diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
new file mode 100644
index 0000000..9dd1a84
--- /dev/null
+++ b/.github/workflows/check_external_links.yml
@@ -0,0 +1,32 @@
+name: Check Sphinx external links
+on:
+  push:
+  schedule:
+    - cron: '0 5 * * 0'  # once every Sunday at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    name: Check for broken Sphinx external links
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: |
+          cd docs  # run_doc_autogen assumes spec is found in ../spec/
+          sphinx-build -b linkcheck ./source ./test_build
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
index 6575870..314b085 100644
--- a/.github/workflows/codespell.yml
+++ b/.github/workflows/codespell.yml
@@ -1,6 +1,6 @@
 name: Codespell
 on:
-  pull_request:
+  push:
   workflow_dispatch:
 
 jobs:
@@ -9,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
new file mode 100644
index 0000000..9b4f05d
--- /dev/null
+++ b/.github/workflows/ruff.yml
@@ -0,0 +1,14 @@
+name: Ruff
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Ruff
+        uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
index 8f16226..6292cad 100644
--- a/.github/workflows/run_all_tests.yml
+++ b/.github/workflows/run_all_tests.yml
@@ -1,6 +1,6 @@
 name: Run all tests
 on:
-  pull_request:
+  push:
   schedule:
     - cron: '0 5 * * 0'  # once every Sunday at midnight ET
   workflow_dispatch:
@@ -12,6 +12,9 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -38,19 +41,13 @@ jobs:
           - { name: macos-python3.12             , requirements: pinned     , python-ver: "3.12", os: macos-latest }
           - { name: macos-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: macos-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -64,19 +61,20 @@ jobs:
         if: ${{ matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (pinned)
         if: ${{ matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (upgraded)
         if: ${{ matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U -e .
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |
@@ -110,6 +108,9 @@ jobs:
     defaults:
      run:
        shell: bash -l {0}  # needed for conda environment to work
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -122,18 +123,13 @@ jobs:
           - { name: conda-linux-python3.12           , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
           - { name: conda-linux-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           auto-activate-base: true
@@ -151,19 +147,20 @@ jobs:
         if: ${{ matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (pinned)
         if: ${{ matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (upgraded)
         if: ${{ matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U -e .
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
index 4883bf4..5aa6f9e 100644
--- a/.github/workflows/run_coverage.yml
+++ b/.github/workflows/run_coverage.yml
@@ -1,6 +1,6 @@
 name: Run code coverage
 on:
-  pull_request:
+  push:
   workflow_dispatch:
 
 jobs:
@@ -13,26 +13,23 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
+      cancel-in-progress: true
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:  # used by codecov-action
       OS: ${{ matrix.os }}
-      PYTHON: '3.11'
+      PYTHON: '3.12'
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.11.0
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON }}
 
@@ -43,17 +40,18 @@ jobs:
 
       - name: Install package
         run: |
-          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip install .
           python -m pip list
 
       - name: Run tests and generate coverage report
         run: |
-          pytest --cov
-          python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
 
-      # TODO uncomment after setting up repo on codecov.io
+      # TODO uncomment after setting up repo on codecov.io and adding token
       # - name: Upload coverage to Codecov
-      #   uses: codecov/codecov-action@v3
+      #   uses: codecov/codecov-action@v4
       #   with:
       #     fail_ci_if_error: true
+      #     file: ./coverage.xml
+      #   env:
+      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml
new file mode 100644
index 0000000..d050de1
--- /dev/null
+++ b/.github/workflows/validate_schema.yml
@@ -0,0 +1,22 @@
+name: Validate schema
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Install HDMF
+      run: |
+        pip install hdmf
+    - name: Download latest nwb schema language specification
+      run: |
+        curl -L https://raw.githubusercontent.com/NeurodataWithoutBorders/nwb-schema/dev/nwb.schema.json -o nwb.schema.json
+    - name: Validate schema specification
+      run: |
+        validate_hdmf_spec spec -m nwb.schema.json
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index a40ad0b..056fce3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,9 +4,6 @@
 # generated docs
 docs/source/_format_auto_docs
 
-# copied spec files
-src/pynwb/ndx_microscopy/spec/*.yaml
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -29,6 +26,7 @@ parts/
 sdist/
 var/
 wheels/
+share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -47,14 +45,18 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
 *.cover
+*.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -64,6 +66,7 @@ coverage.xml
 *.log
 local_settings.py
 db.sqlite3
+db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -76,16 +79,49 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# pyenv
-.python-version
+# IPython
+profile_default/
+ipython_config.py
 
