01Images to traits
Build a phenotyping workflow
Start with reproducible image analysis, add foundation-model segmentation, then benchmark on field data.
- PlantCV
- Meta SAM 3.1
- PhenoBench
Research learning hubCurated and verified · July 2026
Learn AI for Science & digital agriculture.
A focused map of official courses, models, datasets, and tools for scientific machine learning, AI agents & LLMs, crop simulation, plant phenotyping, remote sensing, and 3D reconstruction.
- curated resources
- 73
- focused topics
- 8
- source policy
- official-first
- last verified
- July 2026
Start with a goal
Three practical learning paths
Each path moves from a reliable starting point to a reproducible research workflow.
02Process to prediction
Learn process-based crop models
Move from an approachable water-productivity model to Python workflows and full cropping-system simulation.
- FAO AquaCrop
- PCSE / WOFOST
- APSIM Next Generation
03Leaf to canopy
Measure photosynthesis properly
Read the physiology first, follow shared measurement protocols, then analyse gas-exchange data reproducibly in R.
- Plants in Action
- PROMETHEUS Protocols
- Photosynthesis with R
04Models with mechanisms
Enter AI for Science
Map the field, learn scientific machine learning, then reproduce a domain model with official notebooks.
- AI for Science 101
- MIT SciML
- NVIDIA PhysicsNeMo
Curated catalog
Find the right resource
Pick a dimension on the left—foundations, domain, or publishing—then read each topic from beginner to advanced.
Showing 73 of 73 resources
Core foundations
Deep learning, graphs, classical ML, and the from-scratch explanations worth returning to.
Beginner
PyTorch FoundationOfficial
Updated 2026PyTorch Tutorials
The official path from tensors and training loops to transfer learning, detection, distributed training, and compilation.
- Deep learning
- Python
- Computer vision
Inria / Scikit-learnOfficial
Scikit-learn MOOC
A careful introduction to tabular ML, evaluation, pipelines, model selection, and leakage-aware experimentation.
- Classical ML
- Evaluation
- Pipelines
Andrej KarpathyCommunity
Updated 2026Neural Networks: Zero to Hero
Build neural networks from scratch—backprop, makemore, and a GPT—through carefully narrated, code-along video lectures.
- From scratch
- Backprop
- GPT
3Blue1BrownCommunity
Updated 20263Blue1Brown: Neural Networks
Visual, intuition-first explanations of neural networks, gradient descent, backpropagation, and transformers.
- Intuition
- Visualization
- Math
MIT 6.036 / 6.390Official
MIT Introduction to Machine Learning
Complete written notes on regression, classification, neural networks, and reinforcement learning—useful when a video course moves too fast.
- Notes
- Fundamentals
- Math
Intermediate
PyG TeamOfficial
Updated 2026PyTorch Geometric
Hands-on graph neural networks for molecules, biological networks, meshes, point clouds, and heterogeneous graphs.
- GNN
- Molecules
- Point clouds
Stanford UniversityOfficial
Stanford CS231n
A durable computer-vision foundation covering recognition, optimization, CNNs, transformers, detection, and segmentation.
- Computer vision
- Segmentation
- Transformers
Advanced
Stanford UniversityOfficial
Updated 2026Stanford CS224W
A structured course on graph representation learning, GNNs, graph transformers, knowledge graphs, and applications.
- Graphs
- GNN
- Theory
Lilian WengCommunity
Updated 2026Lil'Log
In-depth technical essays on LLM agents, diffusion, RL, hallucination, and reasoning—widely used as reference explainers.
- Deep dives
- LLM agents
- Reference
AI agents & LLMs
Model APIs, agent frameworks, tool protocols, and agricultural domain models.
Beginner
AnthropicOfficial
Updated 2026Anthropic Claude Docs
Official Claude developer docs: Messages API, tool use, extended thinking, structured outputs, prompt caching, and agent patterns.
- LLM API
- Tool use
- Prompting
OpenAIOfficial
Updated 2026OpenAI Platform Docs
Official OpenAI developer reference for the Responses API, function calling, structured outputs, embeddings, and retrieval.
- LLM API
- Function calling
- Embeddings
Hugging FaceOfficial
Updated 2026Hugging Face Agents Course
A hands-on course on building agents with smolagents, LlamaIndex, and LangGraph, from fundamentals to a capstone project.
- Agents
- Hands-on
- Frameworks
Intermediate
AnthropicOfficial
Updated 2026Claude Agent SDK
Build production agents on the same harness as Claude Code, with subagents, sessions, tool orchestration, and MCP support.
