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bioRxiv · 10.64898/2026.07.07.736730

Optimizing Signal Acquisition and Chemometric Pipelines for Micro NIR Plant Identification: Evaluating Spectral Backgrounds and Data Processing in Herbarium Specimens

Alves, T. C.·de Gasper, A. L.
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Abstract

PremiseRapid and accurate plant species identification is a critical challenge exacerbated by the taxonomic impediment. Although portable near-infrared (Micro NIR) spectroscopy represents a promising solution, the current absence of standardized protocols and a fundamental understanding of how critical acquisition and analysis parameters influence accuracy remain significant barriers. This study focused on the systematic optimization and validation of a comprehensive workflow designed to maximize the reliability of plant identification using this technology. To ensure methodological robustness across diverse foliar matrices, four vascular plant species were strategically selected as a representative test set to encompass morphological extremes, including significant variations in leaf thickness, pubescence, and surface texture. MethodsUsing a portable spectrometer on herbarium specimens (exsiccate) of four vascular plant species, we systematically tested five spectral backgrounds, seven pre-processing methods, and four classification models. Subsequently, we optimized the number of spectral readings and evaluated the influence of the leaf scanning surface (adaxial vs. abaxial) on model accuracy. ResultsThe highest-performing combination was a Shiny Aluminum background, Second Derivative pre-processing, and a Random Forest model, which achieved a mean cross-validated accuracy of 99%. An average of just three spectral readings from the adaxial (upper) leaf face was sufficient to saturate model performance, proving statistically superior to other approaches (p < 0.001). DiscussionThis study establishes a validated, high-accuracy protocol for plant species identification from herbarium specimens using portable NIR, offering a powerful tool for biodiversity studies. Direct applicability to fresh plants in the field requires future validation to account for the spectral influence of moisture variability.

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Alves, T. C., de Gasper, A. L.. 2026-07-07. Optimizing Signal Acquisition and Chemometric Pipelines for Micro NIR Plant Identification: Evaluating Spectral Backgrounds and Data Processing in Herbarium Specimens. https://doi.org/10.64898/2026.07.07.736730

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