iowarp/phenotyping
Plant-phenotyping methods for any source: design and identity checks with MIAPPE-style example schemas and a validator, size and growth traits, treatment and genotype response, fluorescence and spectral signals, and phenotyping reports.
Inspect actual design, identities, methods, units, coverage and timing in phenotyping data. Adapt checks and derived representations to the supplied files and question; bundled schemas are optional examples.
Structure a phenotyping analysis report with evidence and caveats - experiment identity, design, data quality, methods, results with specific supporting references, and open questions. Use when the user asks for a report, summary, or write-up of a phenotyping analysis.
Physics and pitfalls of physiology sensors in plant phenotyping - chlorophyll fluorescence (dark vs light adapted), reflectance spectra and vegetation indices, red edge, water bands, and relative units. Use before interpreting fluorescence, multispectral, or hyperspectral traits.
Check and analyse plant size and growth from image- or scan-derived traits - pixel vs metric units, projected (2D) vs 3D size, saturation and clipping, and growth curves over repeated measures. Use for any question about plant size, biomass proxies, or growth rate.
Analyse how traits respond to treatments in a phenotyping experiment - dose-response vs categorical contrasts, genotype x treatment interaction, replicates, repeated measures, and tray/position effects. Use for questions comparing treatments or genotypes.