From bce1044a40dcd7591dcc4a815683dad07fa70c8c Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 1 Aug 2023 13:53:26 -0400
Subject: [PATCH 1/9] feat: framework for dense annotation conversion script

---
 poetry.lock                                  | 1655 ++++++++----------
 pyproject.toml                               |    2 -
 src/fibsem_tools/metadata/groundtruth.py     |   16 +-
 src/fibsem_tools/metadata/old_to_new_meta.py |   12 +
 4 files changed, 777 insertions(+), 908 deletions(-)
 create mode 100755 src/fibsem_tools/metadata/old_to_new_meta.py

diff --git a/poetry.lock b/poetry.lock
index 95892c4..fdc0c02 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,122 +1,122 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
-version = "2.5.0"
+version = "2.5.2"
 description = "Async client for aws services using botocore and aiohttp"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "aiobotocore-2.5.0-py3-none-any.whl", hash = "sha256:9a2a022d7b78ec9a2af0de589916d2721cddbf96264401b78d7a73c1a1435f3b"},
-    {file = "aiobotocore-2.5.0.tar.gz", hash = "sha256:6a5b397cddd4f81026aa91a14c7dd2650727425740a5af8ba75127ff663faf67"},
+    {file = "aiobotocore-2.5.2-py3-none-any.whl", hash = "sha256:337429ffd3cc367532572d40be809a84c7b5335f3f8eca2f23e09dfaa9a9ef90"},
+    {file = "aiobotocore-2.5.2.tar.gz", hash = "sha256:e7399f21570db1c287f1c0c814dd3475dfe1c8166722e2c77ce67f172cbcfa89"},
 ]
 
 [package.dependencies]
-aiohttp = ">=3.3.1"
-aioitertools = ">=0.5.1"
-botocore = ">=1.29.76,<1.29.77"
-wrapt = ">=1.10.10"
+aiohttp = ">=3.3.1,<4.0.0"
+aioitertools = ">=0.5.1,<1.0.0"
+botocore = ">=1.29.161,<1.29.162"
+wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.27.76,<1.27.77)"]
-boto3 = ["boto3 (>=1.26.76,<1.26.77)"]
+awscli = ["awscli (>=1.27.161,<1.27.162)"]
+boto3 = ["boto3 (>=1.26.161,<1.26.162)"]
 
 [[package]]
 name = "aiohttp"
-version = "3.8.4"
+version = "3.8.5"
 description = "Async http client/server framework (asyncio)"
 category = "main"
 optional = false
 python-versions = ">=3.6"
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 [package.dependencies]
@@ -161,27 +161,6 @@ files = [
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-version = "3.6.2"
-description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "main"
-optional = false
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-sniffio = ">=1.1"
-
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-trio = ["trio (>=0.16,<0.22)"]
-
 [[package]]
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 version = "0.3.3"
@@ -249,14 +228,14 @@ files = [
 
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 name = "botocore"
-version = "1.29.76"
+version = "1.29.161"
 description = "Low-level, data-driven core of boto 3."
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
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 [[package]]
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-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
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 [package.dependencies]
@@ -417,63 +396,72 @@ files = [
 
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 [package.dependencies]
@@ -484,72 +472,72 @@ toml = ["tomli"]
 
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+version = "2023.7.1"
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 category = "main"
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 packaging = ">=20.0"
 partd = ">=1.2.0"
 pyyaml = ">=5.3.1"
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+toolz = ">=0.10.0"
 
 [package.extras]
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-test = ["pandas[test]", "pre-commit", "pytest", "pytest-rerunfailures", "pytest-xdist"]
+distributed = ["distributed (==2023.7.1)"]
+test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist"]
 
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 description = "Distribution utilities"
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 python-versions = "*"
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 description = "Distributed scheduler for Dask"
 category = "main"
 optional = false
-python-versions = ">=3.8"
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 [package.dependencies]
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 cloudpickle = ">=1.5.0"
-dask = "2023.4.0"
+dask = "2023.7.1"
 jinja2 = ">=2.10.3"
 locket = ">=1.0.0"
 msgpack = ">=1.0.0"
 packaging = ">=20.0"
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 toolz = ">=0.10.0"
-tornado = ">=6.0.3"
+tornado = ">=6.0.4"
 urllib3 = ">=1.24.3"
 zict = ">=2.2.0"
 
@@ -579,114 +567,101 @@ files = [
 
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 python-versions = ">=3.7"
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 description = "File-system specification"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
 dev = ["flake8", "markdown", "twine", "wheel"]
 
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-[package.dependencies]
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-
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 name = "h5py"
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 description = "Read and write HDF5 files from Python"
 category = "main"
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-category = "main"
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-python-versions = ">=3.7"
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 files = [
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-sniffio = ">=1.0.0,<2.0.0"
-
-[package.extras]
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-socks = ["socksio (>=1.0.0,<2.0.0)"]
-
-[[package]]
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-python-versions = ">=3.7"
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-httpcore = ">=0.15.0,<0.17.0"
-rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
-sniffio = "*"
-
-[package.extras]
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-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"]
-http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
-
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+numpy = ">=1.17.3"
 
 [[package]]
 name = "identify"
-version = "2.5.22"
+version = "2.5.26"
 description = "File identification library for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -959,14 +831,14 @@ files = [
 
 [[package]]
 name = "linkify-it-py"
-version = "2.0.0"
+version = "2.0.2"
 description = "Links recognition library with FULL unicode support."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -974,7 +846,7 @@ uc-micro-py = "*"
 
 [package.extras]
 benchmark = ["pytest", "pytest-benchmark"]
-dev = ["black", "flake8", "isort", "pre-commit"]
+dev = ["black", "flake8", "isort", "pre-commit", "pyproject-flake8"]
 doc = ["myst-parser", "sphinx", "sphinx-book-theme"]
 test = ["coverage", "pytest", "pytest-cov"]
 
@@ -992,20 +864,21 @@ files = [
 
 [[package]]
 name = "markdown"
-version = "3.3.7"
-description = "Python implementation of Markdown."
+version = "3.4.4"
+description = "Python implementation of John Gruber's Markdown."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
@@ -1037,82 +910,82 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.2"
+version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
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-rtd = ["attrs", "myst-parser (>=0.16.1,<0.17.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
+rtd = ["myst-parser", "sphinx-book-theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
@@ -1141,14 +1014,14 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.4.2"
+version = "1.5.1"
 description = "Project documentation with Markdown."
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
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+platformdirs = ">=2.2.0"
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 pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
 [package.extras]
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 [[package]]
 name = "mkdocs-exclude"
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 [package.extras]
 dmypy = ["psutil (>=4.0)"]
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 [[package]]
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 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
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 [package.dependencies]
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 [[package]]
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@@ -1557,7 +1430,7 @@ pytz = ">=2020.1"
 tzdata = ">=2022.1"
 
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 xml = ["lxml (>=4.6.3)"]
 
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@@ -1598,6 +1471,18 @@ toolz = "*"
 [package.extras]
 complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
 
+[[package]]
+name = "pathspec"
+version = "0.11.2"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "main"
+optional = false
+python-versions = ">=3.7"
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 version = "0.20.1"
@@ -1621,30 +1506,30 @@ xarray = ["xarray"]
 
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 name = "platformdirs"
-version = "3.2.0"
+version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
+category = "main"
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+version = "1.2.0"
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-python-versions = ">=3.6"
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+    {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
+    {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
+    {file = "PyYAML-6.0.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
+    {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
 [[package]]
@@ -1950,38 +1835,20 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
-[[package]]
-name = "rfc3986"
-version = "1.5.0"
-description = "Validating URI References per RFC 3986"
-category = "main"
-optional = false
-python-versions = "*"
-files = [
-    {file = "rfc3986-1.5.0-py2.py3-none-any.whl", hash = "sha256:a86d6e1f5b1dc238b218b012df0aa79409667bb209e58da56d0b94704e712a97"},
-    {file = "rfc3986-1.5.0.tar.gz", hash = "sha256:270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835"},
-]
-
-[package.dependencies]
-idna = {version = "*", optional = true, markers = "extra == \"idna2008\""}
-
-[package.extras]
-idna2008 = ["idna"]
-
 [[package]]
 name = "rich"
-version = "13.3.4"
+version = "13.5.1"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "rich-13.3.4-py3-none-any.whl", hash = "sha256:22b74cae0278fd5086ff44144d3813be1cedc9115bdfabbfefd86400cb88b20a"},
-    {file = "rich-13.3.4.tar.gz", hash = "sha256:b5d573e13605423ec80bdd0cd5f8541f7844a0e71a13f74cf454ccb2f490708b"},
+    {file = "rich-13.5.1-py3-none-any.whl", hash = "sha256:b97381b204a206e1be618f5e1215a57174a1a7732490b3bf6668cf41d30bc72d"},
+    {file = "rich-13.5.1.tar.gz", hash = "sha256:881653ee7037803559d8eae98f145e0a4c4b0ec3ff0300d2cc8d479c71fc6819"},
 ]
 
 [package.dependencies]
-markdown-it-py = ">=2.2.0,<3.0.0"
+markdown-it-py = ">=2.2.0"
 pygments = ">=2.13.0,<3.0.0"
 
 [package.extras]
@@ -1989,20 +1856,20 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "s3fs"
-version = "2023.4.0"
+version = "2023.6.0"
 description = "Convenient Filesystem interface over S3"
 category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
-    {file = "s3fs-2023.4.0-py3-none-any.whl", hash = "sha256:be0afe8f01c67951566d6e9b8a954eaf09b674a4a28002d08eecde29c74a3310"},
-    {file = "s3fs-2023.4.0.tar.gz", hash = "sha256:963ee2e070e03e2952d535dbc6fd2b341869fcd16006cf74b90bcf39fd26cded"},
+    {file = "s3fs-2023.6.0-py3-none-any.whl", hash = "sha256:d1a0a423d0d2e17fb2a193d9531935dc3f45ba742693448a461b6b34f6a92a24"},
+    {file = "s3fs-2023.6.0.tar.gz", hash = "sha256:63fd8ddf05eb722de784b7b503196107f2a518061298cf005a8a4715b4d49117"},
 ]
 
 [package.dependencies]
 aiobotocore = ">=2.5.0,<2.6.0"
 aiohttp = "<4.0.0a0 || >4.0.0a0,<4.0.0a1 || >4.0.0a1"
-fsspec = "2023.4.0"
+fsspec = "2023.6.0"
 
 [package.extras]
 awscli = ["aiobotocore[awscli] (>=2.5.0,<2.6.0)"]
@@ -2049,19 +1916,19 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "67.7.2"
+version = "68.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "setuptools-67.7.2-py3-none-any.whl", hash = "sha256:23aaf86b85ca52ceb801d32703f12d77517b2556af839621c641fca11287952b"},
-    {file = "setuptools-67.7.2.tar.gz", hash = "sha256:f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990"},
+    {file = "setuptools-68.0.0-py3-none-any.whl", hash = "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f"},
+    {file = "setuptools-68.0.0.tar.gz", hash = "sha256:baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -2076,18 +1943,6 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
-[[package]]
-name = "sniffio"
-version = "1.3.0"
-description = "Sniff out which async library your code is running under"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "sniffio-1.3.0-py3-none-any.whl", hash = "sha256:eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384"},
-    {file = "sniffio-1.3.0.tar.gz", hash = "sha256:e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101"},
-]
-
 [[package]]
 name = "sortedcontainers"
 version = "2.4.0"
@@ -2102,14 +1957,14 @@ files = [
 
 [[package]]
 name = "tblib"
-version = "1.7.0"
+version = "2.0.0"
 description = "Traceback serialization library."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
-    {file = "tblib-1.7.0-py2.py3-none-any.whl", hash = "sha256:289fa7359e580950e7d9743eab36b0691f0310fce64dee7d9c31065b8f723e23"},
-    {file = "tblib-1.7.0.tar.gz", hash = "sha256:059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c"},
+    {file = "tblib-2.0.0-py3-none-any.whl", hash = "sha256:9100bfa016b047d5b980d66e7efed952fbd20bd85b56110aaf473cb97d18709a"},
+    {file = "tblib-2.0.0.tar.gz", hash = "sha256:a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7"},
 ]
 
 [[package]]
@@ -2136,14 +1991,14 @@ dev = ["aiohttp (>=3.8.1)", "click (>=8.1.2)", "msgpack (>=1.0.3)"]
 
 [[package]]
 name = "tifffile"
-version = "2023.4.12"
+version = "2023.7.18"
 description = "Read and write TIFF files"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "tifffile-2023.4.12-py3-none-any.whl", hash = "sha256:3161954746fe32c4f4244d0fb2eb0a272f3a3760b78882a42faa83ac5e6e0b74"},
-    {file = "tifffile-2023.4.12.tar.gz", hash = "sha256:2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd"},
+    {file = "tifffile-2023.7.18-py3-none-any.whl", hash = "sha256:a9449ab688b82b69f3ddf80e4e0b4de7b5b02549974a56e112061b816b3c5585"},
+    {file = "tifffile-2023.7.18.tar.gz", hash = "sha256:5a5a624b2f7ab7f37e9ec4174ae2df1805b9658f89013f9b4b5550672f65f2a1"},
 ]
 
