hed-standard · VisLab · Jan 26, 2026 · Jan 26, 2026 · Jan 26, 2026
diff --git a/README.md b/README.md
@@ -2,10 +2,16 @@
 
 # HEDTools - Python
 
+```{index} HEDTools, Python tools, validation, analysis
+```
+
 > Python tools for validation, analysis, and transformation of HED (Hierarchical Event Descriptors) tagged datasets.
 
 ## Overview
 
+```{index} HED, Hierarchical Event Descriptors, BIDS, NWB
+```
+
 HED (Hierarchical Event Descriptors) is a framework for systematically describing both laboratory and real-world events as well as other experimental metadata. HED tags are comma-separated path strings that provide a standardized vocabulary for annotating events and experimental conditions.
 
 **Key Features:**
@@ -20,8 +26,14 @@ HED (Hierarchical Event Descriptors) is a framework for systematically describin
 
 ## Quick start
 
+```{index} quick start, getting started, installation
+```
+
 ### Online tools (no installation required)
 
+```{index} online tools, web tools, hedtools.org
+```
+
 For simple validation or transformation tasks, use the online tools at [https://hedtools.org/hed](https://hedtools.org/hed) - no installation needed!
 
 Browser-based validation (no data upload) is available at [https://www.hedtags.org/hed-javascript](https://www.hedtags.org/hed-javascript)
@@ -30,6 +42,9 @@ A development version of the online tools is available at: [https://hedtools.org
 
 ### Python installation
 
+```{index} installation; Python, pip install, PyPI
+```
+
 **Requirements:** Python 3.10 or higher
 
 Install from PyPI:
@@ -46,6 +61,9 @@ pip install git+https://github.com/hed-standard/hed-python/@main
 
 ### Basic usage
 
+```{index} usage examples, HedString, load_schema_version, validation example
+```
+
 ```python
 from hed import HedString, load_schema_version
 
@@ -65,6 +83,9 @@ else:
 
 ### Command-line tools
 
+```{index} command-line tools, CLI, hedpy, validate-bids, extract-sidecar
+```
+
 HEDTools provides a unified command-line interface with git-like subcommands:
 
 ```bash
@@ -97,6 +118,9 @@ For more examples, see the [user guide](https://www.hedtags.org/hed-python/user_
 
 ### Jupyter notebook examples
 
+```{index} Jupyter notebooks, examples, interactive workflows
+```
+
 **Note:** Example notebooks are available in the [GitHub repository](https://github.com/hed-standard/hed-python/tree/main/examples) only, not in the PyPI package.
 
 The [`examples/`](examples/) directory contains Jupyter notebooks demonstrating common HED workflows with BIDS datasets:
@@ -127,6 +151,9 @@ See [`examples/README.md`](examples/README.md) for more details.
 
 ## Documentation
 
+```{index} documentation, user guide, API reference, Sphinx
+```
+
 📖 **Full Documentation:** [https://www.hedtags.org/hed-python](https://www.hedtags.org/hed-python)
 
 - [User guide](https://www.hedtags.org/hed-python/user_guide.html) - Usage instructions
@@ -135,6 +162,9 @@ See [`examples/README.md`](examples/README.md) for more details.
 
 ### Building docs locally
 
+```{index} building documentation, sphinx-build
+```
+
 ```bash
 # Install documentation dependencies
 pip install -e .[docs]
@@ -152,6 +182,9 @@ make html
 
 ### Formatting with Black
 
+```{index} Black, code formatting, style guide
+```
+
 This project uses [Black](https://black.readthedocs.io/) for consistent code formatting.
 
 ```bash
@@ -184,6 +217,9 @@ black --workers 1 .
 
 ## Related repositories
 
+```{index} HED ecosystem, repositories, hed-schemas, hed-specification
+```
+
 The HED ecosystem consists of several interconnected repositories:
 
 | Repository                                                             | Description                                      |
@@ -198,6 +234,9 @@ The HED ecosystem consists of several interconnected repositories:
 
 ## Contributing
 
+```{index} contributing, development setup, pull requests
+```
+
 We welcome contributions! Here's how you can help:
 
 1. **Report issues:** Use [GitHub Issues](https://github.com/hed-standard/hed-python/issues) for bug reports and feature requests
@@ -234,8 +273,14 @@ For detailed contribution guidelines, please see [CONTRIBUTING.md](CONTRIBUTING.
 
