The IHerbSpec Protocol
Herbarium specimens are an unparalleled record of plant diversity that we can leverage via reflectance spectrometry to illuminate plant structure and function across time, space, and taxa. Yet variation in instrumentation and measurement procedures, along with variable preservation of tissues and sources of contamination such as paper and glue, pose significant challenges to global data harmonization.
The IHerbSpec Protocol was developed to provide clear, community-driven standards for spectral measurement and metadata documentation—establishing best practices to minimize technical errors, maximize data quality, and promote transparency in accordance with the Findable, Accessible, Interoperable, and Reusable (FAIR) principles.
By following this protocol, researchers and collections can generate reproducible, interoperable data that support confident aggregation across institutions and unlock new insights in ecology, evolution, and biodiversity sciences.
👀 Content
You can browse the protocol section by section online, or download the protocol documents and metadata spreadsheets below.
Sections
Preface
Introduces the motivation, development history, and community collaboration behind the protocol, as well as author information and acknowledgements.
Part 1: Overview
Defines the purpose, structure, and guiding principles of the protocol, including minimum requirements and recommended practices.
Part 2: Measurement and Metadata Workflow
Step-by-step workflow for spectral data collection, including setup, measurement sequence, quality control, and metadata entry.
Part 3: Filename Conventions and Formats
Recommended file-naming rules that encode key metadata for traceability and long-term interoperability.
Part 4: Metadata and Databasing
Definitions of metadata fields, controlled vocabularies, and guidelines for archiving and sharing spectral data.
Part 5: Instrumentation and Materials Guidelines
Practical guidance for handling instruments, managing materials, and annotating specimens to ensure data quality.
Part 6: Selecting Tissues for Spectral Measurement
Guidelines for choosing appropriate tissues, understanding sources of variation, and applying decision rules for measurement.
Appendix I: Number of Measurements per Tissue
Empirical justification for recommended numbers of replicate measurements and guidance on averaging strategies.
Appendix II: Tissue Metadata for Quality Control
Examples and scoring guidelines for recording tissue condition, contamination, and preservation status in metadata.
References
We welcome questions, comments, and suggestions to improve the protocol, and encourage more members of the herbarium community to join IHerbSpec.
Please communicate about the protocol via github.com/iherbspec/iherbspec-protocol
or Contact Us to get involved!
📌 Suggested Citation
White DM, NI Ahlstrand, MW Austin, D Bastianelli, S Bazan, K Boughalmi, W Cardinal-McTeague, TLP Couvreur, F Durgante, OM Grace, JA Guzmán Q, K Hansen, M Hopkins, R Jackson, JA Kennedy, S Kothari, AK Lee, É Léveillé-Bourret, JE Meireles, BM Neto-Bradley, CO Nichodemus, NL Quinteros Casaverde, C Rodrigues-Vaz, M Schmull, PS Soltis, D Spalink, CC Vasconcelos, JL Viana, H Tuomisto, T Wells, J Cavender-Bares. 2025. IHerbSpec Protocol v.1.XX https://doi.org/10.5281/zenodo.15849668
📥 Download IHerbSpec Protocol Files
The protocol is archived and version controlled at: 
©️ License
This protocol and all associated figures, tables, and supplementary materials are licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
Users are free to share and adapt the material, provided attribution is given to IHerbSpec Protocol (DOI: 10.5281/zenodo.15849668)
IHerbSpec Protocol (