 [package.dependencies]
@@ -2211,14 +2066,14 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.5.0"
+version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
-    {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
+    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
 [[package]]
@@ -2235,14 +2090,14 @@ files = [
 
 [[package]]
 name = "uc-micro-py"
-version = "1.0.1"
+version = "1.0.2"
 description = "Micro subset of unicode data files for linkify-it-py projects."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "uc-micro-py-1.0.1.tar.gz", hash = "sha256:b7cdf4ea79433043ddfe2c82210208f26f7962c0cfbe3bacb05ee879a7fdb596"},
-    {file = "uc_micro_py-1.0.1-py3-none-any.whl", hash = "sha256:316cfb8b6862a0f1d03540f0ae6e7b033ff1fa0ddbe60c12cbe0d4cec846a69f"},
+    {file = "uc-micro-py-1.0.2.tar.gz", hash = "sha256:30ae2ac9c49f39ac6dce743bd187fcd2b574b16ca095fa74cd9396795c954c54"},
+    {file = "uc_micro_py-1.0.2-py3-none-any.whl", hash = "sha256:8c9110c309db9d9e87302e2f4ad2c3152770930d88ab385cd544e7a7e75f3de0"},
 ]
 
 [package.extras]
@@ -2250,14 +2105,14 @@ test = ["coverage", "pytest", "pytest-cov"]
 
 [[package]]
 name = "urllib3"
-version = "1.26.15"
+version = "1.26.16"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
-    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+    {file = "urllib3-1.26.16-py2.py3-none-any.whl", hash = "sha256:8d36afa7616d8ab714608411b4a3b13e58f463aee519024578e062e141dce20f"},
+    {file = "urllib3-1.26.16.tar.gz", hash = "sha256:8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14"},
 ]
 
 [package.extras]
@@ -2267,24 +2122,24 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.22.0"
+version = "20.24.2"
 description = "Virtual Python Environment builder"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.22.0-py3-none-any.whl", hash = "sha256:48fd3b907b5149c5aab7c23d9790bea4cac6bc6b150af8635febc4cfeab1275a"},
-    {file = "virtualenv-20.22.0.tar.gz", hash = "sha256:278753c47aaef1a0f14e6db8a4c5e1e040e90aea654d0fc1dc7e0d8a42616cc3"},
+    {file = "virtualenv-20.24.2-py3-none-any.whl", hash = "sha256:43a3052be36080548bdee0b42919c88072037d50d56c28bd3f853cbe92b953ff"},
+    {file = "virtualenv-20.24.2.tar.gz", hash = "sha256:fd8a78f46f6b99a67b7ec5cf73f92357891a7b3a40fd97637c27f854aae3b9e0"},
 ]
 
 [package.dependencies]
-distlib = ">=0.3.6,<1"
-filelock = ">=3.11,<4"
-platformdirs = ">=3.2,<4"
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<4"
 
 [package.extras]
-docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
 name = "watchdog"
@@ -2413,14 +2268,14 @@ files = [
 
 [[package]]
 name = "xarray"
-version = "2023.4.2"
+version = "2023.7.0"
 description = "N-D labeled arrays and datasets in Python"
 category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "xarray-2023.4.2-py3-none-any.whl", hash = "sha256:1b6d577c1217ad6bf7458426af19ed7a489ab6c41220ca791f55f5df9648173a"},
-    {file = "xarray-2023.4.2.tar.gz", hash = "sha256:958ec588220352343b910cbc05e54e7ab54d4e8c1c3a7783d6bfe7549d0bd0d2"},
+    {file = "xarray-2023.7.0-py3-none-any.whl", hash = "sha256:af8b55bf78b792b8ad9326eb9d89980602f1a51e93d8465b445aeea3accca27e"},
+    {file = "xarray-2023.7.0.tar.gz", hash = "sha256:dace2fdbf1b7ff185d9c1226a24bf83c2ae52f3253dbfe80e17d1162600d055c"},
 ]
 
 [package.dependencies]
@@ -2489,86 +2344,86 @@ xarray = ">=2023.2.0,<2024.0.0"
 
 [[package]]
 name = "yarl"
-version = "1.9.1"
+version = "1.9.2"
 description = "Yet another URL library"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "yarl-1.9.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:e124b283a04cc06d22443cae536f93d86cd55108fa369f22b8fe1f2288b2fe1c"},
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-    {file = "yarl-1.9.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:ecaa5755a39f6f26079bf13f336c67af589c222d76b53cd3824d3b684b84d1f1"},
-    {file = "yarl-1.9.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:92a101f6d5a9464e86092adc36cd40ef23d18a25bfb1eb32eaeb62edc22776bb"},
-    {file = "yarl-1.9.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:92e37999e36f9f3ded78e9d839face6baa2abdf9344ea8ed2735f495736159de"},
-    {file = "yarl-1.9.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:ef7e2f6c47c41e234600a02e1356b799761485834fe35d4706b0094cb3a587ee"},
-    {file = "yarl-1.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1d7a0075a55380b19aa43b9e8056e128b058460d71d75018a4f9d60ace01e78c"},
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+    {file = "yarl-1.9.2-cp39-cp39-win32.whl", hash = "sha256:b124e2a6d223b65ba8768d5706d103280914d61f5cae3afbc50fc3dfcc016623"},
+    {file = "yarl-1.9.2-cp39-cp39-win_amd64.whl", hash = "sha256:61016e7d582bc46a5378ffdd02cd0314fb8ba52f40f9cf4d9a5e7dbef88dee18"},
+    {file = "yarl-1.9.2.tar.gz", hash = "sha256:04ab9d4b9f587c06d801c2abfe9317b77cdf996c65a90d5e84ecc45010823571"},
 ]
 
 [package.dependencies]
@@ -2577,14 +2432,14 @@ multidict = ">=4.0"
 
 [[package]]
 name = "zarr"
-version = "2.14.2"
+version = "2.16.0"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zarr-2.14.2-py3-none-any.whl", hash = "sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2"},
-    {file = "zarr-2.14.2.tar.gz", hash = "sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc"},
+    {file = "zarr-2.16.0-py3-none-any.whl", hash = "sha256:6cf9e6e4c58b9233262e024394e68921a438a6af5a7428bd6bdb1e4e8d05b69a"},
+    {file = "zarr-2.16.0.tar.gz", hash = "sha256:84e36b695bda0ecea52af9861271984cb22a5c864679907b7b9ba3f79b684f7e"},
 ]
 
 [package.dependencies]
@@ -2610,21 +2465,21 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
+    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "61d553d7954e8589dc0150f8dff3014ee396000c3785bb6521edaf9eae701092"
+content-hash = "92b99a4d75df5f14dcb4e547c4366d9350ab881649047c497e199e61e700c824"
diff --git a/pyproject.toml b/pyproject.toml
index ed6c482..f141f43 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,8 +25,6 @@ pydantic-ome-ngff = "^0.2.0"
 click = "^8.1.3"
 dask = "^2023.3.2"
 textual = "^0.16.0"
-aiohttp = "^3.8.4"
-httpx = {extras = ["http2"], version = "^0.23.3"}
 xarray-datatree = "^0.0.12"
 
 
diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index 1179cd2..ac21ac5 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 from enum import Enum
-from typing import Dict, Generic, List, Literal, Optional, TypeVar, Union
+from typing import Any, Dict, Generic, List, Literal, Optional, TypeVar, Union
 
 from pydantic import BaseModel, root_validator
 from pydantic.generics import GenericModel
@@ -36,14 +36,14 @@ class Label(BaseModel):
 
 class LabelList(BaseModel):
     labels: List[Label]
-    annotation_type: AnnotationType = "semantic"
+    annotation_type: Literal["semantic", "instance"] = "semantic"
 
 
 classNameDict = {
     1: InstanceName(short="ECS", long="Extracellular Space"),
     2: InstanceName(short="Plasma membrane", long="Plasma membrane"),
     3: InstanceName(short="Mito membrane", long="Mitochondrial membrane"),
-    4: InstanceName(short="Mito lumen",long="Mitochondrial lumen"),
+    4: InstanceName(short="Mito lumen", long="Mitochondrial lumen"),
     5: InstanceName(short="Mito DNA", long="Mitochondrial DNA"),
     6: InstanceName(short="Golgi Membrane", long="Golgi apparatus membrane"),
     7: InstanceName(short="Golgi lumen", long="Golgi apparatus lumen"),
@@ -57,7 +57,9 @@ class LabelList(BaseModel):
     15: InstanceName(short="LD lumen", long="Lipid droplet lumen"),
     16: InstanceName(short="ER membrane", long="Endoplasmic reticulum membrane"),
     17: InstanceName(short="ER lumen", long="Endoplasmic reticulum membrane"),
-    18: InstanceName(short="ERES membrane", long="Endoplasmic reticulum exit site membrane"),
+    18: InstanceName(
+        short="ERES membrane", long="Endoplasmic reticulum exit site membrane"
+    ),
     19: InstanceName(short="ERES lumen", long="Endoplasmic reticulum exit site lumen"),
     20: InstanceName(short="NE membrane", long="Nuclear envelope membrane"),
     21: InstanceName(short="NE lumen", long="Nuclear envelope lumen"),
@@ -83,7 +85,9 @@ class LabelList(BaseModel):
     41: InstanceName(short="Endothelial cells", long="Endothelial cells"),
     42: InstanceName(short="Cardiomyocytes", long="Cardiomyocytes"),
     43: InstanceName(short="Epicardial cells", long="Epicardial cells"),
-    44: InstanceName(short="Parietal pericardial cells", long="Parietal pericardial cells"),
+    44: InstanceName(
+        short="Parietal pericardial cells", long="Parietal pericardial cells"
+    ),
     45: InstanceName(short="Red blood cells", long="Red blood cells"),
     46: InstanceName(short="White blood cells", long="White blood cells"),
     47: InstanceName(short="Peroxisome membrane", long="Peroxisome membrane"),
@@ -121,7 +125,7 @@ class AnnotationArrayAttrs(GenericModel, Generic[TName]):
     annotation_type: AnnotationType
 
     @root_validator()
-    def check_encoding(cls, values):
+    def check_encoding(cls, values: Any) -> Any:
         if (typ := values.get("type", False)) and (
             hist := values.get("histogram", False)
         ):
diff --git a/src/fibsem_tools/metadata/old_to_new_meta.py b/src/fibsem_tools/metadata/old_to_new_meta.py
new file mode 100755
index 0000000..6af95b5
--- /dev/null
+++ b/src/fibsem_tools/metadata/old_to_new_meta.py
@@ -0,0 +1,12 @@
+import click
+from fibsem_tools import read_xarray
+
+
+@click.command
+@click.argument("source", type=click.STRING)
+def main(source: str) -> None:
+    read_xarray(source)
+
+
+if __name__ == "__main__":
+    main()

From ffb2c00f0fb08a77cf749fd6946cf1deab16976a Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 1 Aug 2023 14:30:17 -0400
Subject: [PATCH 2/9] fix: remove union operator

---
 src/fibsem_tools/metadata/groundtruth.py     | 6 +++---
 src/fibsem_tools/metadata/old_to_new_meta.py | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index ac21ac5..b4525b7 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -147,9 +147,9 @@ class MultiscaleGroupAttrs(GenericModel, Generic[TName]):
     description: str
     created_by: list[str]
     created_with: list[str]
-    start_date: str | None
-    end_date: str | None
-    duration_days: int | None
+    start_date: Optional[str]
+    end_date: Optional[str]
+    duration_days: Optional[int]
     annotation_type: AnnotationType
 
 
diff --git a/src/fibsem_tools/metadata/old_to_new_meta.py b/src/fibsem_tools/metadata/old_to_new_meta.py
index 6af95b5..e8ff7bc 100755
--- a/src/fibsem_tools/metadata/old_to_new_meta.py
+++ b/src/fibsem_tools/metadata/old_to_new_meta.py
@@ -5,7 +5,7 @@
 @click.command
 @click.argument("source", type=click.STRING)
 def main(source: str) -> None:
-    read_xarray(source)
+    click.echo(read_xarray(source))
 
 
 if __name__ == "__main__":

From 2a1126311105bf66a8e3df6ffac9aca713341810 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 23 Aug 2023 16:33:07 -0400
Subject: [PATCH 3/9] feat: refactor conversion script to use declarative style

---
 src/fibsem_tools/metadata/groundtruth.py     |  82 +++++++++-----
 src/fibsem_tools/metadata/old_to_new_meta.py | 111 ++++++++++++++++++-
 2 files changed, 160 insertions(+), 33 deletions(-)

diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index ac21ac5..094b8c7 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -1,7 +1,8 @@
 from __future__ import annotations
+from datetime import date
 from enum import Enum
-from typing import Any, Dict, Generic, List, Literal, Optional, TypeVar, Union
-
+from typing import Dict, Generic, List, Literal, Optional, TypeVar, Union
+from pydantic_zarr import GroupSpec, ArraySpec
 from pydantic import BaseModel, root_validator
 from pydantic.generics import GenericModel
 
