Dirk Baker

📣3D Visualization of Biological Systems in Paraview
Join our workshop on Thursday/Friday on a powerful tool for visualization: Paraview! 👉https://events.hifis.net/event/3367/ This work is a collaboration between my colleague Tobias Selzner and myself: put biodata into 3d visualizations with us!

Got it working again after deliberately breaking it....

There are photography websites with something like a CC-BY model. There you can even do a copyright violation yourself by not providing attribution, instead of asking AI to violate copyright for you. I've seen too many AI animals (just plain normal animals!) in presentations in 2025.

Goodbye 2025… This was the first full year I spent in Leipzig and I am excited to see what 2026 brings me! I am in the fortunate position that there are a lot of opportunities for me to engage with the community, both scientific and general public. Also expect a Synavis update soon 👀

The main issue to me is the fact that simplifying language changes meaning. A climate model estimate is different to a ballpark figure a layperson would provide. However, this is often simplified into similar terms, potentially leading to the wrong conclusion that researchers are "unsure" about this

Important aspects highlighted here, but: If the general public is as new to the topic as this public-facing video indicates, then it is quite a sad conclusion to years of public information campaigns.

☀️🌾 Virtual world coupling with #photosynthesis evaluation for synthetic data production
doi.org/10.1093/insi... #PlantScience #FSPM #CPlantBox #UnrealEngine

Coding is seldomly the part that gets you published. However, it is important for the longevity of a software - even if not explicitly defined as software "product" in the classical sense. I am migrating the Unreal Engine part of Synavis to a more modular standard: www.dirkbaker.eu#20251005-mig...

Very pleased to see our paper published in its final form! Many thanks to our collaborators and funders at PhotoBoost🙏🏽 Prof. Stephen Long developed the first version of this model and was a wonderfully kind and knowledgeable mentor. This work wouldn’t have been possible without his guidance.

Slightly longer version of my video production statement: www.dirkbaker.eu#20251002-vid...

Video to: Virtual World Coupling with Photosynthesis Evaluation for Synthetic Data Production In this work, we couple the functional-structural plant model CPlantBox to the Unreal Engine by exploiting the implemented lighting pipeline to evaluate light influx on the plant surface. There are…

Check out this video summary of the article Virtual World Coupling with #Photosynthesis Evaluation for Synthetic Data Production by @dhelmrich.bsky.social. Access it at
doi.org/10.6084/m9.f... #PlantScience

My videos are typically not even "in-action": I have a separate video project in UE that I use for the video production, along with a few selected tools for the motion/slide design. Data is imported from experiments through common frameworks, yielding more compatibility with other tools such as DART

This is even more impactful for domains that rely heavily on visual media, such as visualization. There is all sorts of stuff one can do using images alone, particularly cherrypicking. Actually seeing what things look in practice provides more profound insight.

My PhD studies immediately pushed me to writing papers. I learned very early that videos as an additional source of information are very valuable. How many people watch? Not many. However, if it helps a selected few to gain access to the information we write about, great! www.youtube.com/@dirkbaker

Can Virtual World Models accurately inform synthetic data?
We coupled CPlantBox with Unreal Engine to simulate light influx on plant surfaces. The impact? Demonstrated versatility for AI
Read our paper: doi.org/10.1093/insi...
Video: doi.org/10.6084/m9.f...
#SyntheticData #PlantScience #UnrealEngine

📢The Call for Papers for in silico Plant’s Special Issue “Simulating plant-plant interactions and community dynamics” is now open
🔬 Editor: Andrew Friend (University of Cambridge)
ℹ️ Find out more: academic.oup.com/insilicoplan... #PlantScience #DGVM

2/2 A great discussion of a commonly used model, particularly from what it means when its results and quantifications are placed in the context of the functional properties of plants.

Widely used variants of the Farquhar-von-Caemmerer-Berry model can cause errors in parameter estimation Abstract. The Farquhar-von-Caemmerer-Berry (FvCB) model is the most widely used mechanistic model of C3 net CO2 assimilation, and it plays a significant ro

1/2 Recently published by Lochocki and McGrath: A mechanistic model of C3 plant (FvCB) which has seen frequent use in literature yields some key challenges when it comes to the interpretation of the plant photosynthetic parameters. See the full story here: doi.org/10.1093/insi...

Just found this: rdcu.be/eGCek
Coppolino et al. (2025) showcase a datacentric view on digital twin modelling. This goes beyond a typical implementation of the digital twin - it explores the implementation in Gaia-X, the European initiative to build a federated and interoperable service framework.

