Protocol for the Spectral Digitization of Herbarium Specimens
CURRENT VERSION: 1.2
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Herbarium specimens are an unparalleled record of plant diversity that we can leverage via reflectance spectroscopy to illuminate plant biology across time, space, and taxa.
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
Frontmatter introducing the motivation, development history, and community collaboration behind the protocol, as well as author information and acknowledgements.
Changes Since Last Version
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
Downloads
IHerbSpec Metadata Spreadsheet, example spreadsheets, and protocol tables
📥 Download IHerbSpec Protocol Files
Versioned releases of the IHerbSpec Protocol are archived on Zenodo: 
Each archived release includes: - A compiled PDF of the full protocol (stable, citable snapshot) - Protocol source files (Quarto/Markdown and associated assets) for transparency and reproducibility - Metadata templates and controlled vocabularies (CSV files) - Optional rendered HTML files corresponding to the archived version
The website presents the most current living version of the protocol, while Zenodo preserves fixed, citable versions for reference, reuse, and long-term archiving.
©️ 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.18451589)”
👥 Team Science
This protocol reflects a team science approach. We welcome contributions to improve it and invite people interested in spectroscopy of herbarium specimens to join IHerbSpec.
Please Contact Us if you are interested in joining the working group, por to share feedback or suggestions.
You can also post comments or issues on our GitHub repo github.com/IHerbSpec/iherbspec.github.io
Navigate the protocol
Browse additional parts and appendices:
- Part 1 – Overview
- Part 2 – Measurement and Metadata Workflow
- Part 3 – Filename Conventions and Formats
- Part 4 – Metadata and Databasing
- Part 5 – Instrumentation and Materials Guidelines
- Part 6 – Selecting Tissues for Spectral Measurement
- References
- Appendix I – Number of Measurements per Tissue
- Appendix II – Tissue Metadata for Quality Control
Browse Home and Downloads
IHerbSpec Protocol (