@@ -11,7 +12,18 @@ class Config:
         extra = "forbid"
 
 
-class InstanceName(BaseModel):
+T = TypeVar("T")
+
+
+class CellmapWrapper(StrictBase, GenericModel, Generic[T]):
+    cellmap: T
+
+
+class AnnotationWrapper(StrictBase, GenericModel, Generic[T]):
+    annotation: T
+
+
+class InstanceName(StrictBase):
     long: str
     short: str
 
@@ -22,21 +34,21 @@ class Annotated(str, Enum):
     empty: str = "empty"
 
 
-class AnnotationState(BaseModel):
+class AnnotationState(StrictBase):
     present: bool
     annotated: Annotated
 
 
-class Label(BaseModel):
+class Label(StrictBase):
     value: int
     name: InstanceName
     annotationState: AnnotationState
     count: Optional[int]
 
 
-class LabelList(BaseModel):
+class LabelList(StrictBase):
     labels: List[Label]
-    annotation_type: Literal["semantic", "instance"] = "semantic"
+    annotation_type: AnnotationType = "semantic"
 
 
 classNameDict = {
@@ -97,12 +109,12 @@ class LabelList(BaseModel):
 Possibility = Literal["unknown", "absent"]
 
 
-class SemanticSegmentation(BaseModel):
+class SemanticSegmentation(StrictBase):
     type: Literal["semantic_segmentation"] = "semantic_segmentation"
     encoding: Dict[Union[Possibility, Literal["present"]], int]
 
 
-class InstanceSegmentation(BaseModel):
+class InstanceSegmentation(StrictBase):
     type: Literal["instance_segmentation"] = "instance_segmentation"
     encoding: Dict[Possibility, int]
 
@@ -125,7 +137,7 @@ class AnnotationArrayAttrs(GenericModel, Generic[TName]):
     annotation_type: AnnotationType
 
     @root_validator()
-    def check_encoding(cls, values: Any) -> Any:
+    def check_encoding(cls, values):
         if (typ := values.get("type", False)) and (
             hist := values.get("histogram", False)
         ):
@@ -135,7 +147,7 @@ def check_encoding(cls, values: Any) -> Any:
         return values
 
 
-class MultiscaleGroupAttrs(GenericModel, Generic[TName]):
+class AnnotationGroupAttrs(GenericModel, Generic[TName]):
     """
     The metadata for an individual annotated semantic class.
     In a storage hierarchy like zarr or hdf5, this metadata is associated with a
@@ -144,29 +156,45 @@ class MultiscaleGroupAttrs(GenericModel, Generic[TName]):
     """
 
     class_name: TName
-    description: str
-    created_by: list[str]
-    created_with: list[str]
-    start_date: str | None
-    end_date: str | None
-    duration_days: int | None
     annotation_type: AnnotationType
 
 
-class AnnotationProtocol(GenericModel, Generic[TName]):
-    url: str
-    class_names: list[TName]
-
-    class Config:
-        allow_extra = "forbid"
-
-
-class AnnotationCropAttrs(GenericModel, Generic[TName]):
+class CropGroupAttrs(GenericModel, Generic[TName]):
     """
     The metadata for all annotations in a single crop.
     """
 
     name: Optional[str]
     description: Optional[str]
-    protocol: AnnotationProtocol[TName]
+    created_by: list[str]
+    created_with: list[str]
+    start_date: Optional[date]
+    end_date: Optional[date]
+    duration_days: Optional[int]
+    protocol_url: str
+    class_names: list[TName]
+    index: dict[TName, str]
     doi: Optional[str]
+
+
+AnnotationArray = ArraySpec[AnnotationArrayAttrs]
+AnnotationGroup = GroupSpec[
+    CellmapWrapper[AnnotationWrapper[AnnotationGroupAttrs]], AnnotationArray
+]
+CropGroup = GroupSpec[
+    CellmapWrapper[AnnotationWrapper[CropGroupAttrs]], AnnotationGroup
+]
+
+
+def annotation_attrs_wrapper(
+    value: T,
+) -> dict[Literal["cellmap"], dict[Literal["annotation"], T]]:
+    return {"cellmap": {"annotation": value}}
+
+
+def annotation_array_metadata():
+    pass
+
+
+def annotation_group_metadata():
+    pass
diff --git a/src/fibsem_tools/metadata/old_to_new_meta.py b/src/fibsem_tools/metadata/old_to_new_meta.py
index 6af95b5..6631229 100755
--- a/src/fibsem_tools/metadata/old_to_new_meta.py
+++ b/src/fibsem_tools/metadata/old_to_new_meta.py
@@ -1,12 +1,111 @@
+import os
+from typing import Optional
 import click
 from fibsem_tools import read_xarray
+import numpy as np
+import fibsem_tools.metadata.groundtruth as gt
+from pydantic_zarr import GroupSpec, ArraySpec
+from pathlib import Path
+import zarr
+from fibsem_tools.io.util import split_by_suffix
+from numcodecs import Blosc
+from xarray_ome_ngff import get_adapters
 
+ome_adapters = get_adapters("0.4")
+out_chunks = (256,) * 3
 
-@click.command
-@click.argument("source", type=click.STRING)
-def main(source: str) -> None:
-    read_xarray(source)
+annotation_type = gt.SemanticSegmentation(encoding={"absent": 0, "present": 1})
+
+
+def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zarr.Group:
+    tree = read_xarray(source)
+    # todo: don't assume the biggest array is named s0!
+    array_name = "s0"
+    source_xr = tree[array_name].data
+
+    ome_meta = ome_adapters.multiscale_metadata([source_xr], [array_name])
+    if name is None:
+        crop_name = Path(source).stem
+    else:
+        crop_name = name
+
+    uniques = np.unique(source_xr)
+    all_class_names = tuple(g.short for g in gt.classNameDict.values())
+    observed_class_names = [gt.classNameDict.get(u).short for u in uniques]
+    annotation_group_names = tuple(
+        c.lower().replace(" ", "_") for c in observed_class_names
+    )
+    annotation_group_specs: dict[str, GroupSpec] = {}
+
+    for idx, un in enumerate(uniques):
+        class_name = gt.classNameDict.get(un).short
+        data_unique = np.array((source_xr == un).astype("uint8"))
+        num_present = int(data_unique.sum())
+        num_absent = data_unique.size - num_present
+        hist = {"absent": num_absent}
+
+        annotation_group_attrs = gt.AnnotationGroupAttrs(
+            class_name=class_name, description="", annotation_type=annotation_type
+        )
+
+        annotation_array_attrs = gt.AnnotationArrayAttrs(
+            class_name=class_name, histogram=hist, annotation_type=annotation_type
+        )
+        label_array_spec = ArraySpec.from_array(
+            data_unique,
+            chunks=out_chunks,
+            compressor=Blosc(cname="zstd"),
+            attrs=gt.annotation_attrs_wrapper(annotation_array_attrs.dict()),
+        )
 
+        annotation_group_specs[annotation_group_names[idx]] = GroupSpec(
+            attrs={
+                **gt.annotation_attrs_wrapper(annotation_group_attrs.dict()),
+                "multiscales": [ome_meta.dict()],
+            },
+            members={array_name: label_array_spec},
+        )
 
-if __name__ == "__main__":
-    main()
+    crop_attrs = gt.CropGroupAttrs(
+        name=crop_name,
+        description=None,
+        created_by=[],
+        created_with=[],
+        start_date=None,
+        end_date=None,
+        duration_days=None,
+        class_names=all_class_names,
+        index=dict(zip(observed_class_names, annotation_group_specs)),
+    )
+
+    pre, post, _ = split_by_suffix(dest, (".zarr",))
+
+    crop_group_spec = GroupSpec(
+        attrs=gt.annotation_attrs_wrapper(crop_attrs.dict()),
+        members=annotation_group_specs,
+    )
+
+    crop_group = crop_group_spec.to_zarr(
+        zarr.NestedDirectoryStore(pre), path=post, overwrite=False
+    )
+
+    # save data inside arrays
+    for idx, un in enumerate(uniques):
+        data_unique = np.array((source_xr == un).astype("uint8"))
+        arr = zarr.Array(
+            store=crop_group.store,
+            path=os.path.join(observed_class_names[idx], array_name),
+            mode="a",
+            write_empty_chunks=False,
+        )
+        arr[:] = data_unique
+
+    return crop_group
+
+
+@click.command
+@click.argument("source", type=click.STRING)
+@click.argument("dest", type=click.STRING)
+@click.option("--name", type=click.STRING)
+def cli(source, dest, name):
+    split_annotations(source, dest, name)

From fa4639ef4f2fa477ae4600775a52278c98ddd3f6 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 23 Aug 2023 18:58:47 -0400
Subject: [PATCH 4/9] fix: change array access mode to w- for array access in
 cli

---
 poetry.lock                                  | 282 ++++++++++---------
 src/fibsem_tools/metadata/old_to_new_meta.py |   2 +-
 2 files changed, 147 insertions(+), 137 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index cb54833..8299b9e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,25 +1,25 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
-version = "2.5.0"
+version = "2.5.4"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "aiobotocore-2.5.0-py3-none-any.whl", hash = "sha256:9a2a022d7b78ec9a2af0de589916d2721cddbf96264401b78d7a73c1a1435f3b"},
-    {file = "aiobotocore-2.5.0.tar.gz", hash = "sha256:6a5b397cddd4f81026aa91a14c7dd2650727425740a5af8ba75127ff663faf67"},
+    {file = "aiobotocore-2.5.4-py3-none-any.whl", hash = "sha256:4b32218728ca3d0be83835b604603a0cd6c329066e884bb78149334267f92440"},
+    {file = "aiobotocore-2.5.4.tar.gz", hash = "sha256:60341f19eda77e41e1ab11eef171b5a98b5dbdb90804f5334b6f90e560e31fae"},
 ]
 
 [package.dependencies]
-aiohttp = ">=3.3.1"
-aioitertools = ">=0.5.1"
-botocore = ">=1.29.76,<1.29.77"
-wrapt = ">=1.10.10"
+aiohttp = ">=3.3.1,<4.0.0"
+aioitertools = ">=0.5.1,<1.0.0"
+botocore = ">=1.31.17,<1.31.18"
+wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.27.76,<1.27.77)"]
-boto3 = ["boto3 (>=1.26.76,<1.26.77)"]
+awscli = ["awscli (>=1.29.17,<1.29.18)"]
+boto3 = ["boto3 (>=1.28.17,<1.28.18)"]
 
 [[package]]
 name = "aiohttp"
@@ -219,13 +219,13 @@ files = [
 
 [[package]]
 name = "botocore"
-version = "1.29.76"
+version = "1.31.17"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.29.76-py3-none-any.whl", hash = "sha256:70735b00cd529f152992231ca6757e458e5ec25db43767b3526e9a35b2f143b7"},
-    {file = "botocore-1.29.76.tar.gz", hash = "sha256:c2f67b6b3f8acf2968eafca06526f07b9fb0d27bac4c68a635d51abb675134a7"},
+    {file = "botocore-1.31.17-py3-none-any.whl", hash = "sha256:6ac34a1d34aa3750e78b77b8596617e2bab938964694d651939dba2cbde2c12b"},
+    {file = "botocore-1.31.17.tar.gz", hash = "sha256:396459065dba4339eb4da4ec8b4e6599728eb89b7caaceea199e26f7d824a41c"},
 ]
 
 [package.dependencies]
@@ -240,7 +240,6 @@ crt = ["awscrt (==0.16.26)"]
 name = "certifi"
 version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -345,13 +344,13 @@ files = [
 
 [[package]]
 name = "click"
-version = "8.1.3"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
-    {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
 ]
 
 [package.dependencies]
@@ -381,62 +380,63 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.2.3"
+version = "7.3.0"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "coverage-7.2.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:344e714bd0fe921fc72d97404ebbdbf9127bac0ca1ff66d7b79efc143cf7c0c4"},
-    {file = "coverage-7.2.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:974bc90d6f6c1e59ceb1516ab00cf1cdfbb2e555795d49fa9571d611f449bcb2"},
-    {file = "coverage-7.2.3-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:0743b0035d4b0e32bc1df5de70fba3059662ace5b9a2a86a9f894cfe66569013"},
-    {file = "coverage-7.2.3-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5d0391fb4cfc171ce40437f67eb050a340fdbd0f9f49d6353a387f1b7f9dd4fa"},
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 [package.dependencies]
@@ -447,13 +447,13 @@ toml = ["tomli"]
 
 [[package]]
 name = "dask"
-version = "2023.4.0"
+version = "2023.8.1"
 description = "Parallel PyData with Task Scheduling"
 optional = false
 python-versions = ">=3.9"
 files = [
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 [package.dependencies]
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 diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2023.4.0)"]
-test = ["pandas[test]", "pre-commit", "pytest", "pytest-rerunfailures", "pytest-xdist"]
+distributed = ["distributed (==2023.8.1)"]
+test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist"]
 