-# celery beat schedule file
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
 celerybeat-schedule
+celerybeat.pid
 
 # SageMath parsed files
 *.sage.py
@@ -111,9 +147,24 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+.dmypy.json
+dmypy.json
 
-# Mac finder
-.DS_Store
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
 
 # PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+
+# Mac finder
+.DS_Store
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..db3ef69
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1 @@
+# Changelog for ndx-microscopy
diff --git a/NEXTSTEPS.md b/NEXTSTEPS.md
index 0faf651..e67a62a 100644
--- a/NEXTSTEPS.md
+++ b/NEXTSTEPS.md
@@ -4,12 +4,12 @@
 
 ## Creating Your Extension
 
-1. In a terminal, change directory into the new ndx-microscopy directory.
+1. In a terminal, change directory into the new ndx-microscopy directory: `cd ndx-microscopy`
 
-2. Add any packages required by your extension to `requirements.txt` and `setup.py`.
+2. Add any packages required by your extension to the `dependencies` key in `pyproject.toml`.
 
-3. Run `python -m pip install -r requirements.txt -r requirements-dev.txt` to install the `pynwb` package
-and any other packages required to install, develop, and document your extension.
+3. Run `python -m pip install -e .` to install your new extension Python package
+and any other packages required to develop, document, and run your extension.
 
 4. Modify `src/spec/create_extension_spec.py` to define your extension.
 
@@ -19,16 +19,18 @@ and any other packages required to install, develop, and document your extension
 
 6. Define API classes for your new extension data types.
 
-    - As a starting point, `src/pynwb/__init__.py` includes an example for how to use
-      the `pynwb.get_class` to get a basic Python class for your new extension data
+    - As a starting point, `src/pynwb/ndx_microscopy/__init__.py` includes an
+      example for how to use
+      the `pynwb.get_class` to generate a basic Python class for your new extension data
       type. This class contains a constructor and properties for the new data type.
     - Instead of using `pynwb.get_class`, you can define your own custom class for the
       new type, which will allow you to customize the class methods, customize the
-      object mapping, and create convenience functions. See
-      [https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html](https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html)
+      object mapping, and create convenience functions. See the
+      [Extending NWB tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html)
       for more details.
 
-7. Define tests for your new extension data types in `src/pynwb/tests` or `src/matnwb/tests`.
+7. Define tests for your new extension data types in 
+`src/pynwb/ndx_microscopy/tests` or `src/matnwb/tests`.
 A test for the example `TetrodeSeries` data type is provided as a reference and should be
 replaced or removed.
 
@@ -40,10 +42,26 @@ replaced or removed.
      new functions) and **integration tests** (e.g., write the new data types to file, read
      the file, and confirm the read data types are equal to the written data types) is
      highly encouraged.
-
-8. You may need to modify `setup.py` and re-run `python setup.py install` if you
+     - By default, to aid with debugging, the project is configured NOT to run code coverage as
+     part of the tests.
+     Code coverage reporting is useful to help with creation of tests and report test coverage.
+     However, with this option enabled, breakpoints for debugging with pdb are being ignored.
+     To enable this option for code coverage reporting, uncomment out the following line in
+     your `pyproject.toml`: [line](https://github.com/nwb-extensions/ndx-template/blob/11ae225b3fd3934fa3c56e6e7b563081793b3b43/%7B%7B%20cookiecutter.namespace%20%7D%7D/pyproject.toml#L82-L83
+)
+
+7. (Optional) Define custom visualization widgets for your new extension data types in
+`src/pynwb/ndx_microscopy/widgets` so that the visualizations can be displayed with
+[nwbwidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets).
+You will also need to update the `vis_spec` dictionary in 
+`src/pynwb/ndx_microscopy/widgets/__init__.py` so that
+nwbwidgets can find your custom visualizations.
+
+8. You may need to modify `pyproject.toml` and re-run `python -m pip install -e .` if you
 use any dependencies.
 
+9. Update the `CHANGELOG.md` regularly to document changes to your extension.
+
 
 ## Documenting and Publishing Your Extension to the Community
 
@@ -65,16 +83,26 @@ your extension.
 
