protocol.qmd

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title: "IHerbSpec Protocol"
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  og:title: "IHerbSpec Protocol"
  og:description: "Community standards for spectral measurement and metadata documentation of herbarium specimens."
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  twitter:title: "IHerbSpec Protocol"
  twitter:description: "Community standards for spectral measurement and metadata documentation of herbarium specimens."
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      IHerbSpec Protocol (<a href="https://doi.org/10.5281/zenodo.18451589">10.5281/zenodo.18451589</a>)
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## Protocol for the Spectral Digitization of Herbarium Specimens

**CURRENT VERSION: {{< var protocol_version >}}**

Navigate to [Changes Since Last Version](protocol/changes.qmd)

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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](https://doi.org/10.1038/sdata.2016.18)) 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.

- [Preface](protocol/preface.html)  
  *Frontmatter introducing the motivation, development history, and community collaboration behind the protocol, as well as author information and acknowledgements.*  

- [Changes Since Last Version](protocol/changes.qmd)  

- [Part 1: Overview](protocol/part1-overview.qmd)  
  *Defines the purpose, structure, and guiding principles of the protocol, including minimum requirements and recommended practices.*  

- [Part 2: Measurement and Metadata Workflow](protocol/part2-workflow.qmd)  
  *Step-by-step workflow for spectral data collection, including setup, measurement sequence, quality control, and metadata entry.*  

- [Part 3: Filename Conventions and Formats](protocol/part3-filenames.qmd)  
  *Recommended file-naming rules that encode key metadata for traceability and long-term interoperability.*  

- [Part 4: Metadata and Databasing](protocol/part4-metadata.qmd)  
  *Definitions of metadata fields, controlled vocabularies, and guidelines for archiving and sharing spectral data.*  

- [Part 5: Instrumentation and Materials Guidelines](protocol/part5-instrumentation.qmd)  
  *Practical guidance for handling instruments, managing materials, and annotating specimens to ensure data quality.*  

- [Part 6: Selecting Tissues for Spectral Measurement](protocol/part6-guidelines.qmd)  
  *Guidelines for choosing appropriate tissues, understanding sources of variation, and applying decision rules for measurement.*  

- [Appendix I: Number of Measurements per Tissue](protocol/appendix1.qmd)  
  *Empirical justification for recommended numbers of replicate measurements and guidance on averaging strategies.*  

- [Appendix II: Tissue Metadata for Quality Control](protocol/appendix2.qmd)  
  *Examples and scoring guidelines for recording tissue condition, contamination, and preservation status in metadata.*
  
- [References](protocol/references.qmd)  
 
- [Downloads](protocol/tables.qmd)  
  *IHerbSpec Metadata Spreadsheet, example spreadsheets, and protocol tables*

## 📥 Download IHerbSpec Protocol Files

**Versioned releases of the IHerbSpec Protocol are archived on Zenodo:**  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18451589.svg)](https://doi.org/10.5281/zenodo.18451589)


Each archived release includes:

- A compiled PDF of the full protocol (stable, citable snapshot)
- Protocol source files (Quarto/Markdown) and figures
- Metadata templates and controlled vocabularies tables (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.

## 📌 Suggested Citation

IHerbSpec, 2026. Protocol for Spectral Digitization of Herbarium Specimens, v.{{< var protocol_version >}}. Zenodo. [https://doi.org/10.5281/zenodo.18451589](https://doi.org/10.5281/zenodo.18451589)

[Download BibTeX](bibtex/IHerbSpec-Protocol-1.2.bib) (or right click and "Save Link As...")

## ©️ 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](https://doi.org/10.5281/zenodo.18451589))"

## 👥 Get Involved
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This protocol reflects a team science approach. We welcome comments and invite people interested in spectroscopy and preserved plants and fungi to join IHerbSpec and  contribute to our activities.  

### Join the IHerbSpec community

To get announcements and participate in our activities, [Contact Us](https://iherbspec.github.io/contact) or join our **IHerbSpec-all** Google Group by following these instructions:

1) Visit [groups.google.com/u/4/a/g.harvard.edu/g/iherbspec-all](https://groups.google.com/u/4/a/g.harvard.edu/g/iherbspec-all), 
2) click *Ask to join group*, and (optionally) send a brief message to introduce yourself.
3) To participate in protocol discussions, repeat steps 1 and 2 for the Protocol group also: [groups.google.com/u/4/a/g.harvard.edu/g/iherbspec-protocol](https://groups.google.com/u/4/a/g.harvard.edu/g/iherbspec-protocol)  

### Questions and Discussion Forums

IHerbSpec maintains multiple **public communication channels** to support dialogue, transparency, and discovery across the community. You can browse previously discussed topics and ask questions through the following forums:

- **IHerbSpec-Protocol Google Group**
  - Public protocol discussion, clarification, and governance
  - [https://groups.google.com/u/4/a/g.harvard.edu/g/iherbspec-protocol](https://groups.google.com/u/4/a/g.harvard.edu/g/iherbspec-protocol)

- **GitHub Discussions**
  - Public Q&A and ideas related to IHerbSpec and the IHerbSpec Protocol
  - [https://github.com/IHerbSpec/iherbspec.github.io/discussions](https://github.com/IHerbSpec/iherbspec.github.io/discussions)

- **GitHub Issues**
  - Concrete, actionable proposed edits or technical tasks related to the website or protocol source  
  - [https://github.com/IHerbSpec/iherbspec.github.io/issues](https://github.com/IHerbSpec/iherbspec.github.io/issues)

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## Navigate the protocol
- Proceed to [**Preface**](protocol/preface.qmd)  

Browse additional parts and appendices:

- [**Part 1**](protocol/part1-overview.qmd) – Overview  
- [**Part 2**](protocol/part2-workflow.qmd) – Measurement and Metadata Workflow  
- [**Part 3**](protocol/part3-filenames.qmd) – Filename Conventions and Formats  
- [**Part 4**](protocol/part4-metadata.qmd) – Metadata and Databasing  
- [**Part 5**](protocol/part5-instrumentation.qmd) – Instrumentation and Materials Guidelines  
- [**Part 6**](protocol/part6-guidelines.qmd) – Selecting Tissues for Spectral Measurement  
- [**References**](protocol/references.qmd)  
- [**Appendix I**](protocol/appendix1.qmd) – Number of Measurements per Tissue  
- [**Appendix II**](protocol/appendix2.qmd) – Tissue Metadata for Quality Control  

Browse Home and Downloads

- [**Home - IHerbSpec Protocol**](protocol.html)  
- [**Downloads**](protocol/tables.html)