 [[package]]
 name = "distlib"
@@ -487,19 +487,19 @@ files = [
 
 [[package]]
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 jinja2 = ">=2.10.3"
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 msgpack = ">=1.0.0"
@@ -707,13 +707,13 @@ numpy = ">=1.17.3"
 
 [[package]]
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 python-versions = ">=3.8"
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-category = "main"
+version = "3.4.4"
+description = "Python implementation of John Gruber's Markdown."
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 python-versions = ">=3.7"
 files = [
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 [[package]]
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 description = "Optional static typing for Python"
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 python-versions = ">=3.8"
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+    {file = "mypy-1.5.1-cp39-cp39-win_amd64.whl", hash = "sha256:c543214ffdd422623e9fedd0869166c2f16affe4ba37463975043ef7d2ea8770"},
+    {file = "mypy-1.5.1-py3-none-any.whl", hash = "sha256:f757063a83970d67c444f6e01d9550a7402322af3557ce7630d3c957386fa8f5"},
+    {file = "mypy-1.5.1.tar.gz", hash = "sha256:b031b9601f1060bf1281feab89697324726ba0c0bae9d7cd7ab4b690940f0b92"},
 ]
 
 [package.dependencies]
@@ -1409,6 +1409,17 @@ toolz = "*"
 [package.extras]
 complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
 
+[[package]]
+name = "pathspec"
+version = "0.11.2"
+description = "Utility library for gitignore style pattern matching of file paths."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pathspec-0.11.2-py3-none-any.whl", hash = "sha256:1d6ed233af05e679efb96b1851550ea95bbb64b7c490b0f5aa52996c11e92a20"},
+    {file = "pathspec-0.11.2.tar.gz", hash = "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3"},
+]
+
 [[package]]
 name = "pint"
 version = "0.20.1"
@@ -1433,7 +1444,6 @@ xarray = ["xarray"]
 name = "platformdirs"
 version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1763,13 +1773,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "rich"
-version = "13.3.4"
+version = "13.5.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "rich-13.3.4-py3-none-any.whl", hash = "sha256:22b74cae0278fd5086ff44144d3813be1cedc9115bdfabbfefd86400cb88b20a"},
-    {file = "rich-13.3.4.tar.gz", hash = "sha256:b5d573e13605423ec80bdd0cd5f8541f7844a0e71a13f74cf454ccb2f490708b"},
+    {file = "rich-13.5.2-py3-none-any.whl", hash = "sha256:146a90b3b6b47cac4a73c12866a499e9817426423f57c5a66949c086191a8808"},
+    {file = "rich-13.5.2.tar.gz", hash = "sha256:fb9d6c0a0f643c99eed3875b5377a184132ba9be4d61516a55273d3554d75a39"},
 ]
 
 [package.dependencies]
@@ -1839,18 +1849,18 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "67.7.2"
+version = "68.1.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-67.7.2-py3-none-any.whl", hash = "sha256:23aaf86b85ca52ceb801d32703f12d77517b2556af839621c641fca11287952b"},
-    {file = "setuptools-67.7.2.tar.gz", hash = "sha256:f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990"},
+    {file = "setuptools-68.1.2-py3-none-any.whl", hash = "sha256:3d8083eed2d13afc9426f227b24fd1659489ec107c0e86cec2ffdde5c92e790b"},
+    {file = "setuptools-68.1.2.tar.gz", hash = "sha256:3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5,<=7.1.2)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -1909,13 +1919,13 @@ dev = ["aiohttp (>=3.8.1)", "click (>=8.1.2)", "msgpack (>=1.0.3)"]
 
 [[package]]
 name = "tifffile"
-version = "2023.4.12"
+version = "2023.8.12"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "tifffile-2023.4.12-py3-none-any.whl", hash = "sha256:3161954746fe32c4f4244d0fb2eb0a272f3a3760b78882a42faa83ac5e6e0b74"},
-    {file = "tifffile-2023.4.12.tar.gz", hash = "sha256:2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd"},
+    {file = "tifffile-2023.8.12-py3-none-any.whl", hash = "sha256:d1ef06461a947a6800ba6121b330b54a57fb9cbf7e5bc0adab8307081297d66b"},
+    {file = "tifffile-2023.8.12.tar.gz", hash = "sha256:824956b6d974b9d346aae59932bea862a2ad18fcc2b1a820b6941b7f6ddb2bca"},
 ]
 
 [package.dependencies]
@@ -2031,13 +2041,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.22.0"
+version = "20.24.3"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.22.0-py3-none-any.whl", hash = "sha256:48fd3b907b5149c5aab7c23d9790bea4cac6bc6b150af8635febc4cfeab1275a"},
-    {file = "virtualenv-20.22.0.tar.gz", hash = "sha256:278753c47aaef1a0f14e6db8a4c5e1e040e90aea654d0fc1dc7e0d8a42616cc3"},
+    {file = "virtualenv-20.24.3-py3-none-any.whl", hash = "sha256:95a6e9398b4967fbcb5fef2acec5efaf9aa4972049d9ae41f95e0972a683fd02"},
+    {file = "virtualenv-20.24.3.tar.gz", hash = "sha256:e5c3b4ce817b0b328af041506a2a299418c98747c4b1e68cb7527e74ced23efc"},
 ]
 
 [package.dependencies]
@@ -2174,13 +2184,13 @@ files = [
 
 [[package]]
 name = "xarray"
-version = "2023.4.2"
+version = "2023.8.0"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "xarray-2023.4.2-py3-none-any.whl", hash = "sha256:1b6d577c1217ad6bf7458426af19ed7a489ab6c41220ca791f55f5df9648173a"},
-    {file = "xarray-2023.4.2.tar.gz", hash = "sha256:958ec588220352343b910cbc05e54e7ab54d4e8c1c3a7783d6bfe7549d0bd0d2"},
+    {file = "xarray-2023.8.0-py3-none-any.whl", hash = "sha256:eb42b56aea2c7d5db2a7d0c33fb005b78eb5c4421eb747f2ced138c70b5c204e"},
+    {file = "xarray-2023.8.0.tar.gz", hash = "sha256:825c6d64202a731a4e49321edd1e9dfabf4be06802f1b8c8a3c00a3ebfc8cedf"},
 ]
 
 [package.dependencies]
@@ -2333,13 +2343,13 @@ multidict = ">=4.0"
 
 [[package]]
 name = "zarr"
-version = "2.14.2"
+version = "2.16.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zarr-2.14.2-py3-none-any.whl", hash = "sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2"},
-    {file = "zarr-2.14.2.tar.gz", hash = "sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc"},
+    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
+    {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"},
 ]
 
 [package.dependencies]
@@ -2381,4 +2391,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "61d553d7954e8589dc0150f8dff3014ee396000c3785bb6521edaf9eae701092"
+content-hash = "ff5a2e973d9eb2ead8f1a31a014be9fe4e2ede679675d5a5abc04024d351ef95"
diff --git a/src/fibsem_tools/metadata/old_to_new_meta.py b/src/fibsem_tools/metadata/old_to_new_meta.py
index 6631229..120d944 100755
--- a/src/fibsem_tools/metadata/old_to_new_meta.py
+++ b/src/fibsem_tools/metadata/old_to_new_meta.py
@@ -95,7 +95,7 @@ def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zar
         arr = zarr.Array(
             store=crop_group.store,
             path=os.path.join(observed_class_names[idx], array_name),
-            mode="a",
+            mode="w-",
             write_empty_chunks=False,
         )
         arr[:] = data_unique

From b5e405d8b6f23ff8ae956ccbca3b59ec32fd175f Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Thu, 24 Aug 2023 14:40:18 -0400
Subject: [PATCH 5/9] feat: add features to get ground truth conversion script
 working

---
 poetry.lock                                  | 120 +++++++++++++++++--
 pyproject.toml                               |   4 +-
 src/fibsem_tools/cli/zarr-to-json.py         |  28 +++++
 src/fibsem_tools/io/util.py                  |   3 +-
 src/fibsem_tools/io/zarr.py                  |  16 +--
 src/fibsem_tools/metadata/groundtruth.py     |   2 +-
 src/fibsem_tools/metadata/old_to_new_meta.py |  31 +++--
 7 files changed, 175 insertions(+), 29 deletions(-)
 create mode 100644 src/fibsem_tools/cli/zarr-to-json.py

diff --git a/poetry.lock b/poetry.lock
index 8299b9e..1044244 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,9 +1,10 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
 version = "2.5.4"
 description = "Async client for aws services using botocore and aiohttp"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -25,6 +26,7 @@ boto3 = ["boto3 (>=1.28.17,<1.28.18)"]
 name = "aiohttp"
 version = "3.8.5"
 description = "Async http client/server framework (asyncio)"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -133,6 +135,7 @@ speedups = ["Brotli", "aiodns", "cchardet"]
 name = "aioitertools"
 version = "0.11.0"
 description = "itertools and builtins for AsyncIO and mixed iterables"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -147,6 +150,7 @@ typing_extensions = {version = ">=4.0", markers = "python_version < \"3.10\""}
 name = "aiosignal"
 version = "1.3.1"
 description = "aiosignal: a list of registered asynchronous callbacks"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -161,6 +165,7 @@ frozenlist = ">=1.1.0"
 name = "asciitree"
 version = "0.3.3"
 description = "Draws ASCII trees."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -171,6 +176,7 @@ files = [
 name = "async-timeout"
 version = "4.0.3"
 description = "Timeout context manager for asyncio programs"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -182,6 +188,7 @@ files = [
 name = "atomicwrites"
 version = "1.4.1"
 description = "Atomic file writes."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -192,6 +199,7 @@ files = [
 name = "attrs"
 version = "23.1.0"
 description = "Classes Without Boilerplate"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -210,6 +218,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 name = "backoff"
 version = "1.11.1"
 description = "Function decoration for backoff and retry"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -221,6 +230,7 @@ files = [
 name = "botocore"
 version = "1.31.17"
 description = "Low-level, data-driven core of boto 3."
+category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
@@ -240,6 +250,7 @@ crt = ["awscrt (==0.16.26)"]
 name = "certifi"
 version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -251,6 +262,7 @@ files = [
 name = "cfgv"
 version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -262,6 +274,7 @@ files = [
 name = "charset-normalizer"
 version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -346,6 +359,7 @@ files = [
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -360,6 +374,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "cloudpickle"
 version = "2.2.1"
 description = "Extended pickling support for Python objects"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -371,6 +386,7 @@ files = [
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -382,6 +398,7 @@ files = [
 name = "coverage"
 version = "7.3.0"
 description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -449,6 +466,7 @@ toml = ["tomli"]
 name = "dask"
 version = "2023.8.1"
 description = "Parallel PyData with Task Scheduling"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -478,6 +496,7 @@ test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailu
 name = "distlib"
 version = "0.3.7"
 description = "Distribution utilities"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -489,6 +508,7 @@ files = [
 name = "distributed"
 version = "2023.8.1"
 description = "Distributed scheduler for Dask"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -517,6 +537,7 @@ zict = ">=2.2.0"
 name = "entrypoints"
 version = "0.4"
 description = "Discover and load entry points from installed packages."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -528,6 +549,7 @@ files = [
 name = "fasteners"
 version = "0.18"
 description = "A python package that provides useful locks"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -539,6 +561,7 @@ files = [
 name = "filelock"
 version = "3.12.2"
 description = "A platform independent file lock."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -554,6 +577,7 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "p
 name = "frozenlist"
 version = "1.4.0"
 description = "A list-like structure which implements collections.abc.MutableSequence"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -624,6 +648,7 @@ files = [
 name = "fsspec"
 version = "2023.6.0"
 description = "File-system specification"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -659,6 +684,7 @@ tqdm = ["tqdm"]
 name = "ghp-import"
 version = "2.1.0"
 description = "Copy your docs directly to the gh-pages branch."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -676,6 +702,7 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 name = "h5py"
 version = "3.9.0"
 description = "Read and write HDF5 files from Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -709,6 +736,7 @@ numpy = ">=1.17.3"
 name = "identify"
 version = "2.5.27"
 description = "File identification library for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -723,6 +751,7 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -734,6 +763,7 @@ files = [
 name = "importlib-metadata"
 version = "4.13.0"
 description = "Read metadata from Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -753,6 +783,7 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -764,6 +795,7 @@ files = [
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -781,6 +813,7 @@ i18n = ["Babel (>=2.7)"]
 name = "jmespath"
 version = "1.0.1"
 description = "JSON Matching Expressions"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -792,6 +825,7 @@ files = [
 name = "linkify-it-py"
 version = "2.0.2"
 description = "Links recognition library with FULL unicode support."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -812,6 +846,7 @@ test = ["coverage", "pytest", "pytest-cov"]
 name = "locket"
 version = "1.0.0"
 description = "File-based locks for Python on Linux and Windows"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -823,6 +858,7 @@ files = [
 name = "markdown"
 version = "3.4.4"
 description = "Python implementation of John Gruber's Markdown."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -841,6 +877,7 @@ testing = ["coverage", "pyyaml"]
 name = "markdown-it-py"
 version = "2.2.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -867,6 +904,7 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "markupsafe"
 version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -926,6 +964,7 @@ files = [
 name = "mdit-py-plugins"
 version = "0.4.0"
 description = "Collection of plugins for markdown-it-py"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -945,6 +984,7 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -956,6 +996,7 @@ files = [
 name = "mergedeep"
 version = "1.3.4"
 description = "A deep merge function for 🐍."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -967,6 +1008,7 @@ files = [
 name = "mkdocs"
 version = "1.5.2"
 description = "Project documentation with Markdown."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -998,6 +1040,7 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 name = "mkdocs-exclude"
 version = "1.0.2"
 description = "A mkdocs plugin that lets you exclude files or trees."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1011,6 +1054,7 @@ mkdocs = "*"
 name = "mrcfile"
 version = "1.4.3"
 description = "MRC file I/O library"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1025,6 +1069,7 @@ numpy = ">=1.16.0"
 name = "msgpack"
 version = "1.0.5"
 description = "MessagePack serializer"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1097,6 +1142,7 @@ files = [
 name = "multidict"
 version = "6.0.4"
 description = "multidict implementation"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1180,6 +1226,7 @@ files = [
 name = "mypy"
 version = "1.5.1"
 description = "Optional static typing for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1226,6 +1273,7 @@ reports = ["lxml"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1237,6 +1285,7 @@ files = [
 name = "nodeenv"
 version = "1.8.0"
 description = "Node.js virtual environment builder"
+category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
 files = [
@@ -1251,6 +1300,7 @@ setuptools = "*"
 name = "numcodecs"
 version = "0.11.0"
 description = "A Python package providing buffer compression and transformation codecs for use"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1283,6 +1333,7 @@ zfpy = ["zfpy (>=1.0.0)"]
 name = "numpy"
 version = "1.25.2"
 description = "Fundamental package for array computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1317,6 +1368,7 @@ files = [
 name = "packaging"
 version = "23.1"
 description = "Core utilities for Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1328,6 +1380,7 @@ files = [
 name = "pandas"
 version = "2.0.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1395,6 +1448,7 @@ xml = ["lxml (>=4.6.3)"]
 name = "partd"
 version = "1.4.0"
 description = "Appendable key-value storage"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1413,6 +1467,7 @@ complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
 name = "pathspec"
 version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1424,6 +1479,7 @@ files = [
 name = "pint"
 version = "0.20.1"
 description = "Physical quantities module"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1444,6 +1500,7 @@ xarray = ["xarray"]
 name = "platformdirs"
 version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1459,6 +1516,7 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 name = "pluggy"
 version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1474,6 +1532,7 @@ testing = ["pytest", "pytest-benchmark"]
 name = "pre-commit"
 version = "2.21.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1492,6 +1551,7 @@ virtualenv = ">=20.10.0"
 name = "psutil"
 version = "5.9.5"
 description = "Cross-platform lib for process and system monitoring in Python."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1518,6 +1578,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "py"
 version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1529,6 +1590,7 @@ files = [
 name = "pydantic"
 version = "1.10.12"
 description = "Data validation and settings management using python type hints"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1579,13 +1641,14 @@ email = ["email-validator (>=1.0.3)"]
 
