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Dirk Baker

@dhelmrich.bsky.social
830 followers 365 following 23 posts

Doctor in Computational Engineering from University of Iceland 🇮🇸 - currently RSE at Helmholtz Centre for Environmental Research 🇩🇪 I express my work-related opinions and announcements here. orcid.org/0000-0003-1542-1062 www.dirkbaker.eu

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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 11/08/2026
A functional-structural plant model to evaluate sunburn susceptibility across diverse vineyard configurations by Christopher Bahr, Dominik Schmidt, Katrin Kahlen doi.org/10.1093/insi... #PlantScience #FSPM
doi.org
Simulating berry sunburn with the functional–structural plant model Virtual Riesling
Abstract. Berry sunburn in grapes is a disorder likely linked to climate change that can severely reduce yield and fruit quality. It is driven by heat impa
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Dirk Baker @dhelmrich.bsky.social · 22/06/2026
Job Alert ⚠️ We search for a DevOps Research Software Engineer to join our HIFIS team in the Helmholtz-Centre for Environmental Research in Leipzig, Germany 👉 recruitingapp-5128.de.umantis.com/Vacancies/34...
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 11/05/2026
Metabolic modeling links leaf anatomy to environment-specific benefits on the C3-C4 spectrum by Tiago M. Machado, Alejandro León-Ramírez, Sezin Dogan, Andreas P.M. Weber, Urte Schlüter, and Nadine Töpfer buff.ly/DadgXje via @biorxiv-plants.bsky.social #PlantScience #Photosynthesis
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 29/04/2026
🌿Are you teaching or learning plant modeling? Discover our latest article type: Methods for Plant Modeling articles describe software, tools, models, and other resources in an accessible way, making them suitable for educational use. 📰 See the collection at buff.ly/P1GV8q6
Learn how to use plant models!
Methods for Plant Modelling
Every article contains an introduction to the model, essential equations, and instructions
EXPLORE THE COLLECTION! - in silico plants
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Reposted by Dirk Baker
eurobioimaging.bsky.social @eurobioimaging.bsky.social · 11/04/2026
Explore image data analysis the FAIR way with @galaxyproject.bsky.social ! Join us April 16 🕒️ 15:00–17:00 CEST for a hands‑on introduction to web‑based, HPC‑ready workflows. #Galaxy #ImageAnalysis #FAIRdata #BioImaging #Workshop 🌌 us02web.zoom.us/meeting/regi...
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 09/04/2026
💻 🍃 Virtual world coupling with #photosynthesis evaluation for synthetic data production by @dhelmrich.bsky.social Mona Giraud, Jens Henrik Gobbert, Hanno Scharr, Morris Riedel, Ebba Pora Hvannberg, Andrea Schnepf @agrosphere-ibg-3.bsky.social buff.ly/ncZrjvV #PlantScience #CPlantBox
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Dirk Baker @dhelmrich.bsky.social · 03/04/2026
Would it not be nice to have the choice of backends when combining a virtual scene with AI?
Visual description of the Synavis plugin with its dependencies, surrounding authoring of the virtual scene, coupling between virtual scene and training, and the training itself. Synavis will support two backends, webRTC for image streaming and ADIOS for data-centric coupling.
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 26/02/2026
NEW! Validation of root hair upscaling in rhizosphere solute transport models by Christian Kuppe, Andrea Schnepf, and Johannes Postma doi.org/10.1093/insi... @agrosphere-ibg-3.bsky.social
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Dirk Baker @dhelmrich.bsky.social · 09/02/2026
📣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!
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Dirk Baker @dhelmrich.bsky.social · 15/01/2026
Got it working again after deliberately breaking it....
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Dirk Baker @dhelmrich.bsky.social · 01/01/2026
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.
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Dirk Baker @dhelmrich.bsky.social · 31/12/2025
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 👀
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Dirk Baker @dhelmrich.bsky.social · 11/11/2025
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.
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 23/10/2025
☀️🌾 Virtual world coupling with #photosynthesis evaluation for synthetic data production doi.org/10.1093/insi... #PlantScience #FSPM #CPlantBox #UnrealEngine
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Dirk Baker @dhelmrich.bsky.social · 08/10/2025
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...
dirkbaker.eu
Dirk Baker
Dirk Baker - Research & Software Engineer - Personal Website
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Reposted by Dirk Baker
Supreeta Vijayakumar @svijayakumar32.bsky.social · 05/10/2025
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.