 7. Add a license file. Permissive licenses should be used if possible. **A [BSD license](https://opensource.org/licenses/BSD-3-Clause) is recommended.**
 
-8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/CodyCBakerPhD/ndx-microscopy/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
+8. Update the `CHANGELOG.md` to document changes to your extension.
+
+8. Push your repository to GitHub. A default set of GitHub Actions workflows is set up to
+test your code on Linux, Windows, Mac OS, and Linux using conda; upload code coverage
+stats to codecov.io; check for spelling errors; check for style errors; and check for broken
+links in the documentation. For the code coverage workflow to work, you will need to
+set up the repo on codecov.io and uncomment the "Upload coverage to Codecov" step
+in `.github/workflows/run_coverage.yml`.
+
+8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/alessandratrapani/ndx-microscopy/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
 
 9. Publish your updated extension on [PyPI](https://pypi.org/).
-    - Follow these directions: https://packaging.python.org/tutorials/packaging-projects/
-    - You may need to modify `setup.py`
+    - Follow these directions: https://packaging.python.org/en/latest/tutorials/packaging-projects/
+    - You may need to modify `pyproject.toml`
     - If your extension version is 0.1.0, then this page should exist: https://pypi.org/project/ndx-microscopy/0.1.0
 
-   Once your GitHub release and ``setup.py`` are ready, publishing on PyPI:
+   Once your GitHub release and `pyproject.toml` are ready, publishing on PyPI:
     ```bash
-    python setup.py sdist bdist_wheel
+    python -m pip install --upgrade build twine
+    python -m build
     twine upload dist/*
     ```
 
@@ -104,11 +132,12 @@ with information on where to find your NWB extension.
       ```yaml
       name: ndx-microscopy
       version: 0.1.0
-      src: https://github.com/CodyCBakerPhD/ndx-microscopy
+      src: https://github.com/alessandratrapani/ndx-microscopy
       pip: https://pypi.org/project/ndx-microscopy/
-      license: MIT
-      maintainers:
-        - CodyCBakerPhD
+      license: BSD-3
+      maintainers: 
+        - alessandratrapani
+        - codycbakerphd
       ```
 