 [[package]]
 name = "pydantic-ome-ngff"
-version = "0.2.3"
+version = "0.3.0"
 description = "Pydantic models for the OME-NGFF"
+category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "pydantic_ome_ngff-0.2.3-py3-none-any.whl", hash = "sha256:458ea3e9b83ba444c7db5b0145b61a3e021d69854e306a37ee29412666f823b2"},
-    {file = "pydantic_ome_ngff-0.2.3.tar.gz", hash = "sha256:7726d7febc447ba6ea8fcc0a645c261b21c7d924529f80c353eab4c133f14c26"},
+    {file = "pydantic_ome_ngff-0.3.0-py3-none-any.whl", hash = "sha256:f474a391a82795a3e143727f9e7d68d348c59645388dc5bc6ed2fae23362ad55"},
+    {file = "pydantic_ome_ngff-0.3.0.tar.gz", hash = "sha256:6ad92fd28c0e17fe933895a9d541e7640a951553bd2b756e76b4801d44aacafe"},
 ]
 
 [package.dependencies]
@@ -1595,6 +1658,7 @@ pydantic = ">=1.10.4,<2.0.0"
 name = "pydantic-zarr"
 version = "0.5.0"
 description = "pydantic models for zarr"
+category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
@@ -1610,6 +1674,7 @@ zarr = ">=2.14.2,<3.0.0"
 name = "pygments"
 version = "2.16.1"
 description = "Pygments is a syntax highlighting package written in Python."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1624,6 +1689,7 @@ plugins = ["importlib-metadata"]
 name = "pytest"
 version = "6.2.5"
 description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1648,6 +1714,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 name = "pytest-cov"
 version = "3.0.0"
 description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1666,6 +1733,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1680,6 +1748,7 @@ six = ">=1.5"
 name = "pytz"
 version = "2023.3"
 description = "World timezone definitions, modern and historical"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1691,6 +1760,7 @@ files = [
 name = "pyyaml"
 version = "6.0.1"
 description = "YAML parser and emitter for Python"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1740,6 +1810,7 @@ files = [
 name = "pyyaml-env-tag"
 version = "0.1"
 description = "A custom YAML tag for referencing environment variables in YAML files. "
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1754,6 +1825,7 @@ pyyaml = "*"
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1775,6 +1847,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "rich"
 version = "13.5.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1793,6 +1866,7 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 name = "s3fs"
 version = "2023.6.0"
 description = "Convenient Filesystem interface over S3"
+category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -1813,6 +1887,7 @@ boto3 = ["aiobotocore[boto3] (>=2.5.0,<2.6.0)"]
 name = "scipy"
 version = "1.9.3"
 description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1851,6 +1926,7 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 name = "setuptools"
 version = "68.1.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1867,6 +1943,7 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1878,6 +1955,7 @@ files = [
 name = "sortedcontainers"
 version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1889,6 +1967,7 @@ files = [
 name = "tblib"
 version = "2.0.0"
 description = "Traceback serialization library."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1900,6 +1979,7 @@ files = [
 name = "textual"
 version = "0.16.0"
 description = "Modern Text User Interface framework"
+category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -1921,6 +2001,7 @@ dev = ["aiohttp (>=3.8.1)", "click (>=8.1.2)", "msgpack (>=1.0.3)"]
 name = "tifffile"
 version = "2023.8.12"
 description = "Read and write TIFF files"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1938,6 +2019,7 @@ all = ["defusedxml", "fsspec", "imagecodecs (>=2023.8.12)", "lxml", "matplotlib"
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1949,6 +2031,7 @@ files = [
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1960,6 +2043,7 @@ files = [
 name = "toolz"
 version = "0.12.0"
 description = "List processing tools and functional utilities"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1971,6 +2055,7 @@ files = [
 name = "tornado"
 version = "6.3.3"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -1991,6 +2076,7 @@ files = [
 name = "typing-extensions"
 version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2002,6 +2088,7 @@ files = [
 name = "tzdata"
 version = "2023.3"
 description = "Provider of IANA time zone data"
+category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -2013,6 +2100,7 @@ files = [
 name = "uc-micro-py"
 version = "1.0.2"
 description = "Micro subset of unicode data files for linkify-it-py projects."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2027,6 +2115,7 @@ test = ["coverage", "pytest", "pytest-cov"]
 name = "urllib3"
 version = "1.26.16"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -2043,6 +2132,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "virtualenv"
 version = "20.24.3"
 description = "Virtual Python Environment builder"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2063,6 +2153,7 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 name = "watchdog"
 version = "3.0.0"
 description = "Filesystem events monitoring"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2102,6 +2193,7 @@ watchmedo = ["PyYAML (>=3.10)"]
 name = "wrapt"
 version = "1.15.0"
 description = "Module for decorators, wrappers and monkey patching."
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 files = [
@@ -2186,6 +2278,7 @@ files = [
 name = "xarray"
 version = "2023.8.0"
 description = "N-D labeled arrays and datasets in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2210,6 +2303,7 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"]
 name = "xarray-datatree"
 version = "0.0.12"
 description = "Hierarchical tree-like data structures for xarray"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2224,6 +2318,7 @@ xarray = ">=2022.6.0"
 name = "xarray-multiscale"
 version = "2.1.0"
 description = ""
+category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
@@ -2239,25 +2334,27 @@ xarray = ">=2022.03.0"
 
 [[package]]
 name = "xarray-ome-ngff"
-version = "1.2.0"
+version = "1.2.1"
 description = "xarray and ome-ngff"
+category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "xarray_ome_ngff-1.2.0-py3-none-any.whl", hash = "sha256:4ac8bb126dfb40e5dcce86c1f8671db5a617e5fd97cdec5178f411ee62e3e861"},
-    {file = "xarray_ome_ngff-1.2.0.tar.gz", hash = "sha256:814661a48574c837f07fb15a96c0dc0a6c92b0b1c5e02732c77b04ade823b520"},
+    {file = "xarray_ome_ngff-1.2.1-py3-none-any.whl", hash = "sha256:938d853cedbc64383c20368a1c0dd2ebb576adff7a5b31cf2d69c62e485958ad"},
+    {file = "xarray_ome_ngff-1.2.1.tar.gz", hash = "sha256:5f1701cfc1f2cfb15906e1b3c4532c24707a4972b360a40c0efd7c9169eb17bd"},
 ]
 
 [package.dependencies]
 pint = ">=0.20.1,<0.21.0"
-pydantic = ">=1.10.4,<2.0.0"
-pydantic-ome-ngff = ">=0.2.0,<0.3.0"
+pydantic = ">=1.10.7,<2.0.0"
+pydantic-ome-ngff = ">=0.3.0,<0.4.0"
 xarray = ">=2023.2.0,<2024.0.0"
 
 [[package]]
 name = "yarl"
 version = "1.9.2"
 description = "Yet another URL library"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2345,6 +2442,7 @@ multidict = ">=4.0"
 name = "zarr"
 version = "2.16.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2366,6 +2464,7 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 name = "zict"
 version = "3.0.0"
 description = "Mutable mapping tools"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2377,6 +2476,7 @@ files = [
 name = "zipp"
 version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2391,4 +2491,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "ff5a2e973d9eb2ead8f1a31a014be9fe4e2ede679675d5a5abc04024d351ef95"
+content-hash = "a9859268b74e57c2a73d7ad777478d43cbe9757f47eeeba4dd3394988dee0edf"
diff --git a/pyproject.toml b/pyproject.toml
index bf5e3ce..50e9bd6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,11 +17,11 @@ xarray = ">=2022.03.0"
 pydantic = "^1.8.2"
 backoff = "^1.10.0"
 s3fs = ">=2022.2.0"
-xarray-ome-ngff = "^1.2.0"
+xarray-ome-ngff = "^1.2.1"
 pint = "^0.20.1"
 xarray-multiscale = "^2.0.0"
 tifffile = "^2023.2.28"
-pydantic-ome-ngff = "^0.2.0"
+pydantic-ome-ngff = "^0.3.0"
 click = "^8.1.3"
 dask = "^2023.3.2"
 textual = "^0.16.0"
diff --git a/src/fibsem_tools/cli/zarr-to-json.py b/src/fibsem_tools/cli/zarr-to-json.py
new file mode 100644
index 0000000..e05c9c2
--- /dev/null
+++ b/src/fibsem_tools/cli/zarr-to-json.py
@@ -0,0 +1,28 @@
+from typing import Union
+import click
+from pydantic_zarr import GroupSpec, ArraySpec
+import zarr
+from fibsem_tools import read
+from fibsem_tools.io.util import split_by_suffix
+from rich import print
+
+def parse_zarr_path(path: str) -> Union[ArraySpec, GroupSpec]:
+    pre, post, suffix = split_by_suffix(path, ('.n5', '.zarr'))
+    obj = read(path)
+    if isinstance(obj, zarr.Array):
+        result = ArraySpec.from_zarr(obj)
+    elif isinstance(obj, zarr.Group):
+        result = GroupSpec.from_zarr(obj)
+    else:
+        raise ValueError(f'Got an unparseable object: {type(obj)}')
+    return result
+
+
+@click.command()
+@click.argument('path', type=click.STRING)
+def cli(path: str):
+    result = parse_zarr_path(path)
+    print(result.json(indent=2))
+
+if __name__ == "__main__":
+    cli()
diff --git a/src/fibsem_tools/io/util.py b/src/fibsem_tools/io/util.py
index 3e1e88a..774ab44 100644
--- a/src/fibsem_tools/io/util.py
+++ b/src/fibsem_tools/io/util.py
@@ -127,7 +127,8 @@ def split_by_suffix(uri: PathLike, suffixes: Sequence[str]) -> Tuple[str, str, s
     suffixed = [Path(part).suffix in suffixes for part in parts]
 
     if not any(suffixed):
-        raise ValueError(f"No path elements found with the suffix(es) {suffixes}")
+        msg = f"No path elements found with the suffix(es) {suffixes} in {uri}"
+        raise ValueError(msg)
 
     index = [idx for idx, val in enumerate(suffixed) if val][-1]
     if index == (len(parts) - 1):
diff --git a/src/fibsem_tools/io/zarr.py b/src/fibsem_tools/io/zarr.py
index 5c5ba13..f913ce2 100644
--- a/src/fibsem_tools/io/zarr.py
+++ b/src/fibsem_tools/io/zarr.py
@@ -12,7 +12,7 @@
 import numpy as np
 import xarray
 import zarr
-from zarr.storage import FSStore, contains_array, contains_group
+from zarr.storage import FSStore, contains_array, contains_group, BaseStore
 from dask import bag, delayed
 from distributed import Client, Lock
 from toolz import concat
@@ -168,15 +168,17 @@ def get_url(node: Union[zarr.Group, zarr.Array]):
         cannot be resolved to a url"""
         )
 
