.)
January 14, 2025 at 9:26 PM
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.)
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.
Today in Oak Ridge, Tennessee, USA - a beautiful place to live and work. Looking north to my roots in Kentucky.
January 11, 2025 at 3:34 PM
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.
Today in Oak Ridge, Tennessee, USA - a beautiful place to live and work. Looking north to my roots in Kentucky.
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.
January 8, 2025 at 2:32 AM
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.
Reposted by Larry M. York
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!
January 6, 2025 at 5:19 PM
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!
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
www.rhizovision.com
January 6, 2025 at 8:07 PM
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
www.rhizovision.com
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...
Humanoid robots - YouTube
youtube.com
January 5, 2025 at 2:44 AM
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...
So fungal people. Is this a thing? Measuring respiration of fungus growing on agar in petri dish? Well if not, it is now. 🥸
December 31, 2024 at 5:40 PM
So fungal people. Is this a thing? Measuring respiration of fungus growing on agar in petri dish? Well if not, it is now. 🥸
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.
December 25, 2024 at 8:37 PM
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.
Cultured fungi can be really beautiful and interesting to look at. We should take more pictures.
December 25, 2024 at 2:18 AM
Cultured fungi can be really beautiful and interesting to look at. We should take more pictures.