- Agents
- Python & TS
- MCP
OpenAIOfficial
Updated 2026OpenAI Agents SDK
A lightweight framework for multi-agent workflows with handoffs, guardrails, sessions, and built-in tracing.
- Agents
- Orchestration
- Tracing
MCP ProjectOfficial
Updated 2026Model Context Protocol
The open standard for connecting LLMs to tools and data sources, with a growing ecosystem of interoperable servers.
- Interoperability
- Tools
- Standard
Hugging FaceOfficial
Updated 2026smolagents
A minimal library for code-writing agents—define tools, pick any model, and run agentic loops in a few lines of Python.
- Code agents
- Lightweight
- Python
Shanghai AI LabOfficial
Updated 2024SeedLLM 丰登
The first seed-industry LLM, trained for variety selection, agronomic traits, cultivation, and promotion-region reasoning.
- Agri LLM
- Breeding
- Chinese
Advanced
LangChainOfficial
Updated 2026LangGraph
A low-level orchestration framework for durable, stateful multi-agent systems with explicit graphs, memory, and human-in-the-loop.
- Stateful agents
- Graphs
- Python
AgriAgent (open source)Community
Updated 2024AgriAgent
An open Chinese agricultural multimodal model on MiniCPM-Llama3-V that diagnoses crop disease and answers farming questions.
- Agri VLM
- Disease ID
- Chinese
AgriGPT (arXiv)Community
Updated 2025AgriGPT
A domain LLM ecosystem for agriculture built on a multi-agent data engine and the Agri-342K instruction dataset.
- Agri LLM
- Dataset
- Ecosystem
Plant physiology & measurement
Photosynthesis, fluorescence, canopy measurement protocols, and how to analyse what comes off the instrument.
Beginner
Australian Society of Plant ScientistsOfficial
Plants in Action
An open plant-physiology textbook covering photosynthesis, water relations, growth, and stress—the background a modelling or imaging paper assumes you already have.
- Textbook
- Photosynthesis
- Water relations
PrometheusWiki communityOfficial
PROMETHEUS Protocols
Community-maintained protocols for gas exchange, fluorescence, sensing, and environment measurement, written so a method can be repeated by someone else.
- Protocols
- Gas exchange
- Sensing
PhotosynQOfficial
PhotosynQ
A handheld MultispeQ plus shared protocols and data, giving fluorescence and leaf measurements at field scale without a lab bench.
- MultispeQ
- Fluorescence
- Field
Intermediate
Jiedong Zhu (bookdown)Community
Photosynthesis Data Analysis with R
A practical Chinese walkthrough for fitting A/Ci and light-response curves and cleaning LI-COR output in R.
- R
- A/Ci curves
- Chinese
LI-COR EnvironmentalOfficial
LI-6800 Photosynthesis System
Manuals, application notes, and configuration guidance for the gas-exchange and fluorescence system most photosynthesis papers rely on.
- Gas exchange
- Instrument
- Manuals
METER GroupOfficial
Researcher's Guide to Leaf Area Index
How LAI is defined, measured directly and optically, and where each method's error comes from—useful before trusting an LAI product.
- LAI
- Canopy
- Measurement error
Advanced
JB Hyperspectral DevicesOfficial
FloX SIF Monitoring
Continuous field measurement of solar-induced fluorescence and reflectance—the ground reference behind canopy-scale SIF work.
- SIF
- Hyperspectral
- Canopy
Crop models
Process-based crop simulation, from an approachable water model to full cropping systems and virtual plants.
Beginner
FAO Land and WaterOfficial
FAO AquaCrop 7.1
An approachable crop water-productivity model with official handbooks, reference manuals, and 43 video tutorials.
- Water productivity
- Irrigation
Crops in Silico consortiumOfficial
Crops in Silico
A multi-scale plant modelling initiative that shows how gene, cell, plant, and field models are coupled into one simulation.
- Multi-scale
- Community
- Simulation
Intermediate
Wageningen modelling communityOfficial
Updated 2026PCSE / WOFOST
A Python crop simulation environment with WOFOST, LINGRA, and LINTUL—well suited to optimization and data assimilation.
- Python
- WOFOST
- Data assimilation
BioCroOfficial
Updated 2026BioCro
Modular C++ and R crop-growth simulation with practical guides for photosynthesis, environment, and model development.
- R
- C++
- Photosynthesis
Advanced
APSIM InitiativeOfficial
Updated 2026APSIM Next Generation
Model soil, water, nitrogen, crops, rotations, and management scenarios in a mature agricultural systems framework.
- Systems model
- Scenario analysis
DSSAT FoundationOfficial
Updated 2026DSSAT Cropping System Model
Learn genotype–soil–weather–management simulation for yield forecasting, cultivar calibration, and climate risk studies.