+def get_store(path: PathLike) -> zarr.storage.BaseStore:
+    if isinstance(path, Path):
+        path = str(path)
+    
+    return DEFAULT_ZARR_STORE(path)
 
 def access_zarr(
-    store: PathLike, path: PathLike, **kwargs: Any
+    store: Union[PathLike, BaseStore], path: PathLike, **kwargs: Any
 ) -> zarr.Array | zarr.Group:
-    if isinstance(store, Path):
-        store = str(store)
-
-    if isinstance(store, str):
-        store = DEFAULT_ZARR_STORE(store)
+    if isinstance(store, (Path, str)):
+        store = get_store(store)
 
     # set default dimension separator to /
     if "shape" in kwargs and "dimension_separator" not in kwargs:
diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index 094b8c7..b708f97 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -171,7 +171,7 @@ class CropGroupAttrs(GenericModel, Generic[TName]):
     start_date: Optional[date]
     end_date: Optional[date]
     duration_days: Optional[int]
-    protocol_url: str
+    protocol_url: Optional[str]
     class_names: list[TName]
     index: dict[TName, str]
     doi: Optional[str]
diff --git a/src/fibsem_tools/metadata/old_to_new_meta.py b/src/fibsem_tools/metadata/old_to_new_meta.py
index 120d944..f024a63 100755
--- a/src/fibsem_tools/metadata/old_to_new_meta.py
+++ b/src/fibsem_tools/metadata/old_to_new_meta.py
@@ -1,16 +1,21 @@
 import os
 from typing import Optional
 import click
+from xarray import DataArray
 from fibsem_tools import read_xarray
+from fibsem_tools import access
 import numpy as np
+from fibsem_tools.io.zarr import get_store
 import fibsem_tools.metadata.groundtruth as gt
 from pydantic_zarr import GroupSpec, ArraySpec
 from pathlib import Path
 import zarr
+from zarr.storage import contains_array, contains_group
 from fibsem_tools.io.util import split_by_suffix
 from numcodecs import Blosc
 from xarray_ome_ngff import get_adapters
-
+import dask.array as da
+from zarr.errors import ContainsArrayError, ContainsGroupError
 ome_adapters = get_adapters("0.4")
 out_chunks = (256,) * 3
 
@@ -18,10 +23,19 @@
 
 
 def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zarr.Group:
+    pre, post, _ = split_by_suffix(dest, (".zarr",))
+    # fail fast if there's already a group there
+    store = get_store(pre)
+    if contains_group(store, post):
+        raise ContainsGroupError(f'{store.path}/{post}')
+    
+    if contains_array(store, post):
+        raise ContainsArrayError(f'{store.path}/{post}')
+
     tree = read_xarray(source)
     # todo: don't assume the biggest array is named s0!
     array_name = "s0"
-    source_xr = tree[array_name].data
+    source_xr: DataArray = tree[array_name].data
 
     ome_meta = ome_adapters.multiscale_metadata([source_xr], [array_name])
     if name is None:
@@ -29,7 +43,7 @@ def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zar
     else:
         crop_name = name
 
-    uniques = np.unique(source_xr)
+    uniques = da.unique(source_xr.data).compute()
     all_class_names = tuple(g.short for g in gt.classNameDict.values())
     observed_class_names = [gt.classNameDict.get(u).short for u in uniques]
     annotation_group_names = tuple(
@@ -39,7 +53,7 @@ def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zar
 
     for idx, un in enumerate(uniques):
         class_name = gt.classNameDict.get(un).short
-        data_unique = np.array((source_xr == un).astype("uint8"))
+        data_unique = (source_xr == un).astype("uint8").compute()
         num_present = int(data_unique.sum())
         num_absent = data_unique.size - num_present
         hist = {"absent": num_absent}
@@ -78,8 +92,6 @@ def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zar
         index=dict(zip(observed_class_names, annotation_group_specs)),
     )
 
-    pre, post, _ = split_by_suffix(dest, (".zarr",))
-
     crop_group_spec = GroupSpec(
         attrs=gt.annotation_attrs_wrapper(crop_attrs.dict()),
         members=annotation_group_specs,
@@ -90,12 +102,12 @@ def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zar
     )
 
     # save data inside arrays
+
     for idx, un in enumerate(uniques):
         data_unique = np.array((source_xr == un).astype("uint8"))
         arr = zarr.Array(
             store=crop_group.store,
-            path=os.path.join(observed_class_names[idx], array_name),
-            mode="w-",
+            path=os.path.join(crop_group.path, annotation_group_names[idx], array_name),
             write_empty_chunks=False,
         )
         arr[:] = data_unique
@@ -109,3 +121,6 @@ def split_annotations(source: str, dest: str, name: Optional[str] = None) -> zar
 @click.option("--name", type=click.STRING)
 def cli(source, dest, name):
     split_annotations(source, dest, name)
+
+if __name__ == '__main__':
+    cli()
\ No newline at end of file

From bb07ffc90fb3c807b5d81aefda25d6616e3329ff Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Thu, 24 Aug 2023 17:15:12 -0400
Subject: [PATCH 6/9] feat: global cli access

---
 pyproject.toml                                         | 2 ++
 src/fibsem_tools/cli/__init__.py                       | 0
 src/fibsem_tools/cli/{zarr-to-json.py => zarr2json.py} | 8 +++++---
 3 files changed, 7 insertions(+), 3 deletions(-)
 create mode 100644 src/fibsem_tools/cli/__init__.py
 rename src/fibsem_tools/cli/{zarr-to-json.py => zarr2json.py} (77%)

diff --git a/pyproject.toml b/pyproject.toml
index 50e9bd6..8819f90 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,6 +39,8 @@ requests = "^2.28.2"
 
 [tool.poetry.scripts]
 tiff2zarr = 'fibsem_tools.cli.tiff2zarr:run'
+zarr-scan = 'fibsem_tools.cli.zarr_scan:cli'
+zarr2json = 'fibsem_tools.cli.zarr2json:cli'
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
diff --git a/src/fibsem_tools/cli/__init__.py b/src/fibsem_tools/cli/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/fibsem_tools/cli/zarr-to-json.py b/src/fibsem_tools/cli/zarr2json.py
similarity index 77%
rename from src/fibsem_tools/cli/zarr-to-json.py
rename to src/fibsem_tools/cli/zarr2json.py
index e05c9c2..333b190 100644
--- a/src/fibsem_tools/cli/zarr-to-json.py
+++ b/src/fibsem_tools/cli/zarr2json.py
@@ -6,23 +6,25 @@
 from fibsem_tools.io.util import split_by_suffix
 from rich import print
 
+
 def parse_zarr_path(path: str) -> Union[ArraySpec, GroupSpec]:
-    pre, post, suffix = split_by_suffix(path, ('.n5', '.zarr'))
+    pre, post, suffix = split_by_suffix(path, (".n5", ".zarr"))
     obj = read(path)
     if isinstance(obj, zarr.Array):
         result = ArraySpec.from_zarr(obj)
     elif isinstance(obj, zarr.Group):
         result = GroupSpec.from_zarr(obj)
     else:
-        raise ValueError(f'Got an unparseable object: {type(obj)}')
+        raise ValueError(f"Got an unparseable object: {type(obj)}")
     return result
 
 
 @click.command()
-@click.argument('path', type=click.STRING)
+@click.argument("path", type=click.STRING)
 def cli(path: str):
     result = parse_zarr_path(path)
     print(result.json(indent=2))
 
+
 if __name__ == "__main__":
     cli()

From 29e06a0883bf7c32e4bdaa91a11569082281fde6 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Sat, 26 Aug 2023 23:47:40 -0400
Subject: [PATCH 7/9] docs: start having docs

---
 docs/api/cli/tiff2zarr.md                |   1 +
 docs/api/cli/zarr2json.md                |   1 +
 docs/api/cli/zarr_scan.md                |   1 +
 docs/api/io/core.md                      |   1 +
 docs/api/io/dask.md                      |   1 +
 docs/api/io/dat.md                       |   1 +
 docs/api/io/h5.md                        |   1 +
 docs/api/io/mrc.md                       |   1 +
 docs/api/io/multiscale.md                |   1 +
 docs/api/io/neuroglancer.md              |   1 +
 docs/api/io/server.md                    |   1 +
 docs/api/io/tif.md                       |   1 +
 docs/api/io/util.md                      |   1 +
 docs/api/io/xr.md                        |   1 +
 docs/api/io/zarr.md                      |   1 +
 docs/api/metadata/groundtruth.md         |   1 +
 docs/index.md                            |   3 +
 mkdocs.yml                               |  70 +++
 poetry.lock                              | 697 ++++++++++++++++++-----
 pyproject.toml                           |   9 +-
 src/fibsem_tools/cli/tiff2zarr.py        |   5 +-
 src/fibsem_tools/cli/zarr2json.py        |  10 +-
 src/fibsem_tools/cli/zarr_scan.py        |  65 ++-
 src/fibsem_tools/metadata/groundtruth.py |  89 ++-
 24 files changed, 811 insertions(+), 153 deletions(-)
 create mode 100644 docs/api/cli/tiff2zarr.md
 create mode 100644 docs/api/cli/zarr2json.md
 create mode 100644 docs/api/cli/zarr_scan.md
 create mode 100644 docs/api/io/core.md
 create mode 100644 docs/api/io/dask.md
 create mode 100644 docs/api/io/dat.md
 create mode 100644 docs/api/io/h5.md
 create mode 100644 docs/api/io/mrc.md
 create mode 100644 docs/api/io/multiscale.md
 create mode 100644 docs/api/io/neuroglancer.md
 create mode 100644 docs/api/io/server.md
 create mode 100644 docs/api/io/tif.md
 create mode 100644 docs/api/io/util.md
 create mode 100644 docs/api/io/xr.md
 create mode 100644 docs/api/io/zarr.md
 create mode 100644 docs/api/metadata/groundtruth.md
 create mode 100644 docs/index.md
 create mode 100644 mkdocs.yml