 ## Configuration
 
+```{index} configuration, schema caching, cache directory
+```
+
 ### Schema caching
 
+~~~{index} schema; caching, ~/.hedtools
+~~~
+
 By default, HED schemas are cached in `~/.hedtools/` (location varies by OS).
 
 ```python

diff --git a/docs/api/errors.rst b/docs/api/errors.rst
@@ -1,5 +1,5 @@
-Errors
-======
+Python HEDTools error handling
+==============================
 
 Error handling and reporting classes for HED validation and processing.
 

diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -1,7 +1,7 @@
 Python HEDTools API
 ===================
 
-This section contains the complete API reference for HED Python tools.
+This section contains the complete API reference for Python HEDTools.
 
 .. toctree::
    :maxdepth: 2
@@ -15,7 +15,7 @@ This section contains the complete API reference for HED Python tools.
 Core modules overview
 ---------------------
 
-The HED Python tools package is organized into several key modules:
+The Python HEDTools package is organized into several key modules:
 
 * **Models**: Core data structures for HED annotations and tags
 * **Schema**: HED schema management and validation

diff --git a/docs/api/models.rst b/docs/api/models.rst
@@ -1,5 +1,5 @@
-Models
-======
+Python HEDTools models
+=============================
 
 Core data models for working with HED data structures.
 

diff --git a/docs/api/schema.rst b/docs/api/schema.rst
@@ -1,5 +1,5 @@
-Schema
-======
+Python HEDTools schema
+======================
 
 HED schema management and validation tools.
 

diff --git a/docs/api/tools.rst b/docs/api/tools.rst
@@ -1,5 +1,5 @@
-Tools
-=====
+Python HEDTools tools
+=============================
 
 Utility functions and data processing tools for HED operations.
 

diff --git a/docs/api/validator.rst b/docs/api/validator.rst
@@ -1,5 +1,5 @@
-Validator
-=========
+Python HEDTools validator
+=========================
 
 Validation tools for HED data structures and annotations.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -45,7 +45,7 @@ Python HEDTools API
    API <api/index>
 
 
-Index
-=====
+Python HEDtools index
+----------------------
 
 * :ref:`genindex`
diff --git a/docs/overview.md b/docs/overview.md
@@ -1,7 +1,13 @@
 # Python HEDTools overview
 
+```{index} single: HED; overview
+```
+
 ## What is HED?
 
+```{index} HED, Hierarchical Event Descriptors, controlled vocabulary, BIDS, NWB
+```
+
 HED (Hierarchical Event Descriptors) is a framework for systematically describing events and experimental metadata in machine-actionable form. HED provides:
 
 - **Controlled vocabulary** for annotating experimental data and events
@@ -10,7 +16,10 @@ HED (Hierarchical Event Descriptors) is a framework for systematically describin
 
 For more information, visit the HED project [homepage](https://www.hedtags.org) and the [resources page](https://www.hedtags.org/hed-resources). The [table-remodeler](https://www.hedtags.org/table-remodeler) tools are now in a separate repository.
 
-## What is HEDTools?
+## What are Python HEDTools?
+
+```{index} hedtools, validation, BIDS integration, NWB support
+```
 
 The **hedtools** Python package (`hed-python` repository) provides:
 
@@ -36,6 +45,9 @@ The **hedtools** Python package (`hed-python` repository) provides:
 
 ## Installation
 
+```{index} installation, pip, PyPI
+```
+
 ### From PyPI (recommended)
 
 Install the latest stable release:
@@ -112,6 +124,9 @@ pip install -e .
 
 ### Basic validation example
 
+```{index} validation; HED string, HedString
+```
+
 ```python
 from hed import HedString, load_schema, get_printable_issue_string
 
@@ -130,6 +145,9 @@ else:
 
 ### BIDS dataset validation
 
+```{index} BIDS; validation, BidsDataset
+```
+
 ```python
 from hed.tools import BidsDataset
 
@@ -145,6 +163,9 @@ else:
 
 ### Working with sidecars
 
+```{index} sidecar, JSON sidecar, Sidecar class
+```
+
 ```python
 from hed import Sidecar, load_schema_version