- Yield
- Calibration
- Climate risk
CropboxOfficial
Cropbox.jl
A declarative Julia framework for building, calibrating, evaluating, and visualizing crop and physiological models.
- Julia
- Model development
- Experimental
Plant Simulation Lab, UC DavisOfficial
Helios
A C++ framework for 3D plant architecture with ray-traced radiation, energy balance, photosynthesis, and synthetic imagery.
- 3D canopy
- Ray tracing
- C++
LESS developersOfficial
LESS
A large-scale 3D radiative-transfer model that simulates reflectance, thermal imagery, LiDAR, and SIF over realistic canopies.
- Radiative transfer
- LiDAR
- Simulation
Plant phenotyping
Image-to-trait workflows, segmentation models, field benchmarks, and the metadata standards behind them.
Beginner
IPPNOfficial
International Plant Phenotyping Network
The field's umbrella network: working groups, facilities, events, and a reliable map of who does what in phenotyping.
- Community
- Facilities
- Events
Intermediate
Donald Danforth Plant Science CenterOfficial
Updated 2026PlantCV
Reproducible RGB, NIR, thermal, fluorescence, hyperspectral, morphology, and geospatial plant-image workflows.
- Python
- Image analysis
- Hyperspectral
PhenoCam workflowOfficial
PhenoAI
A focused workflow for PhenoCam time-series quality control, vegetation segmentation, indices, and phenology extraction.
- Phenology
- Time series
- DeepLabV3+
Kreshuk LabOfficial
Updated 2025PlantSeg v2
Napari-based 2D and 3D cell segmentation tuned for densely packed plant tissues and microscopy workflows.
- Microscopy
- 3D cells
- Napari
Open3DOfficial
Open3D Tutorials
Python and C++ tutorials for point clouds, meshes, RGB-D data, registration, reconstruction, and 3D machine learning.
- Point cloud
- Mesh
- 3D vision
Breeding API communityOfficial
BrAPI
The common API for plant breeding and phenotyping data, so trials, germplasm, and observations move between systems without custom exports.
- API
- Breeding data
- Interoperability
ELIXIR / EMPHASISOfficial
MIAPPE
The minimum information checklist for a plant phenotyping experiment—apply it while collecting, not when a reviewer asks.
- Metadata
- FAIR data
- Checklist
Advanced
University of Bonn / PhenoRobOfficial
Updated 2026PhenoBench
A field benchmark for crop, weed, plant-instance, leaf-instance, and hierarchical panoptic segmentation from UAV imagery.
- UAV
- Segmentation
- Codabench
ICRISATOfficial
Updated 2025ICRISAT Legume 3D Point Clouds
Multispectral 3D scans of four legume crops with organ-level leaf, petiole, and stem labels plus MIAPPE metadata.
- Point cloud
- Organ labels
- MIAPPE
Meta ResearchOfficial
Updated 2026Meta SAM 3.1
Concept-prompted detection, segmentation, and tracking for images and video, with notebooks and fine-tuning code.
- Segmentation
- Tracking
- Foundation model
John Innes CentreOfficial
MorphoGraphX
Visualize and quantify 4D live-imaged tissues, cell geometry, growth, fluorescence, and morphogenesis.
- 4D imaging
- Morphogenesis
- Cells
University of Bonn / StachnissLabOfficial
Pheno4D
Spatio-temporal point clouds of maize and tomato with leaf instance labels—a rare benchmark for 4D plant growth analysis.
- Point cloud
- 4D growth
- Instance labels
GeoAI & 3D
Earth observation platforms, geospatial foundation models, photogrammetry, and point-cloud workflows.
Beginner
European Space AgencyOfficial
Updated 2026ESA WorldCereal
Global crop extent and crop-type mapping with a MOOC, reference data, notebooks, and a processing hub.
- Global crops
- MOOC
- Processing hub
FAOOfficial
FAO SEPAL Classification
A low-code workflow for mosaics, training samples, and RF/SVM/gradient-boosting land and crop classification.
- Low code
- Sentinel
- Classification
QGIS ProjectOfficial
QGIS User Guide
The practical entry point to projections, vector and raster handling, and map layout before moving into scripted geospatial work.
- GIS
- Projections
- Cartography
Intermediate
Google Earth EngineOfficial
Updated 2025AlphaEarth Satellite Embeddings
Annual precomputed Earth representations for few-shot classification, clustering, land cover, and agricultural mapping.
- Embeddings
- Few-shot
- Earth Engine
WorldCereal / open communityOfficial
Updated 2026Fields of The World
Global field-boundary data, pretrained segmentation models, CLI, QGIS tooling, and browser inference.