 14. Edit `staged-extensions/ndx-microscopy/README.md`
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..54e6545
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,179 @@
+
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS     =
+SPHINXBUILD    = sphinx-build
+SPHINXAPIDOC   = sphinx-apidoc
+PAPER          =
+BUILDDIR       = build
+SRCDIR         = ../src
+RSTDIR         = source
+CONFDIR        = $(PWD)/source
+
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext fulldoc allclean
+
+help:
+	@echo "To update documentation sources from the format specification please use \`make apidoc'"
+	@echo ""
+	@echo "To build the documentation please use \`make <target>' where <target> is one of"
+	@echo "  fulldoc    to rebuild the apidoc, html, and latexpdf all at once"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  apidoc     to to build RST from source code"
+	@echo "  clean      to clean all documents built by Sphinx in _build"
+	@echo "  allclean   to clean all autogenerated documents both from Sphinx and apidoc"
+
+allclean:
+	-rm -rf $(BUILDDIR)/* $(RSTDIR)/modules.rst
+	-rm $(RSTDIR)/_format_auto_docs/*.png
+	-rm $(RSTDIR)/_format_auto_docs/*.pdf
+	-rm $(RSTDIR)/_format_auto_docs/*.rst
+	-rm $(RSTDIR)/_format_auto_docs/*.inc
+
+clean:
+	-rm -rf $(BUILDDIR)/* $(RSTDIR)/modules.rst
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" 	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/sample.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sample.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/sample"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/sample"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" 	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" 	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " 	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " 	      "results in $(BUILDDIR)/doctest/output.txt."
+
+apidoc:
+	PYTHONPATH=$(CONFDIR):$(PYTHONPATH) nwb_generate_format_docs
+	@echo
+	@echo "Generate rst source files from NWB spec."
+
+fulldoc:
+	$(MAKE) allclean
+	@echo
+	@echo "Rebuilding apidoc, html, latexpdf"
+	$(MAKE) apidoc
+	$(MAKE) html
+	$(MAKE) latexpdf
diff --git a/docs/README.md b/docs/README.md
new file mode 100644
index 0000000..9a3a30d
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,121 @@
+
+# Getting started
+
+## Generate Documentation
+
+* To generate the HTML version of your documentation run ``make html``.
+* The [hdmf-docutils](https://pypi.org/project/hdmf-docutils/) package must be installed.
+
+## Customize Your Extension Documentation
+
+* **extension description**
+  * Edit ``source/description.rst`` to describe your extension.
+
+* **release notes**
+  * Edit ``source/release_notes.rst`` to document improvements and fixes of your extension.
+
+* **documentation build settings**
+  * Edit ``source/conf.py`` to customize your extension documentation configuration.
+  * Edit ``source/conf_doc_autogen.py`` to customize the format documentation auto-generation based on
+    the YAML specification files.
+
+
+# Overview
+
+The specification documentation uses Sphinx [http://www.sphinx-doc.org/en/stable/index.html](http://www.sphinx-doc.org/en/stable/index.html)
+
+## Rebuilding All
+
+To rebuild the full documentation in html, latex, and PDF simply run:
+
+```
+make fulldoc
+```
+
+This is a convenience function that is equivalent to:
+
+```
+make allclean
+make apidoc
+make html
+make latexpdf
+```
+
+## Generating the format documentation from the format spec
+
+The format documentation is auto-generated from the format specification (YAML) sources via:
+
+```
+make apidoc
+```
+
+This will invoke the executable:
+
+```
+hdmf_generate_format_docs
+```
+
+The script automatically generates a series of .rst, .png, and .pdf files that are stored in the folder `source/format_auto_docs`. The generated .rst files are included in `source/format.rst` and the png and pdf files are used as figures in the autogenerated docs.
+
+The folder `source/format_auto_docs` is reserved for autogenerated files, i.e., files in the folder should not be added or edited by hand as they will be deleted and rebuilt during the full built of the documentation.
+
+By default the Sphinx configuration is setup to always regenerate the sources whenever the docs are being built (see next section). This behavior can be customized via the `spec_doc_rebuild_always` parameter in `source/conf.py`
+
+## Building a specific document type
+
+To build the documentation, run:
+
+```
+make <doctype>
+```
+
+where `<doctype>` is, e.g., `latexpdf`, `html`, `singlehtml`, or `man`. For a complete list of supported doc-types, see:
+
+```
+make help
+```
+
+## Cleaning up
+
+`make clean` cleans up all builds of the documentation located in `_build`.
+
+`make allclean` cleans up all builds of the documentation located in `_build` as well as all autogenerated sources stored in `source/format_auto_docs`.
+
+## Configuration
+
+The build of the documentation can be customized via a broad range of Sphinx options in:
+
+`source/conf_doc_autogen.py`
+
+In addition to standard Sphinx options, there are a number of additional options used to customize the content and structure of the autogenerated documents, e.g.:
+