diff --git a/docs/api/cli/tiff2zarr.md b/docs/api/cli/tiff2zarr.md
new file mode 100644
index 0000000..a44fc61
--- /dev/null
+++ b/docs/api/cli/tiff2zarr.md
@@ -0,0 +1 @@
+::: fibsem_tools.cli.tiff2zarr
\ No newline at end of file
diff --git a/docs/api/cli/zarr2json.md b/docs/api/cli/zarr2json.md
new file mode 100644
index 0000000..2bf6808
--- /dev/null
+++ b/docs/api/cli/zarr2json.md
@@ -0,0 +1 @@
+::: fibsem_tools.cli.zarr2json
\ No newline at end of file
diff --git a/docs/api/cli/zarr_scan.md b/docs/api/cli/zarr_scan.md
new file mode 100644
index 0000000..08a0eef
--- /dev/null
+++ b/docs/api/cli/zarr_scan.md
@@ -0,0 +1 @@
+::: fibsem_tools.cli.zarr_scan
\ No newline at end of file
diff --git a/docs/api/io/core.md b/docs/api/io/core.md
new file mode 100644
index 0000000..a4c565f
--- /dev/null
+++ b/docs/api/io/core.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.core
\ No newline at end of file
diff --git a/docs/api/io/dask.md b/docs/api/io/dask.md
new file mode 100644
index 0000000..929ce5b
--- /dev/null
+++ b/docs/api/io/dask.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.dask
\ No newline at end of file
diff --git a/docs/api/io/dat.md b/docs/api/io/dat.md
new file mode 100644
index 0000000..d5b7b2b
--- /dev/null
+++ b/docs/api/io/dat.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.dat
\ No newline at end of file
diff --git a/docs/api/io/h5.md b/docs/api/io/h5.md
new file mode 100644
index 0000000..f0aa228
--- /dev/null
+++ b/docs/api/io/h5.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.h5
\ No newline at end of file
diff --git a/docs/api/io/mrc.md b/docs/api/io/mrc.md
new file mode 100644
index 0000000..b5010fc
--- /dev/null
+++ b/docs/api/io/mrc.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.mrc
\ No newline at end of file
diff --git a/docs/api/io/multiscale.md b/docs/api/io/multiscale.md
new file mode 100644
index 0000000..80aec97
--- /dev/null
+++ b/docs/api/io/multiscale.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.multiscale
\ No newline at end of file
diff --git a/docs/api/io/neuroglancer.md b/docs/api/io/neuroglancer.md
new file mode 100644
index 0000000..2506359
--- /dev/null
+++ b/docs/api/io/neuroglancer.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.neuroglancer
\ No newline at end of file
diff --git a/docs/api/io/server.md b/docs/api/io/server.md
new file mode 100644
index 0000000..d50cbb8
--- /dev/null
+++ b/docs/api/io/server.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.server
\ No newline at end of file
diff --git a/docs/api/io/tif.md b/docs/api/io/tif.md
new file mode 100644
index 0000000..cc36ff5
--- /dev/null
+++ b/docs/api/io/tif.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.tif
\ No newline at end of file
diff --git a/docs/api/io/util.md b/docs/api/io/util.md
new file mode 100644
index 0000000..8cd0d52
--- /dev/null
+++ b/docs/api/io/util.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.util
\ No newline at end of file
diff --git a/docs/api/io/xr.md b/docs/api/io/xr.md
new file mode 100644
index 0000000..14010e0
--- /dev/null
+++ b/docs/api/io/xr.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.xr
\ No newline at end of file
diff --git a/docs/api/io/zarr.md b/docs/api/io/zarr.md
new file mode 100644
index 0000000..2f8f512
--- /dev/null
+++ b/docs/api/io/zarr.md
@@ -0,0 +1 @@
+::: fibsem_tools.io.zarr
\ No newline at end of file
diff --git a/docs/api/metadata/groundtruth.md b/docs/api/metadata/groundtruth.md
new file mode 100644
index 0000000..2e2fd6f
--- /dev/null
+++ b/docs/api/metadata/groundtruth.md
@@ -0,0 +1 @@
+::: fibsem_tools.metadata.groundtruth
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..74e2a7b
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,3 @@
+# FIB-SEM tools
+
+This is a python library used by the [cellmap](https://www.janelia.org/project-team/cellmap) project team to store and manipulate large FIB-SEM images.  
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..a4fecc5
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,70 @@
+site_name: "fibsem-tools"
+site_url: https://janelia-cellmap.github.io/fibsem-tools/
+site_author: Davis Bennett
+site_description: >-
+  Documentation for fibsem-tools
+
+# Repository
+repo_name: janelia-cellmap/pydantic-zarr
+repo_url: https://github.com/janelia-cellmap/pydantic-zarr
+
+# Copyright
+copyright: Copyright &copy; 2016 - 2023 HHMI / Janelia
+
+theme:
+  name: material
+  palette: 
+  # Palette toggle for light mode
+  - scheme: default
+    toggle:
+      icon: material/brightness-7 
+      name: Switch to dark mode
+
+  # Palette toggle for dark mode
+  - scheme: slate
+    toggle:
+      icon: material/brightness-4
+      name: Switch to light mode
+
+nav:
+    - About: index.md
+    - Usage: usage.md
+    - API:
+      - io:
+        - core: api/io/core.md
+        - dask: api/io/dask.md
+        - dat: api/io/dat.md
+        - hdf5: api/io/h5.md
+        - mrc: api/io/mrc.md
+        - multiscale: api/io/multiscale.md
+        - neuroglancer: api/io/neuroglancer.md
+        - tif: api/io/tif.md
+        - util: api/io/util.md
+        - xarray: api/io/xr.md
+        - zarr: api/io/zarr.md
+      - metadata:
+        - groundtruth: api/metadata/groundtruth.md
+      - cli:
+        - tiff2zarr: api/cli/tiff2zarr.md
+        - zarr_scan: api/cli/zarr_scan.md
+        - zarr2json: api/cli/zarr2json.md
+
+plugins:
+- mkdocstrings:
+    handlers:
+        python:
+          options:
+            show_signature_annotations: true
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - toc:
+      baselevel: 2
+      toc_depth: 4
+      permalink: "#"
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 1044244..dc9747e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
 version = "2.5.4"
 description = "Async client for aws services using botocore and aiohttp"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -26,7 +25,6 @@ boto3 = ["boto3 (>=1.28.17,<1.28.18)"]
 name = "aiohttp"
 version = "3.8.5"
 description = "Async http client/server framework (asyncio)"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -135,7 +133,6 @@ speedups = ["Brotli", "aiodns", "cchardet"]
 name = "aioitertools"
 version = "0.11.0"
 description = "itertools and builtins for AsyncIO and mixed iterables"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -150,7 +147,6 @@ typing_extensions = {version = ">=4.0", markers = "python_version < \"3.10\""}
 name = "aiosignal"
 version = "1.3.1"
 description = "aiosignal: a list of registered asynchronous callbacks"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -165,7 +161,6 @@ frozenlist = ">=1.1.0"
 name = "asciitree"
 version = "0.3.3"
 description = "Draws ASCII trees."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -176,7 +171,6 @@ files = [
 name = "async-timeout"
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 description = "Timeout context manager for asyncio programs"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -184,22 +178,10 @@ files = [
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 ]
 
-[[package]]
-name = "atomicwrites"
-version = "1.4.1"
-description = "Atomic file writes."
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
-]
-
 [[package]]
 name = "attrs"
 version = "23.1.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -214,11 +196,21 @@ docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-
 tests = ["attrs[tests-no-zope]", "zope-interface"]
 tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
+[[package]]
+name = "babel"
+version = "2.12.1"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+]
+
 [[package]]
 name = "backoff"
 version = "1.11.1"
 description = "Function decoration for backoff and retry"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -226,11 +218,74 @@ files = [
     {file = "backoff-1.11.1.tar.gz", hash = "sha256:ccb962a2378418c667b3c979b504fdeb7d9e0d29c0579e3b13b86467177728cb"},
 ]
 
+[[package]]
+name = "beautifulsoup4"
+version = "4.12.2"
+description = "Screen-scraping library"
+optional = false
+python-versions = ">=3.6.0"
+files = [
+    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
+    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+]
+
+[package.dependencies]
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
+[[package]]
+name = "black"
+version = "23.7.0"
+description = "The uncompromising code formatter."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "black-23.7.0-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:5c4bc552ab52f6c1c506ccae05681fab58c3f72d59ae6e6639e8885e94fe2587"},
+    {file = "black-23.7.0-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:552513d5cd5694590d7ef6f46e1767a4df9af168d449ff767b13b084c020e63f"},
+    {file = "black-23.7.0-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:86cee259349b4448adb4ef9b204bb4467aae74a386bce85d56ba4f5dc0da27be"},
+    {file = "black-23.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:501387a9edcb75d7ae8a4412bb8749900386eaef258f1aefab18adddea1936bc"},
+    {file = "black-23.7.0-cp310-cp310-win_amd64.whl", hash = "sha256:fb074d8b213749fa1d077d630db0d5f8cc3b2ae63587ad4116e8a436e9bbe995"},
+    {file = "black-23.7.0-cp311-cp311-macosx_10_16_arm64.whl", hash = "sha256:b5b0ee6d96b345a8b420100b7d71ebfdd19fab5e8301aff48ec270042cd40ac2"},
+    {file = "black-23.7.0-cp311-cp311-macosx_10_16_universal2.whl", hash = "sha256:893695a76b140881531062d48476ebe4a48f5d1e9388177e175d76234ca247cd"},
+    {file = "black-23.7.0-cp311-cp311-macosx_10_16_x86_64.whl", hash = "sha256:c333286dc3ddca6fdff74670b911cccedacb4ef0a60b34e491b8a67c833b343a"},
+    {file = "black-23.7.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:831d8f54c3a8c8cf55f64d0422ee875eecac26f5f649fb6c1df65316b67c8926"},
+    {file = "black-23.7.0-cp311-cp311-win_amd64.whl", hash = "sha256:7f3bf2dec7d541b4619b8ce526bda74a6b0bffc480a163fed32eb8b3c9aed8ad"},
+    {file = "black-23.7.0-cp38-cp38-macosx_10_16_arm64.whl", hash = "sha256:f9062af71c59c004cd519e2fb8f5d25d39e46d3af011b41ab43b9c74e27e236f"},
+    {file = "black-23.7.0-cp38-cp38-macosx_10_16_universal2.whl", hash = "sha256:01ede61aac8c154b55f35301fac3e730baf0c9cf8120f65a9cd61a81cfb4a0c3"},
+    {file = "black-23.7.0-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:327a8c2550ddc573b51e2c352adb88143464bb9d92c10416feb86b0f5aee5ff6"},
+    {file = "black-23.7.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6d1c6022b86f83b632d06f2b02774134def5d4d4f1dac8bef16d90cda18ba28a"},
+    {file = "black-23.7.0-cp38-cp38-win_amd64.whl", hash = "sha256:27eb7a0c71604d5de083757fbdb245b1a4fae60e9596514c6ec497eb63f95320"},
+    {file = "black-23.7.0-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:8417dbd2f57b5701492cd46edcecc4f9208dc75529bcf76c514864e48da867d9"},
+    {file = "black-23.7.0-cp39-cp39-macosx_10_16_universal2.whl", hash = "sha256:47e56d83aad53ca140da0af87678fb38e44fd6bc0af71eebab2d1f59b1acf1d3"},
+    {file = "black-23.7.0-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:25cc308838fe71f7065df53aedd20327969d05671bac95b38fdf37ebe70ac087"},
+    {file = "black-23.7.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:642496b675095d423f9b8448243336f8ec71c9d4d57ec17bf795b67f08132a91"},
+    {file = "black-23.7.0-cp39-cp39-win_amd64.whl", hash = "sha256:ad0014efc7acf0bd745792bd0d8857413652979200ab924fbf239062adc12491"},
+    {file = "black-23.7.0-py3-none-any.whl", hash = "sha256:9fd59d418c60c0348505f2ddf9609c1e1de8e7493eab96198fc89d9f865e7a96"},
+    {file = "black-23.7.0.tar.gz", hash = "sha256:022a582720b0d9480ed82576c920a8c1dde97cc38ff11d8d8859b3bd6ca9eedb"},
+]
+
+[package.dependencies]
+click = ">=8.0.0"
+mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
 [[package]]
 name = "botocore"
 version = "1.31.17"
 description = "Low-level, data-driven core of boto 3."
-category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
@@ -250,7 +305,6 @@ crt = ["awscrt (==0.16.26)"]
 name = "certifi"
 version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -262,7 +316,6 @@ files = [
 name = "cfgv"
 version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -274,7 +327,6 @@ files = [
 name = "charset-normalizer"
 version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -359,7 +411,6 @@ files = [
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -374,7 +425,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "cloudpickle"
 version = "2.2.1"
 description = "Extended pickling support for Python objects"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -386,7 +436,6 @@ files = [
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 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
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 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -398,7 +447,6 @@ files = [
 name = "coverage"
 version = "7.3.0"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -462,11 +510,21 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
+[[package]]
+name = "cssselect"
+version = "1.2.0"
+description = "cssselect parses CSS3 Selectors and translates them to XPath 1.0"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "cssselect-1.2.0-py2.py3-none-any.whl", hash = "sha256:da1885f0c10b60c03ed5eccbb6b68d6eff248d91976fcde348f395d54c9fd35e"},
+    {file = "cssselect-1.2.0.tar.gz", hash = "sha256:666b19839cfaddb9ce9d36bfe4c969132c647b92fc9088c4e23f786b30f1b3dc"},
+]
+
 [[package]]
 name = "dask"
 version = "2023.8.1"
 description = "Parallel PyData with Task Scheduling"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -496,7 +554,6 @@ test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailu
 name = "distlib"
 version = "0.3.7"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -508,7 +565,6 @@ files = [
 name = "distributed"
 version = "2023.8.1"
 description = "Distributed scheduler for Dask"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -537,7 +593,6 @@ zict = ">=2.2.0"
 name = "entrypoints"
 version = "0.4"
 description = "Discover and load entry points from installed packages."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -545,11 +600,24 @@ files = [
     {file = "entrypoints-0.4.tar.gz", hash = "sha256:b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4"},
 ]
 
+[[package]]
+name = "exceptiongroup"
+version = "1.1.3"
+description = "Backport of PEP 654 (exception groups)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"},
+    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
 [[package]]
 name = "fasteners"
 version = "0.18"
 description = "A python package that provides useful locks"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -561,7 +629,6 @@ files = [
 name = "filelock"
 version = "3.12.2"
 description = "A platform independent file lock."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -577,7 +644,6 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "p
 name = "frozenlist"
 version = "1.4.0"
 description = "A list-like structure which implements collections.abc.MutableSequence"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -648,7 +714,6 @@ files = [
 name = "fsspec"
 version = "2023.6.0"
 description = "File-system specification"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -684,7 +749,6 @@ tqdm = ["tqdm"]
 name = "ghp-import"
 version = "2.1.0"
 description = "Copy your docs directly to the gh-pages branch."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -698,11 +762,24 @@ python-dateutil = ">=2.8.1"
 [package.extras]
 dev = ["flake8", "markdown", "twine", "wheel"]
 
