My favourite aspect of our research is interdiscipinarity. Thinking about plant physiology, global change, machine learning, instrument building, then deep in irish winter mud as we install some more minirhizotron tubes with @ianpalk.bsky.social and @ryanbrennan.bsky.social Cool science coming up!
November 7, 2025 at 5:35 PM
My favourite aspect of our research is interdiscipinarity. Thinking about plant physiology, global change, machine learning, instrument building, then deep in irish winter mud as we install some more minirhizotron tubes with @ianpalk.bsky.social and @ryanbrennan.bsky.social Cool science coming up!
🌱 #Fieldwork days at The Jena Experiment - @jena-experiment.bsky.social!
Scanning roots with a minirhizotron, tracking seasonal changes & traits, plus plant surveys & soil checks. Led by PhD candidate Srijna Saxena with support from Tom Künne. Can’t wait to see what the data reveal!
#RootTraits
Scanning roots with a minirhizotron, tracking seasonal changes & traits, plus plant surveys & soil checks. Led by PhD candidate Srijna Saxena with support from Tom Künne. Can’t wait to see what the data reveal!
#RootTraits
August 8, 2025 at 9:29 AM
🌱 #Fieldwork days at The Jena Experiment - @jena-experiment.bsky.social!
Scanning roots with a minirhizotron, tracking seasonal changes & traits, plus plant surveys & soil checks. Led by PhD candidate Srijna Saxena with support from Tom Künne. Can’t wait to see what the data reveal!
#RootTraits
Scanning roots with a minirhizotron, tracking seasonal changes & traits, plus plant surveys & soil checks. Led by PhD candidate Srijna Saxena with support from Tom Künne. Can’t wait to see what the data reveal!
#RootTraits
Last week of fieldwork (for me!) this week for the summer.
We installed minirhizotron tubes at the flux collars in our open and treed bog for incoming postdoc Miranda Hunter’s project looking at above- and belowground productivity/phenology
Ended the trip with a nice poutine by the river !
We installed minirhizotron tubes at the flux collars in our open and treed bog for incoming postdoc Miranda Hunter’s project looking at above- and belowground productivity/phenology
Ended the trip with a nice poutine by the river !
August 13, 2026 at 12:27 PM
Last week of fieldwork (for me!) this week for the summer.
We installed minirhizotron tubes at the flux collars in our open and treed bog for incoming postdoc Miranda Hunter’s project looking at above- and belowground productivity/phenology
Ended the trip with a nice poutine by the river !
We installed minirhizotron tubes at the flux collars in our open and treed bog for incoming postdoc Miranda Hunter’s project looking at above- and belowground productivity/phenology
Ended the trip with a nice poutine by the river !
This week some of our @psb-trinity.bsky.social group were installing minirhizotron (root observatory) tubes at the Majadas de Tiétar eddy covariance site in Extremadura, Spain.
April 24, 2026 at 6:46 PM
This week some of our @psb-trinity.bsky.social group were installing minirhizotron (root observatory) tubes at the Majadas de Tiétar eddy covariance site in Extremadura, Spain.
Mutualisms shape root traits and carbon cycling under global change
nph.onlinelibrary.wiley.com/doi/10.1111/...
#Commentary by Arnaud et al. highlighting the recent work by Milligan et al.
nph.onlinelibrary.wiley.com/share/YYUPBV...
nph.onlinelibrary.wiley.com/doi/10.1111/...
#Commentary by Arnaud et al. highlighting the recent work by Milligan et al.
nph.onlinelibrary.wiley.com/share/YYUPBV...
November 25, 2025 at 2:45 AM
Mutualisms shape root traits and carbon cycling under global change
nph.onlinelibrary.wiley.com/doi/10.1111/...
#Commentary by Arnaud et al. highlighting the recent work by Milligan et al.
nph.onlinelibrary.wiley.com/share/YYUPBV...
nph.onlinelibrary.wiley.com/doi/10.1111/...
#Commentary by Arnaud et al. highlighting the recent work by Milligan et al.
nph.onlinelibrary.wiley.com/share/YYUPBV...
Mutualisms shape root traits and #carbon cycling under global change
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
👆 A #Commentary by Arnaud et al. on this article by Milligan et al. 👇
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#LatestIssue #PlantScience
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
👆 A #Commentary by Arnaud et al. on this article by Milligan et al. 👇
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#LatestIssue #PlantScience
December 18, 2025 at 1:02 PM
Mutualisms shape root traits and #carbon cycling under global change
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
👆 A #Commentary by Arnaud et al. on this article by Milligan et al. 👇
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#LatestIssue #PlantScience
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
👆 A #Commentary by Arnaud et al. on this article by Milligan et al. 👇
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#LatestIssue #PlantScience
This was our office for the day with Jirka Bednařík as we tried out a couple new ways to drill minirhizotron holes.