+* `spec_show_yaml_src` - Boolean indicating whether the YAML sources should be included for the different Neurodata types
+* `spec_generate_src_file` - Boolean indicating whether the YAML sources of the neurodata_types should be rendered in a separate section (True) or in the same location as the main documentation
+* `spec_show_hierarchy_plots` - Boolean indicating whether we should generate and show figures of the hierarchy defined by the specifications as part of the documentation
+* `spec_file_per_type` - Boolean indicating whether we should generate separate .inc reStructuredText for each neurodata_type (True)
+or should all text be added to the main file (False)
+* `spec_show_subgroups_in_tables` - Should subgroups of the main groups be rendered in the table as well. Usually this is disabled since groups are rendered as separate sections in the text
+* `spec_appreviate_main_object_doc_in_tables` - Abbreviate the documentation of the main object for which a table is rendered in the table. This is commonly set to True as doc of the main object is already rendered as the main intro for the section describing the object
+* `spec_show_title_for_tables` - Add a title for the table showing the specifications.
+* `spec_show_subgroups_in_seperate_table` - Should top-level subgroups be listed in a separate table or as part of the main dataset and attributes table
+* `spec_table_depth_char` - Char to be used as prefix to indicate the depth of an object in the specification hierarchy. NOTE: The char used should be supported by LaTeX.
+* `spec_add_latex_clearpage_after_ndt_sections` - Add a LaTeX clearpage after each main section describing a neurodata_type. This helps in LaTeX to keep the ordering of figures, tables, and code blocks consistent in particular when the hierarchy_plots are included.
+* `spec_resolve_type_inc` - Resolve includes to always show the full list of objects that are part of a type (True) or to show only the parts that are actually new to a current type while only linking to base types (False)
+
+In addition, the location of the input format specification can be customized as follows:
+
+* `spec_input_spec_dir` - Directory where the YAML files for the namespace to be documented are located
+* `spec_input_namespace_filename` - Name of the YAML file with the specification of the Namespace to be documented
+* `spec_input_default_namespace` - Name of the default namespace in the file
+
+Finally, the name and location of output files can be customized as follows:
+
+* `spec_output_dir` - Directory where the autogenerated files should be stored
+* `spec_output_master_filename` - Name of the master .rst file that includes all the autogenerated docs
+* `spec_output_doc_filename` - Name of the file where the main documentation goes
+* `spec_output_src_filename` - Name of the file where the sources of the format spec go. NOTE: This file is only generated if `spec_generate_src_file` is enabled
+* `spec_output_doc_type_hierarchy_filename` - Name of the file containing the type hierarchy. (Included in `spec_output_doc_filename`)
+
+In the regular Sphinx `source/conf.py` file, we can then also set:
+
+* `spec_doc_rebuild_always` - Boolean to define whether to always rebuild the source docs from YAML when doing a regular build of the sources (e.g., via `make html`) even if the folder with the source files already exists
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..dc1312a
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/_static/theme_overrides.css b/docs/source/_static/theme_overrides.css
new file mode 100644
index 0000000..63ee6cc
--- /dev/null
+++ b/docs/source/_static/theme_overrides.css
@@ -0,0 +1,13 @@
+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..002c717
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,112 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'ndx-microscopy'
+copyright = '2024, Alessandra Trapani, Cody Baker'
+author = 'Alessandra Trapani, Cody Baker'
+
+version = '0.1.0'
+release = 'alpha'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+language = 'en'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
+
+# -- Options for intersphinx extension ---------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#configuration
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+}
+
+
+############################################################################
+#  CUSTOM CONFIGURATIONS ADDED BY THE NWB TOOL FOR GENERATING FORMAT DOCS
+###########################################################################
+
+import sphinx_rtd_theme  # noqa: E402
+import textwrap  # noqa: E402
+
+# -- Options for intersphinx  ---------------------------------------------
+intersphinx_mapping.update({
+    'core': ('https://nwb-schema.readthedocs.io/en/latest/', None),
+    'hdmf-common': ('https://hdmf-common-schema.readthedocs.io/en/latest/', None),
+})
+
+# -- Generate sources from YAML---------------------------------------------------
+# Always rebuild the source docs from YAML even if the folder with the source files already exists
+spec_doc_rebuild_always = True
+
+
+def run_doc_autogen(_):
+    # Execute the autogeneration of Sphinx format docs from the YAML sources
+    import sys
+    import os
