@Abe_404

Postdoc | @DIKU_Institut | #RootPainter | Image Segmentation | Interactive Deep Learning | Phenotyping 🌱

colab.research.google.com/drive/104narYAvTBt-X4QEDrBSOZm_DRaAKHtA?usp=sharing
Joined May 2017
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RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation. Now in @NewPhyt nph.onlinelibrary.wiley.com/…

RootPainter: deep learning segmentation of biological images with corrective annotation

Convolutional neural networks (CNNs) are a powerful tool for plant image analysis, but challenges remain in making them more accessible to researchers without a machine-learning background. We pre...

nph.onlinelibrary.wiley.com
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scholar.google.com/citations…

Abraham George Smith - Cited by 1,077

University of Copenhagen - Interactive Machine Learning - Machine Teaching - Computer Vision - Deep Learning - Phenotyping

scholar.google.com
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Transformers Outperform ConvNets for Root Segmentation: A Systematic Comparison Across Nine Datasets biorxiv.org/content/10.64898…
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PhD Project iapetus.ac.uk/studentships/s… Sounding out the deep: using AI and passive acoustic monitoring to reveal spatial and temporal patterns in deep-sea ecosystems Where: University of Glasgow, UK Online Applicant Q&A Workshop Wednesday 26th November
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Accurate, user-friendly, and free AI stomata quantification with #RootPainter using corrective annotation. Works across species & imaging setups. See our new paper "#Stomata morphology measurement with interactive machine learning: accuracy, speed, and biological relevance"
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doi.org/10.1186/s13007-025-0… <-- Link to the paper.

Stomata morphology measurement with interactive machine learning: accuracy, speed, and biological...

Plant Methods - Stomatal morphology plays a critical role in regulating plant gas exchange influencing water use efficiency and ecological adaptability. While traditional methods for analyzing...

link.springer.com
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Five seasons with DeepRootLab: A unique facility for easier deep root research in the field biorxiv.org/content/10.1101/… -- I really enjoyed this collaboration with @EusunHan et al - more work coming soon.

Five seasons with DeepRootLab: A unique facility for easier deep root research in the field

Deep-rooted crops accessing water and nutrients from deep soil layers enhance the resource base for crop production. However, studying these roots in field conditions is labor-intensive, limiting...

biorxiv.org
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New instructions for installing the RootPainter trainer (server) on windows 11 have been added to the GitHub repository.
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The instructions are available here: github.com/Abe404/root_paint…

root_painter/docs/windows_11_trainer_install.md at master · Abe404/root_painter

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation - Abe404/root_painter

github.com
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Abraham George Smith retweeted
Larry M. York@LarryMattYork23 Nov 2024
There's a science party on Bluesky. Join us.
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Abraham George Smith retweeted
Laurence De Clippele@LDeClippele20 Nov 2024
🎓🐟 PhD Opportunity! 🐟🎓 Explore how coastal habitats support fisheries using #bioacoustics & #MachineLearning! 🌊 Study marine ecosystems 🌐 Develop AI tools 💡 Drive sustainability 📍 University of Glasgow 📆 Apply by 3 January 🔗 shorturl.at/4qt5K
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New paper 📊🌱: 'Automated seminal root angle measurement with corrective annotation' academic.oup.com/aobpla/arti… Excited to share our new free #OpenSource tool for root scientists! With Marta Malinowska, Torben Asp, & team @QGG_AU #AI #OpenScience #ROOTS

Automated seminal root angle measurement with corrective annotation

Abstract. Measuring seminal root angle is an important aspect of root phenotyping, yet automated methods are lacking. We introduce SeminalRootAngle, a nove

academic.oup.com
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📢New Root paper: Accesible AI model for ecologists fails to catch roots in complex mature forest soil images from minirhizotrons 😭. More collaborative work needed! tiny.cc/0yhozz lead by @GraceHandyPGR w @Abe_404 @YaffarDaniela @nanimuelbert @iEESParis @BIFoRUoB
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Richard Nair@richardnair16 Sep 2024
📢📢full funded (EU-UK) PhD project with me @TCD_NatSci doing cutting edge stuff with automated root measurements to understand ecosystem greenhouse gas fluxes: findaphd.com/phds/project/ro… #roots #phdposition #rootecology
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PhD position in Data-driven plant phenotyping for discovering novel perennial traits with @EusunHan phd.tech.au.dk/for-applicant…
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Laurence De Clippele@LDeClippele11 Jun 2024
How do you boost AI model training efficiency? A team of Benthic Ecologists and Machine Learning Scientists dived into this at the @maf_world training school! More on this topic coming soon ….! #AI #RootPainter #iML #BenthicEcology
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Poppy Clark@H_Poppy_Clark29 May 2024
🚨New paper alert!🚨 Our work demonstrating the suitability of RootPainter, an interactive machine learning tool, to marine image analysis is now out in @royalsociety Open Science (1/3): royalsocietypublishing.org/d…
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Poppy Clark@H_Poppy_Clark29 May 2024
Be sure to check out the paper and our handy handbook (zenodo.org/records/10013240) to see just how accessible RootPainter is, even for users without machine learning experience Huge thanks to my collaborators @Abe_404 @DanielMcKayFle1 Ann Larsson @MBC_UoA and @LDeClippele ! (3/3)

Marine Image Analysis Handbook for RootPainter

This handbook details use of the open-source and user friendly machine learning tool, RootPainter, for analysis of marine image data. This tool can be used to extract area measurements for a given...

zenodo.org
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Abraham George Smith retweeted
Richard Nair@richardnair2 May 2024
if you're looking for a PhD and are interested in #roots, #belowground dynamics, and links between plant physiology, soils and biogeochemistry, or using AI to help sample all the above, get in touch. I am definately recruiting at least one funded student this year, maybe more...
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Laurence De Clippele@LDeClippele20 Mar 2024
Final days to apply to the Ecological Data Science Leverhulme DTP which offers an exciting array of data science and machine learning projects! More info here: ecological-data-science.gith… Deadline: 5pm (GMT) on the 22nd March 2024. @TiffanyVlaar @Abe_404 @UofG_EcoDataSci
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Laurence De Clippele@LDeClippele14 Feb 2024
📢PhD opportunities in Ecological Data Science as part of *Leverhulme DTP* On offer: fully funded deep-learning PhD project working with exciting long-term deep-sea acoustic and image datasets!🪸🐟📸🎤👩‍💻 👉More info here: ecological-data-science.gith… #DeepSea #MachineLearning
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