🌽 A data-driven sensitivity analysis of #maize stalk #models reveals the dominant factors influencing stalk strength
doi.org/10.1093/insi... #PlantScience

Satellite data, especially solar-induced chlorophyll fluorescence, accurately tracks plant growth and carbon uptake, highlighting physiology's key role in carbon cycling. This study boosts our understanding of global carbon dynamics.👇
@forestecosyst.bsky.social
www.sciencedirect.com/science/arti...

Fig. 1.Graphical representation of the experimental design. The diagram illustrates the experimental layout, showing that Vitis vinifera L. cv. Tempranillo Clone 232 grafted onto 110R and SO4 rootstocks was divided into two groups. A first group of five plants per combination were used for measuring water relations and xylem vulnerability to embolism under laboratory conditions, while a second group of six plants per combination were maintained under field conditions. The field plants were subjected to a progressive drought and quick water recovery, with various gas exchange, water relations, and xylem anatomy parameters measured at different stages. See ‘Material and methods’ for further details.

💧SPECIAL ISSUE RESEARCH💧

🍇 Grapevine shows hydraulic vulnerability segmentation within the scion *and* rootstock. Rootstock choice impacts scion drought resistance by modifying leaf minimum conductance without altering embolism resistance- Flor et al.

🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪

Save the dates!
11th International #FSPM 2026 Conference
Montpellier, France | October 12th to 16th, 2026

www.fspm2026.org @PlantScience

Falling ice drives glacial retreat in Greenland The Greenland ice sheet is melting at an increasing rate, a process accelerated by glacier calving, in which huge chunks of ice break free and crash into the sea, generating large waves that push warm...

Glacier calving, in which huge chunks of ice break free and crash into the sea, generates large waves that push warmer water to the surface. A new study now shows that this mechanism is amplifying glacial melt.

ethz.ch/en/news-and-...

Renaturierungsmaßnahmen wie das Anpflanzen von Hecken verbessern die Bedingungen für verschiedene Tierarten beispielsweise in der Agrarlandschaft und fördern so die biologische Vielfalt. ©André Künzelmann / UFZ

Angesichts wirtschaftlicher und sicherheitspolitischer Herausforderungen droht der Schutz der #Biodiversität aus dem Blick zu geraten. Forschende wie Josef Settele vom #UFZ mahnen deshalb eindringlich, die Möglichkeiten der EU-Renaturierungs-Verordnung (NRR), zu nutzen.
www.ufz.de/index.php?de...

Uncertain times? Also for researchers. The @ufz.de has started backing up critical databases - in fear of them being deleted or otherwise made unavailable. This endeavor is only possible because of the @helmholtz.de Federated IT: www.hifis.net/use-case/202...

💻 Simulating rhizodeposition patterns around growing and exuding root systems
doi.org/10.1093/insi... #roots #model #PlantScience

I'm a doctor! My thesis was defended on the 22nd May at the University of Iceland! I am grateful for this opportunity and this shows the spirit of international collaboration that is the lifeblood of science and engineering. Grateful to everybody involved! 🇮🇸 🇩🇪 🇪🇺

banner for the summer school with the name and date on it

The 2nd edition of 𝐈𝐧𝐭𝐞𝐫𝐧𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐒𝐮𝐦𝐦𝐞𝐫 𝐒𝐜𝐡𝐨𝐨𝐥 𝐨𝐧 𝐌𝐨𝐝𝐞𝐥𝐢𝐧𝐠 𝐖𝐚𝐭𝐞𝐫 𝐅𝐥𝐮𝐱𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐒𝐨𝐢𝐥-𝐏𝐥𝐚𝐧𝐭 𝐒𝐲𝐬𝐭𝐞𝐦 will be held at UCLouvain, BE, 8-12 Sept 2025.

The course will focus on water flow in the soil-rhizosphere-plant system, plant physiology and rhizosphere hydraulics.

www.uclouvain.be/en/research-...

Two-panel figure illustrating root hydraulic conductance in wheat cultivars. Panel (a) shows a line graph of pressure chamber measurements of root hydraulic conductance (Krs) over the years of release from 1900 to 2000, with a downward trend indicated by a dashed line and shaded confidence interval. Panel (b) presents CPlantBox simulations comparing root hydraulic conductance (Krs) over time (in days) for two cultivars: S. Dickkopf (1895) and Tommi (2002), with the older cultivar showing higher conductance.

New paper out in @plantphys.bsky.social :

Juan Baca Cabrera combined #field & #lab/ #structural & #functional / #invivo & #insilico data to analyse how root #hydraulic traits decreased in German winter #wheat cultivars over 100 years of breeding

academic.oup.com/plphys/advan...