It's good news for the caprecaillie and bad news for us: the petrol auger was more of a hazard than a use. Quieter methods worked better.
It's good news for the caprecaillie and bad news for us: the petrol auger was more of a hazard than a use. Quieter methods worked better.
June 27, 2025 at 7:29 PM
This was our office for the day with Jirka Bednařík as we tried out a couple new ways to drill minirhizotron holes.
It's good news for the caprecaillie and bad news for us: the petrol auger was more of a hazard than a use. Quieter methods worked better.
It's good news for the caprecaillie and bad news for us: the petrol auger was more of a hazard than a use. Quieter methods worked better.
If you're curious what I'm up to, I'm working on engineering new and improved technology for an automated minirhizotron! This will be a crucial instrument for my PhD research on soil respiration. Follow my progress on @psb-trinity.bsky.social!
#rootecology #ecology
#rootecology #ecology
Building on the @richardnair.bsky.social et al. 2023 automated minirhizotron paper (doi.org/10.1093/jxb/erac427), we're back at it with v2.0!
It's still a pile of wires on the bench, but we're upgrading both the hardware and the neural networks.
First installations of v2.0 are coming this winter!
It's still a pile of wires on the bench, but we're upgrading both the hardware and the neural networks.
First installations of v2.0 are coming this winter!
November 4, 2025 at 12:55 PM
If you're curious what I'm up to, I'm working on engineering new and improved technology for an automated minirhizotron! This will be a crucial instrument for my PhD research on soil respiration. Follow my progress on @psb-trinity.bsky.social!
#rootecology #ecology
#rootecology #ecology
Building on the @richardnair.bsky.social et al. 2023 automated minirhizotron paper (doi.org/10.1093/jxb/erac427), we're back at it with v2.0!
It's still a pile of wires on the bench, but we're upgrading both the hardware and the neural networks.
First installations of v2.0 are coming this winter!
It's still a pile of wires on the bench, but we're upgrading both the hardware and the neural networks.
First installations of v2.0 are coming this winter!
November 4, 2025 at 12:50 PM
Building on the @richardnair.bsky.social et al. 2023 automated minirhizotron paper (doi.org/10.1093/jxb/erac427), we're back at it with v2.0!
It's still a pile of wires on the bench, but we're upgrading both the hardware and the neural networks.
First installations of v2.0 are coming this winter!
It's still a pile of wires on the bench, but we're upgrading both the hardware and the neural networks.
First installations of v2.0 are coming this winter!
The HydroScale project team braved the first snow of the season during minirhizotron installation in the open, post-disturbance stand just off Rokytská slať today.
The ground is soft there so we drill by hand. How deep can we go?
The ground is soft there so we drill by hand. How deep can we go?
November 14, 2024 at 8:54 PM
The HydroScale project team braved the first snow of the season during minirhizotron installation in the open, post-disturbance stand just off Rokytská slať today.
The ground is soft there so we drill by hand. How deep can we go?
The ground is soft there so we drill by hand. How deep can we go?
What about the roots? 🌱👇
Roots were monitored with a minirhizotron system over a period of 800 days. Although sowing order did not affect root productivity, it did change their vertical distribution ⬇️
Roots were monitored with a minirhizotron system over a period of 800 days. Although sowing order did not affect root productivity, it did change their vertical distribution ⬇️
March 20, 2025 at 10:06 AM
What about the roots? 🌱👇
Roots were monitored with a minirhizotron system over a period of 800 days. Although sowing order did not affect root productivity, it did change their vertical distribution ⬇️
Roots were monitored with a minirhizotron system over a period of 800 days. Although sowing order did not affect root productivity, it did change their vertical distribution ⬇️
Trying to beat the rain, to install minirhizotron observation tubes across our paired invaded and invaded riverbank sites - to look at Himalayan balsam rooting strategies
February 21, 2024 at 10:49 AM
Trying to beat the rain, to install minirhizotron observation tubes across our paired invaded and invaded riverbank sites - to look at Himalayan balsam rooting strategies
🚨Publication Alert🚨Root mixture analysis: methods and vision. Marco Lombardi et al. doi.org/10.1016/j.tp... - A 🧪 rational why we need (better) tools to study (crop) #root mixtures to move toward #sustainable #production of #food #feed #energy. Download 50 days: authors.elsevier.com/a/1lZUN4rGdj...