+    conf_file_dir = os.path.dirname(os.path.abspath(__file__))
+    sys.path.append(conf_file_dir)  # Need so that generate format docs can find the conf_doc_autogen file
+    from conf_doc_autogen import spec_output_dir
+
+    if spec_doc_rebuild_always or not os.path.exists(spec_output_dir):
+        sys.path.append('./docs')  # needed to enable import of generate_format docs
+        from hdmf_docutils.generate_format_docs import main as generate_docs
+        generate_docs()
+
+
+def setup(app):
+    app.connect('builder-inited', run_doc_autogen)
+    # overrides for wide tables in RTD theme
+    try:
+        app.add_css_file("theme_overrides.css")  # Used by newer Sphinx versions
+    except AttributeError:
+        app.add_stylesheet("theme_overrides.css")  # Used by older version of Sphinx
+
+# -- Customize sphinx settings
+numfig = True
+autoclass_content = 'both'
+autodoc_docstring_signature = True
+autodoc_member_order = 'bysource'
+add_function_parentheses = False
+
+
+# -- HTML sphinx options
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# LaTeX Sphinx options
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    'preamble': textwrap.dedent(
+        '''
+        \\setcounter{tocdepth}{3}
+        \\setcounter{secnumdepth}{6}
+        \\usepackage{enumitem}
+        \\setlistdepth{100}
+        '''),
+}
diff --git a/docs/source/conf_doc_autogen.py b/docs/source/conf_doc_autogen.py
new file mode 100644
index 0000000..aed891b
--- /dev/null
+++ b/docs/source/conf_doc_autogen.py
@@ -0,0 +1,90 @@
+# -*- coding: utf-8 -*-
+# Configuration file for generating sources for the format documentation from the YAML specification files
+
+import os
+
+# -- Input options for the specification files to be used -----------------------
+
+# Directory where the YAML files for the namespace to be documented are located
+spec_input_spec_dir = '..\spec'
+
+# Name of the YAML file with the specification of the Namespace to be documented
+spec_input_namespace_filename = 'ndx-microscopy.namespace.yaml'
+
+# Name of the default namespace in the file
+spec_input_default_namespace = 'ndx-microscopy'
+
+
+# -- Options for customizing the locations of output files
+
+# Directory where the autogenerated files should be stored
+spec_output_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_format_auto_docs")
+
+# Name of the master rst file that includes all the autogenerated docs
+spec_output_master_filename = 'format_spec_main.inc'
+
+# Name of the file where the main documentation goes
+spec_output_doc_filename = 'format_spec_doc.inc'
+
+# Name of the file where the sources of the format spec go. NOTE: This file is only generated if
+# spec_generate_src_file is enabled
+spec_output_src_filename = 'format_spec_sources.inc'
+
+# Name of the file containing the type hierarchy. (Included in spec_output_doc_filename)
+spec_output_doc_type_hierarchy_filename = 'format_spec_type_hierarchy.inc'
+
+# Clean up the output directory before we build if the git hash is out of date
+spec_clean_output_dir_if_old_git_hash = True
+
+# Do not rebuild the format sources if we have previously build the sources and the git hash matches
+spec_skip_doc_autogen_if_current_git_hash = False
+
+
+# -- Options for the generation of the documentation from source ----------------
+
+# Should the YAML sources be included for the different modules
+spec_show_yaml_src = True
+
+# Show figure of the hierarchy of objects defined by the spec
+spec_show_hierarchy_plots = True
+
+# Should the sources of the neurodata_types (YAML) be rendered in a separate section (True) or
+# in the same location as the base documentation
+spec_generate_src_file = True
+
+# Should separate .inc reStructuredText files be generated for each neurodata_type (True)
+# or should all text be added to the main file
+spec_file_per_type = True
+
+# Should top-level subgroups be listed in a separate table or as part of the main dataset and attributes table
+spec_show_subgroups_in_seperate_table = True
+
+# Abbreviate the documentation of the main object for which a table is rendered in the table.
+# This is commonly set to True as doc of the main object is alrready rendered as the main intro for the
+# section describing the object
+spec_appreviate_main_object_doc_in_tables = True
+
+# Show a title for the tables
+spec_show_title_for_tables = True
+
+# Char to be used as prefix to indicate the depth of an object in the specification hierarchy
+spec_table_depth_char = '.'  # '→' '.'
+
+# Add a LaTeX clearpage after each main section describing a neurodata_type. This helps in LaTeX to keep the ordering
+# of figures, tables, and code blocks consistent in particular when the hierarchy_plots are included
+spec_add_latex_clearpage_after_ndt_sections = True
+
+# Resolve includes to always show the full list of objects that are part of a type (True)
+# or to show only the parts that are actually new to a current type while only linking to base types
+spec_resolve_type_inc = False
+
+# Default type map to be used. This is the type map where dependent namespaces are stored. In the case of
+# NWB this is spec_default_type_map = pynwb.get_type_map()
+import pynwb  # noqa: E402
+spec_default_type_map = pynwb.get_type_map()
+
