04 — Methods

Analytical Methods

Tutorials, videos, and tools used in crop science research — covering UAV image analysis, machine learning, 3D measurement, and more. Shared openly to support reproducibility and knowledge exchange.

Python & Coding
Series

Python Vibe Coding Course (5 Parts)

A structured guide for researchers: local environment setup → LLM-assisted coding → reproducibility → publishing with your paper

Tutorial

Cloud-Based Python Vibe Coding — Google Colab

For those who want to try Python without local setup. When to choose Colab vs. the Python Vibe Coding Course (local), with a pointer to a step-by-step blog walkthrough

Machine Learning
Tutorial

First Steps in Machine Learning — Random Forest and SHAP

For those who finished the Python Vibe Coding Course and want to actually implement machine learning. A hands-on Random Forest + SHAP walkthrough you can run locally

UAV Image Analysis
Blog

Feature extraction from UAV orthoimages using QGIS

Step-by-step guide to calculating vegetation indices (SR, canopy height) via raster computation and exporting field-level CSV data

Blog

Texture analysis of UAV orthoimages using QGIS and Orfeo Toolbox

Running Haralick texture extraction with QGIS + OTB and applying results to crop growth estimation

Video

Multispectral orthoimage development with Metashape

YouTube — Step-by-step tutorial for generating multispectral orthoimages from UAV imagery using Agisoft Metashape

3D Modeling
Blog

Measurement of plant volume and surface area using 3D mesh data collected by LumaAI

Workflow for generating 3D models from video with LumaAI and measuring plant volume and surface area in Meshmixer

Software
Software

LAYZER: Leaf Area analYZER

Zenodo / DOI: 10.5281/zenodo.18500958 — Python desktop app for automated leaf area measurement from RGB images using Excess Green (ExG) index and Otsu thresholding. Open source (CC BY 4.0)

Software

Vegetation Image Analysis Web App

Free Streamlit web app — upload a vegetation image to instantly obtain analysis results

Other
Blog

Building a Research Portfolio Website with No Coding

Use Claude Code (Claude Desktop) to build and update your site with plain-language instructions — no HTML required. Hosted free with GitHub + Cloudflare Pages