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Dirk Baker @dhelmrich.bsky.social · 02/10/2025
Slightly longer version of my video production statement: www.dirkbaker.eu#20251002-vid...
dirkbaker.eu
Dirk Baker
Dirk Baker - Research & Software Engineer - Personal Website
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 01/10/2025
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
doi.org
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…
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Dirk Baker @dhelmrich.bsky.social · 23/09/2025
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
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Dirk Baker @dhelmrich.bsky.social · 22/09/2025
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
doi.org
Validate User
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 17/09/2025
📢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
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Dirk Baker @dhelmrich.bsky.social · 17/09/2025
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...
doi.org
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
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Dirk Baker @dhelmrich.bsky.social · 16/09/2025
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.
rdcu.be
Simulation as a Service in Data Spaces: A Digital Twin-based Approach
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 26/08/2025
🌽 A data-driven sensitivity analysis of #maize stalk #models reveals the dominant factors influencing stalk strength doi.org/10.1093/insi... #PlantScience
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Reposted by Dirk Baker
Forest Ecosystems @forestecosyst.bsky.social · 27/08/2025
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...
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Reposted by Dirk Baker
Journal of Experimental Botany @jxbotany.bsky.social · 22/08/2025
💧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 🧪
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.
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 22/08/2025
Save the dates! 11th International #FSPM 2026 Conference Montpellier, France | October 12th to 16th, 2026 www.fspm2026.org @PlantScience
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Reposted by Dirk Baker
ETH Zurich @ethz.ch · 14/08/2025
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-...
ethz.ch
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...
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Reposted by Dirk Baker
UFZ @ufz.de · 03/07/2025
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...
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
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Dirk Baker @dhelmrich.bsky.social · 25/06/2025
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...
hifis.net
Backing Up Critical US Databases
In light of the uncertainty surrounding the sustainability of key databases in the Earth and Environment domain, UFZ created a local backup using Helmholtz Cloud services.
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 20/06/2025
💻 Simulating rhizodeposition patterns around growing and exuding root systems doi.org/10.1093/insi... #roots #model #PlantScience
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Dirk Baker @dhelmrich.bsky.social · 29/05/2025
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! 🇮🇸 🇩🇪 🇪🇺
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Reposted by Dirk Baker
Guillaume Lobet @guillaumelobet.bsky.social · 08/04/2025
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-...
banner for the summer school with the name and date on it
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Guillaume Lobet @guillaumelobet.bsky.social · 25/04/2025
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...
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.
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Reposted by Dirk Baker
Matthias C. Rillig @mrillig.bsky.social · 19/04/2025
Deyi Hou et al. in Science Global soil pollution by toxic metals threatens agriculture and human health www.science.org/doi/10.1126/...
science.org
Global soil pollution by toxic metals threatens agriculture and human health
Toxic metal pollution is ubiquitous in soils, yet its worldwide distribution is unknown. We analyzed a global database of soil pollution by arsenic, cadmium, cobalt, chromium, copper, nickel, and lead...
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Kelly Zamudio @kzutaustin.bsky.social · 19/04/2025
Congratulations to lab member Gabi Alves Ferreira who lead us in this fun project! She modeled how range shifts of neotropical frogs with climate change will change phylogenetic diversity and endemism in the new communities. So great to see this published #ProudPI 💪🐸 www.nature.com/articles/s41...
nature.com
Climate change is projected to shrink phylogenetic endemism of Neotropical frogs - Nature Communications
Climate change is a major threat to biodiversity. This study predicts that climate change will reshape Neotropical frog diversity, causing losses in phylogenetic diversity and phylogenetic endemism, w...
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Dirk Baker @dhelmrich.bsky.social · 01/04/2025
Synavis is back 👉 link.springer.com/chapter/10.1... Our conference paper is now online! HPC use-cases for plant science, and a case for having exclusive-use visualization nodes for larger-scale use-cases that involve rendering. Especially in times of AI factories and Tensor chips.
link.springer.com
Adapting Agricultural Virtual Environments in Game Engines to Improve HPC Accessibility
E-infrastructures deliver basic supercomputing and storage capabilities but can benefit from innovative higher-level services that enable use-cases in critical domains, such as environmental and agric...