- Field boundaries
- Segmentation
- QGIS
Google for DevelopersOfficial
Google Earth Engine Tutorials
Official JavaScript and Python learning paths for planetary-scale imagery, time series, classification, and export.
- Geospatial
- JavaScript
- Python
OpenDroneMap CommunityOfficial
OpenDroneMap
Turn drone imagery into orthophotos, point clouds, DSM/DTM, multispectral products, and textured 3D models.
- UAV
- Photogrammetry
- Point cloud
Advanced
IBM / NASA / TorchGeoOfficial
Updated 2026TerraTorch + Prithvi-EO-2.0
Fine-tune open geospatial foundation models for multi-temporal classification and segmentation, including crop mapping.
- Earth observation
- HLS
- Foundation model
NASA HarvestOfficial
Updated 2026NASA Harvest Presto
A lightweight self-supervised time-series transformer for Sentinel-1/2, weather, and terrain in low-label crop mapping.
- Time series
- Few-shot
- Crop mapping
NASA EarthdataOfficial
NASA ARSET: ML for Agriculture
A complete remote-sensing ML workflow using Sentinel-2, crop labels, cloud data engineering, and TensorFlow.
- Remote sensing
- Cloud
- Crop classification
AI for Science
Scientific machine learning, physics-informed models, and domain foundation models with runnable code.
Beginner
AI4Science101 CommunityCommunity
AI for Science 101
A readable field map spanning graph learning, molecular simulation, causal ML, structural biology, and quantum science.
- Field map
- Reading
Intermediate
DeepChemOfficial
Updated 2026DeepChem Tutorials
Notebook-first learning for molecular property prediction, drug discovery, quantum chemistry, and materials science.
- Molecules
- Materials
- Notebooks
Google DeepMindOfficial
AlphaFold Server & Database
Explore predicted protein structures and test biomolecular interactions with AlphaFold 3 through the official server.
- Structural biology
- Protein
FutureHouseOfficial
Updated 2026PaperQA2
A citation-grounded literature search and scientific question-answering workflow that can also use local models.
- Literature
- RAG
- Research agents
Advanced
MIT 18.337Official
Updated 2026MIT Parallel Computing & SciML
A rigorous course on automatic differentiation, ODE/PDE solvers, PINNs, probabilistic programming, GPUs, and HPC.
- PINN
- Differential equations
- HPC
NVIDIAOfficial
Updated 2026NVIDIA PhysicsNeMo
Production-grade Physics AI tutorials for neural operators, PINNs, MeshGraphNet, weather, fluids, and molecular systems.
- Physics ML
- Neural operators
- Python
Chan Zuckerberg BiohubOfficial
Updated 2026Biohub ESM
Current ESM code for protein language models, embeddings, structure prediction, and protein interaction research.
- Protein LM
- ESMC
- ESMFold2
Microsoft Research AI for ScienceOfficial
Updated 2026Microsoft Aurora
A foundation model for weather, air quality, waves, and tropical cyclones, with official ERA5 examples.
- Earth systems
- Weather
- Foundation model
Writing & figures
Manuscript language, controlled terminology, and figure galleries you can copy patterns from.
Beginner
University of ManchesterOfficial
Academic Phrasebank
Section-by-section sentence patterns for academic English—the fastest cure for a stalled introduction or discussion.
- Academic English
- Sentence patterns
Purdue UniversityOfficial
Purdue OWL
Reference-grade guidance on grammar, style, and citation formats, maintained by a university writing lab rather than a content farm.
- Grammar
- Citation
- Style
OverleafOfficial
Overleaf Templates
Journal, thesis, CV, and poster LaTeX templates that compile in the browser—start from a working document instead of a blank preamble.
- LaTeX
- Templates
- Manuscripts
Yan HoltzCommunity
From Data to Viz
A decision tree from data type to appropriate chart, with the common mistakes each chart invites spelled out.
- Chart choice
- Caveats
- R & Python
Intermediate
Planteome ProjectOfficial
Planteome
Reference ontologies for plant traits, anatomy, and growth stages—use these terms and your data stays searchable across species.
- Ontology
- Traits
- Terminology
Yan HoltzCommunity
The R Graph Gallery
Hundreds of ggplot2 charts with reproducible code—the fastest way to go from a figure in your head to publishable output.
- ggplot2
- R
- Reproducible code
Apache Software FoundationOfficial
Apache ECharts Examples
Editable interactive chart examples—useful when a figure needs to live on a web page or dashboard rather than in a PDF.
- Interactive
- Web
- Dashboards