+# Default specification classes for groups datasets and namespaces. In the case of NWB these are the NWB-specfic
+# spec classes. In the general cases these are the spec classes from HDMF
+spec_group_spec_cls = pynwb.spec.NWBGroupSpec
+spec_dataset_spec_cls = pynwb.spec.NWBDatasetSpec
+spec_namespace_spec_cls = pynwb.spec.NWBNamespace
diff --git a/docs/source/credits.rst b/docs/source/credits.rst
new file mode 100644
index 0000000..da5cda1
--- /dev/null
+++ b/docs/source/credits.rst
@@ -0,0 +1,21 @@
+*******
+Credits
+*******
+
+.. note::
+    Add the credits for your extension here
+
+Acknowledgments
+===============
+
+
+Authors
+=======
+
+
+*****
+Legal
+*****
+
+License
+=======
diff --git a/docs/source/description.rst b/docs/source/description.rst
new file mode 100644
index 0000000..6f8553e
--- /dev/null
+++ b/docs/source/description.rst
@@ -0,0 +1,5 @@
+Overview
+========
+
+.. note::
+    Add the description of your extension here
diff --git a/docs/source/format.rst b/docs/source/format.rst
new file mode 100644
index 0000000..4b88782
--- /dev/null
+++ b/docs/source/format.rst
@@ -0,0 +1,12 @@
+
+.. _ndx-microscopy:
+
+**************
+ndx-microscopy
+**************
+
+Version |release| |today|
+
+.. .. contents::
+
+.. include:: _format_auto_docs/format_spec_main.inc
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..207c9a0
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,30 @@
+Specification for the ndx-microscopy extension
+==============================================
+
+.. toctree::
+    :numbered:
+    :maxdepth: 8
+    :caption: Table of Contents
+
+    description
+
+.. toctree::
+    :numbered:
+    :maxdepth: 3
+    :caption: Extension Specification
+
+    format
+
+.. toctree::
+    :maxdepth: 2
+    :caption: History & Legal
+
+    release_notes
+    credits
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/release_notes.rst b/docs/source/release_notes.rst
new file mode 100644
index 0000000..39ccd1c
--- /dev/null
+++ b/docs/source/release_notes.rst
@@ -0,0 +1,5 @@
+Release Notes
+=============
+
+.. note::
+    Add the release notes of your extension here
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 9955dec..0db92de 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,2 +1,14 @@
-pytest
-pytest-cov
+# pinned dependencies to reproduce an entire development environment to
+# run tests, check code style, and generate documentation
+black==24.4.2
+codespell==2.3.0
+coverage==7.5.4
+hdmf==3.14.1
+hdmf-docutils==0.4.7
+pre-commit==3.5.0  # latest pre-commit does not support py3.8
+pynwb==2.8.0
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-subtests==0.12.1
+python-dateutil==2.8.2
+ruff==0.4.10
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index f6c4008..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,17 +0,0 @@
-[wheel]
-universal = 1
-
-[flake8]
-max-line-length = 120
-max-complexity = 17
-exclude =
-  .git,
-  .tox,
-  __pycache__,
-  build/,
-  dist/,
-  docs/source/conf.py
-  versioneer.py
-
-[metadata]
-description-file = README.md
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 33da03e..0000000
--- a/setup.py
+++ /dev/null
@@ -1,69 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import os
-from shutil import copy2
-
-from setuptools import find_packages, setup
-
-# load README.md/README.rst file
-try:
-    if os.path.exists("README.md"):
-        with open("README.md", "r") as fp:
-            readme = fp.read()
-            readme_type = "text/markdown; charset=UTF-8"
-    elif os.path.exists("README.rst"):
-        with open("README.rst", "r") as fp:
-            readme = fp.read()
-            readme_type = "text/x-rst; charset=UTF-8"
-    else:
-        readme = ""
-except Exception:
-    readme = ""
-
-setup_args = {
-    "name": "ndx-microscopy",
-    "version": "0.1.0",
-    "description": "An example extension to demonstrate the TAB proposal for enhancements to optical physiology neurodata types.",
-    "long_description": readme,
-    "long_description_content_type": readme_type,
-    "author": "Cody Baker and Alessandra Trapani",
-    "author_email": "cody.baker@catalystneuro.com",
-    "url": "",
-    "license": "MIT",
-    "install_requires": [
-        "pynwb>=1.5.0,<3",
-        "hdmf>=2.5.6,<4",
-    ],
-    "packages": find_packages("src/pynwb", exclude=["tests", "tests.*"]),
-    "package_dir": {"": "src/pynwb"},
-    "package_data": {
-        "ndx_microscopy": [
-            "spec/ndx-microscopy.namespace.yaml",
-            "spec/ndx-microscopy.extensions.yaml",
-        ]
-    },
-    "classifiers": [
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: MIT License",
-    ],
-    "keywords": ["NeurodataWithoutBorders", "NWB", "nwb-extension", "ndx-extension"],
-    "zip_safe": False,
-}
-
-
-def _copy_spec_files(project_dir):
-    ns_path = os.path.join(project_dir, "spec", "ndx-microscopy.namespace.yaml")
-    ext_path = os.path.join(project_dir, "spec", "ndx-microscopy.extensions.yaml")
-
-    dst_dir = os.path.join(project_dir, "src", "pynwb", "ndx_microscopy", "spec")
-    if not os.path.exists(dst_dir):
-        os.mkdir(dst_dir)
-
-    copy2(ns_path, dst_dir)
-    copy2(ext_path, dst_dir)
-
-
-if __name__ == "__main__":
-    _copy_spec_files(os.path.dirname(__file__))
-    setup(**setup_args)