August 8, 2025 at 10:46 AM
🚨Publication Alert🚨Root mixture analysis: methods and vision. Marco Lombardi et al. doi.org/10.1016/j.tp... - A 🧪 rational why we need (better) tools to study (crop) #root mixtures to move toward #sustainable #production of #food #feed #energy. Download 50 days: authors.elsevier.com/a/1lZUN4rGdj...
Images from our Minirhizotron setup at Oulanka National Park to look at roots. So many fungi growing belowground. Fanning exploration, tight root wrapping symbiosis, areal flushing, or polygonal networks. Anyone wanna train a CNN to auto-detect and classify them?
#mycorrhiza #fungi #minirhizotron
#mycorrhiza #fungi #minirhizotron
August 16, 2026 at 12:48 PM
Images from our Minirhizotron setup at Oulanka National Park to look at roots. So many fungi growing belowground. Fanning exploration, tight root wrapping symbiosis, areal flushing, or polygonal networks. Anyone wanna train a CNN to auto-detect and classify them?
#mycorrhiza #fungi #minirhizotron
#mycorrhiza #fungi #minirhizotron
Johannes is also interested in the role of species-specific root trait expression and distribution in peatland methane emissions. Check out Johannes’s R package for Minirhizotron root trait analysis in R at github.com/jcunow/RootScanR 2/3
GitHub - jcunow/RootScanR
Contribute to jcunow/RootScanR development by creating an account on GitHub.
github.com
May 20, 2025 at 11:07 AM
Johannes is also interested in the role of species-specific root trait expression and distribution in peatland methane emissions. Check out Johannes’s R package for Minirhizotron root trait analysis in R at github.com/jcunow/RootScanR 2/3
Very happy to have contributed to this comparison of #minirhizotron segmentation methods. Generalisation is very important for new techniques doi.org/10.1186/s130...
November 8, 2023 at 7:48 AM
Very happy to have contributed to this comparison of #minirhizotron segmentation methods. Generalisation is very important for new techniques doi.org/10.1186/s130...
Sink or source driven? A new contribution on blog: A Paradigm Shift in Plant Growth: Why Roots May Act as Protagonists of a Never-ending Story plantlifebelowground.wordpress.com/2025/03/26/a...
A Paradigm Shift in Plant Growth: Why Roots May Act as Protagonists of a Never-ending Story
Research and commentary by Bertold Mariën from Umeå University in Sweden. Above are minirhizotron photos of the fine roots of deciduous trees. In 2015, Körner1 posited the need for a paradigm shift…
plantlifebelowground.wordpress.com
March 26, 2025 at 6:57 AM
Sink or source driven? A new contribution on blog: A Paradigm Shift in Plant Growth: Why Roots May Act as Protagonists of a Never-ending Story plantlifebelowground.wordpress.com/2025/03/26/a...
Learn about measuring root dynamics using minirhizotron imaging in tropical forests! Featuring @rich_norby and @CordeiroLonghi at the @TropiRoot @NewPhyt workshop hosted at @stri_panama. Filmed by @anaendara at the @PARCHED_Panama plots!
youtube.com/watch?v=uHZqG5…
youtube.com/watch?v=uHZqG5…
December 9, 2024 at 12:21 AM
Learn about measuring root dynamics using minirhizotron imaging in tropical forests! Featuring @rich_norby and @CordeiroLonghi at the @TropiRoot @NewPhyt workshop hosted at @stri_panama. Filmed by @anaendara at the @PARCHED_Panama plots!
youtube.com/watch?v=uHZqG5…
youtube.com/watch?v=uHZqG5…
in rhizotron or minirhizotron images, which has historically been a difficult task to automate. Hand annotation of rhizotron images is laborious and often subjective; SAM, initialized with GeomPrompt local ridge prompts has the potential to [5/7 of https://arxiv.org/abs/2505.21644v1]
May 29, 2025 at 6:00 AM
in rhizotron or minirhizotron images, which has historically been a difficult task to automate. Hand annotation of rhizotron images is laborious and often subjective; SAM, initialized with GeomPrompt local ridge prompts has the potential to [5/7 of https://arxiv.org/abs/2505.21644v1]
This study used innovative minirhizotron imaging and isotopic tracers to investigate deep root growth and function in winter wheat. Key findings: Deep rooting positively correlated with uptake of deep-placed nitrogen and water, and reduced water stress.
October 6, 2025 at 4:49 PM
This study used innovative minirhizotron imaging and isotopic tracers to investigate deep root growth and function in winter wheat. Key findings: Deep rooting positively correlated with uptake of deep-placed nitrogen and water, and reduced water stress.