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Dirk Baker @dhelmrich.bsky.social · 31/03/2025
Published 👉 doi.org/10.1016/j.pl... VRoot: A VR-Based Application for Manual Root System Architecture Reconstruction, Plant Phenomics (2025) A study on the use of VR for MRI root system extractions, along with a user study providing good quantitative indicators for the value of VR in these tasks 🎉
doi.org
Redirecting
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in silico Plants @insilicoplants.bsky.social · 20/12/2024
Introducing the new #CPlantBox 📰 Story: buff.ly/4ghASQi via @botanyone 🔬 Research: buff.ly/3PKZw18 #PlantScience 🧪#FSPM
botany.one
Introducing the new CPlantBox
Computational model may help unravel the complex processes of drought tolerance.
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Dirk Baker @dhelmrich.bsky.social · 13/12/2024
#Cloud infrastructures are now the backbone of industry and #science! View yourself as an engineer and would like to join a team that is passionate about research data and supporting scientists? Job posting at UFZ in Leipzig 👉 recruitingapp-5128.de.umantis.com/Vacancies/30...
recruitingapp-5128.de.umantis.com
Cloud Infrastructure and DevOps Engineer – Research data management (f/m/x)
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Reposted by Dirk Baker
in silico Plants @insilicoplants.bsky.social · 03/07/2024
⭐ NEW⭐ Insights from utilizing data of different quality levels for simulating #barley performance under Nordic conditions: #APSIM model evaluation #PlantScience by Mercy Appiah, Gennady Bracho-Mujica, Simon Svane, Merete Styczen, Kurt-Christian Kersebaum & Reimund Rötter doi.org/10.1093/insi...
A pyramid portraying quality levels of data suitable for different modeling tasks. At the bottom is model application. For this level, final yield is required and estimated management soil and weather data is desirable. Farm surveys are the source of this data. Next is calibration and evaluation. Yield components are required, anthesis and maturity dates, in season LAI/total aboveground biomass, and management inputs are desired. National variety trials are the source of this data. Next is comparison. On-site, rainfall data and all management inputs are required. Remaining weather data from nearby station and four in-season leaf area index/total above ground biomass/grain data and in-season tissue nitrogen are desired. This data comes from agronomic experiments. Finally, at the top, is improvement. On-site weather, soil, and leaf area index/total above ground biomass/green data required. Rooting depth is desired. The source of this data is specific high-quality field experiments.
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Dirk Baker @dhelmrich.bsky.social · 14/05/2024
Registrations still open: Virtual Worlds for #MachineLearning, #free #online course of the Jülich Supercomputing Centre and PhenoRob where we discuss synthetic data, and how to map between the real and the virtual world. We have guest speakers! indico3-jsc.fz-juelich.de/e/unrealml
indico3-jsc.fz-juelich.de
Virtual Worlds for Machine Learning
This course will take place as an online event. The link to the streaming platform will be provided to the registrants only.The Unreal Engine is one of the state-of-the-art 3D rendering engines, mainl...
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Marc Somssich @somssich.bsky.social · 26/04/2024
"Ohne Mutationen keine Diversität – Von pflanzlicher Auslese, Züchtung und Grüner Gentechnik" Forum article on plant breeding and NGTs by Christopher Grefen for the Journal Nachhaltigkeits Recht. www.biblioscout.net/article/10.3... #PlantScience #PlantGMOs #PlantNGTs
biblioscout.net
Article - Ohne Mutationen keine Diversität – Von pflanzlicher Auslese, Züchtung und Grüner Gentechnik
<p>Seit dem Übergang vom nomadischen zum sesshaften Leben greift der Mensch aktiv in die ihn umgebende Natur ein. Die Domestizierung verschiedener Ar...
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in silico Plants @insilicoplants.bsky.social · 12/04/2024
💻🌿Synthetic data for training image processing artificial intelligence #FSPM #CPlantBox @unrealengine.bsky.social botany.one/2024/04/harn... from @botany.one
botany.one
Harnessing the Power of Synthetic Data for Deep Learning Image Analysis
The Synavis framework provides a solution to overcome data scarcity for training deep learning biological image analysis models.
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in silico Plants @insilicoplants.bsky.social · 03/01/2024
💻🌿 A new framework that supports direct and scalable coupling of realistic #FSPM visualization with #UnrealEngine #Synavis #FSPM #CPlantBox doi.org/10.1093/insi... from Dirk Helmrich, Felix Bauer, Mona Giraud, Andrea Schnepf, Jens Henrik Göbbert, Hanno Scharr, Ebba Hvannberg and Morris Riedel
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