+[[package]]
+name = "griffe"
+version = "0.35.0"
+description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "griffe-0.35.0-py3-none-any.whl", hash = "sha256:52b1dc86dfca6db5877d65a07997f8363f61f14266064cf1cae41b70aac9f395"},
+    {file = "griffe-0.35.0.tar.gz", hash = "sha256:d313f102da3d155fe0a3d284acb0fc93059ee6788903a2e983eb4f64a713fac1"},
+]
+
+[package.dependencies]
+colorama = ">=0.4"
+
 [[package]]
 name = "h5py"
 version = "3.9.0"
 description = "Read and write HDF5 files from Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -736,7 +813,6 @@ numpy = ">=1.17.3"
 name = "identify"
 version = "2.5.27"
 description = "File identification library for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -751,7 +827,6 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -763,7 +838,6 @@ files = [
 name = "importlib-metadata"
 version = "4.13.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -783,7 +857,6 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -795,7 +868,6 @@ files = [
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -813,7 +885,6 @@ i18n = ["Babel (>=2.7)"]
 name = "jmespath"
 version = "1.0.1"
 description = "JSON Matching Expressions"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -825,7 +896,6 @@ files = [
 name = "linkify-it-py"
 version = "2.0.2"
 description = "Links recognition library with FULL unicode support."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -846,7 +916,6 @@ test = ["coverage", "pytest", "pytest-cov"]
 name = "locket"
 version = "1.0.0"
 description = "File-based locks for Python on Linux and Windows"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -854,11 +923,117 @@ files = [
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 ]
 
+[[package]]
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+    {file = "lxml-4.9.3-pp38-pypy38_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:9719fe17307a9e814580af1f5c6e05ca593b12fb7e44fe62450a5384dbf61b4b"},
+    {file = "lxml-4.9.3-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:3331bece23c9ee066e0fb3f96c61322b9e0f54d775fccefff4c38ca488de283a"},
+    {file = "lxml-4.9.3-pp39-pypy39_pp73-macosx_11_0_x86_64.whl", hash = "sha256:ed667f49b11360951e201453fc3967344d0d0263aa415e1619e85ae7fd17b4e0"},
+    {file = "lxml-4.9.3-pp39-pypy39_pp73-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_24_i686.whl", hash = "sha256:8b77946fd508cbf0fccd8e400a7f71d4ac0e1595812e66025bac475a8e811694"},
+    {file = "lxml-4.9.3-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:e4da8ca0c0c0aea88fd46be8e44bd49716772358d648cce45fe387f7b92374a7"},
+    {file = "lxml-4.9.3-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:fe4bda6bd4340caa6e5cf95e73f8fea5c4bfc55763dd42f1b50a94c1b4a2fbd4"},
+    {file = "lxml-4.9.3-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:f3df3db1d336b9356dd3112eae5f5c2b8b377f3bc826848567f10bfddfee77e9"},
+    {file = "lxml-4.9.3.tar.gz", hash = "sha256:48628bd53a426c9eb9bc066a923acaa0878d1e86129fd5359aee99285f4eed9c"},
+]
+
+[package.extras]
+cssselect = ["cssselect (>=0.7)"]
+html5 = ["html5lib"]
+htmlsoup = ["BeautifulSoup4"]
+source = ["Cython (>=0.29.35)"]
+
 [[package]]
 name = "markdown"
 version = "3.4.4"
 description = "Python implementation of John Gruber's Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -877,7 +1052,6 @@ testing = ["coverage", "pyyaml"]
 name = "markdown-it-py"
 version = "2.2.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -900,11 +1074,26 @@ profiling = ["gprof2dot"]
 rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
+name = "markdown2"
+version = "2.4.10"
+description = "A fast and complete Python implementation of Markdown"
+optional = false
+python-versions = ">=3.5, <4"
+files = [
+    {file = "markdown2-2.4.10-py2.py3-none-any.whl", hash = "sha256:e6105800483783831f5dc54f827aa5b44eb137ecef5a70293d8ecfbb4109ecc6"},
+    {file = "markdown2-2.4.10.tar.gz", hash = "sha256:cdba126d90dc3aef6f4070ac342f974d63f415678959329cc7909f96cc235d72"},
+]
+
+[package.extras]
+all = ["pygments (>=2.7.3)", "wavedrom"]
+code-syntax-highlighting = ["pygments (>=2.7.3)"]
+wavedrom = ["wavedrom"]
+
 [[package]]
 name = "markupsafe"
 version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -964,7 +1153,6 @@ files = [
 name = "mdit-py-plugins"
 version = "0.4.0"
 description = "Collection of plugins for markdown-it-py"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -984,7 +1172,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -996,7 +1183,6 @@ files = [
 name = "mergedeep"
 version = "1.3.4"
 description = "A deep merge function for 🐍."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1008,7 +1194,6 @@ files = [
 name = "mkdocs"
 version = "1.5.2"
 description = "Project documentation with Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1036,11 +1221,25 @@ watchdog = ">=2.0"
 i18n = ["babel (>=2.9.0)"]
 min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pathspec (==0.11.1)", "platformdirs (==2.2.0)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
 
+[[package]]
+name = "mkdocs-autorefs"
+version = "0.5.0"
+description = "Automatically link across pages in MkDocs."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "mkdocs_autorefs-0.5.0-py3-none-any.whl", hash = "sha256:7930fcb8ac1249f10e683967aeaddc0af49d90702af111a5e390e8b20b3d97ff"},
+    {file = "mkdocs_autorefs-0.5.0.tar.gz", hash = "sha256:9a5054a94c08d28855cfab967ada10ed5be76e2bfad642302a610b252c3274c0"},
+]
+
+[package.dependencies]
+Markdown = ">=3.3"
+mkdocs = ">=1.1"
+
 [[package]]
 name = "mkdocs-exclude"
 version = "1.0.2"
 description = "A mkdocs plugin that lets you exclude files or trees."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1050,11 +1249,89 @@ files = [
 [package.dependencies]
 mkdocs = "*"
 
+[[package]]
+name = "mkdocs-material"
+version = "9.2.3"
+description = "Documentation that simply works"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "mkdocs_material-9.2.3-py3-none-any.whl", hash = "sha256:1cbac871826bbe0b5a42d7a86cfe729e03cef60cbd4d7425c640115bf1936360"},
+    {file = "mkdocs_material-9.2.3.tar.gz", hash = "sha256:7a8c5638e28cb1c0a0c7596dd85835c461a73637ce8640ea9302dbc674c2aa29"},
+]
+
+[package.dependencies]
+babel = ">=2.10.3"
+colorama = ">=0.4"
+jinja2 = ">=3.0"
+lxml = ">=4.6"
+markdown = ">=3.2"
+mkdocs = ">=1.5.2"
+mkdocs-material-extensions = ">=1.1"
+paginate = ">=0.5.6"
+pygments = ">=2.14"
+pymdown-extensions = ">=9.9.1"
+readtime = ">=2.0"
+regex = ">=2022.4.24"
+requests = ">=2.26"
+
+[[package]]
+name = "mkdocs-material-extensions"
+version = "1.1.1"
+description = "Extension pack for Python Markdown and MkDocs Material."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "mkdocs_material_extensions-1.1.1-py3-none-any.whl", hash = "sha256:e41d9f38e4798b6617ad98ca8f7f1157b1e4385ac1459ca1e4ea219b556df945"},
+    {file = "mkdocs_material_extensions-1.1.1.tar.gz", hash = "sha256:9c003da71e2cc2493d910237448c672e00cefc800d3d6ae93d2fc69979e3bd93"},
+]
+
+[[package]]
+name = "mkdocstrings"
+version = "0.22.0"
+description = "Automatic documentation from sources, for MkDocs."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "mkdocstrings-0.22.0-py3-none-any.whl", hash = "sha256:2d4095d461554ff6a778fdabdca3c00c468c2f1459d469f7a7f622a2b23212ba"},
+    {file = "mkdocstrings-0.22.0.tar.gz", hash = "sha256:82a33b94150ebb3d4b5c73bab4598c3e21468c79ec072eff6931c8f3bfc38256"},
+]
+
+[package.dependencies]
+importlib-metadata = {version = ">=4.6", markers = "python_version < \"3.10\""}
+Jinja2 = ">=2.11.1"
+Markdown = ">=3.3"
+MarkupSafe = ">=1.1"
+mkdocs = ">=1.2"
+mkdocs-autorefs = ">=0.3.1"
+mkdocstrings-python = {version = ">=0.5.2", optional = true, markers = "extra == \"python\""}
+pymdown-extensions = ">=6.3"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.10\""}
+
+[package.extras]
+crystal = ["mkdocstrings-crystal (>=0.3.4)"]
+python = ["mkdocstrings-python (>=0.5.2)"]
+python-legacy = ["mkdocstrings-python-legacy (>=0.2.1)"]
+
+[[package]]
+name = "mkdocstrings-python"
+version = "1.5.2"
+description = "A Python handler for mkdocstrings."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "mkdocstrings_python-1.5.2-py3-none-any.whl", hash = "sha256:ed37ca6d216986e2ac3530c19c3e7be381d1e3d09ea414e4ff467d6fd2cbd9c1"},
+    {file = "mkdocstrings_python-1.5.2.tar.gz", hash = "sha256:81eb4a93bc454a253daf247d1a11397c435d641c64fa165324c17c06170b1dfb"},
+]
+
+[package.dependencies]
+griffe = ">=0.35"
+mkdocstrings = ">=0.20"
+
 [[package]]
 name = "mrcfile"
 version = "1.4.3"
 description = "MRC file I/O library"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1069,7 +1346,6 @@ numpy = ">=1.16.0"
 name = "msgpack"
 version = "1.0.5"
 description = "MessagePack serializer"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1142,7 +1418,6 @@ files = [
 name = "multidict"
 version = "6.0.4"
 description = "multidict implementation"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1226,7 +1501,6 @@ files = [
 name = "mypy"
 version = "1.5.1"
 description = "Optional static typing for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1273,7 +1547,6 @@ reports = ["lxml"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1285,7 +1558,6 @@ files = [
 name = "nodeenv"
 version = "1.8.0"
 description = "Node.js virtual environment builder"
-category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
 files = [
@@ -1300,7 +1572,6 @@ setuptools = "*"
 name = "numcodecs"
 version = "0.11.0"
 description = "A Python package providing buffer compression and transformation codecs for use"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1333,7 +1604,6 @@ zfpy = ["zfpy (>=1.0.0)"]
 name = "numpy"
 version = "1.25.2"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1368,7 +1638,6 @@ files = [
 name = "packaging"
 version = "23.1"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1376,11 +1645,20 @@ files = [
     {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
+[[package]]
+name = "paginate"
+version = "0.5.6"
+description = "Divides large result sets into pages for easier browsing"
+optional = false
+python-versions = "*"
+files = [
+    {file = "paginate-0.5.6.tar.gz", hash = "sha256:5e6007b6a9398177a7e1648d04fdd9f8c9766a1a945bceac82f1929e8c78af2d"},
+]
+
 [[package]]
 name = "pandas"
 version = "2.0.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1448,7 +1726,6 @@ xml = ["lxml (>=4.6.3)"]
 name = "partd"
 version = "1.4.0"
 description = "Appendable key-value storage"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1467,7 +1744,6 @@ complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
 name = "pathspec"
 version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1479,7 +1755,6 @@ files = [
 name = "pint"
 version = "0.20.1"
 description = "Physical quantities module"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1500,7 +1775,6 @@ xarray = ["xarray"]
 name = "platformdirs"
 version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1516,7 +1790,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 name = "pluggy"
 version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1532,7 +1805,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "pre-commit"
 version = "2.21.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1551,7 +1823,6 @@ virtualenv = ">=20.10.0"
 name = "psutil"
 version = "5.9.5"
 description = "Cross-platform lib for process and system monitoring in Python."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1574,23 +1845,10 @@ files = [
 [package.extras]
 test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 
-[[package]]
-name = "py"
-version = "1.11.0"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
-    {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
-    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
-]
-
 [[package]]
 name = "pydantic"
 version = "1.10.12"
 description = "Data validation and settings management using python type hints"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1643,7 +1901,6 @@ email = ["email-validator (>=1.0.3)"]
 name = "pydantic-ome-ngff"
 version = "0.3.0"
 description = "Pydantic models for the OME-NGFF"
-category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
@@ -1658,7 +1915,6 @@ pydantic = ">=1.10.4,<2.0.0"
 name = "pydantic-zarr"
 version = "0.5.0"
 description = "pydantic models for zarr"
-category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
@@ -1674,7 +1930,6 @@ zarr = ">=2.14.2,<3.0.0"
 name = "pygments"
 version = "2.16.1"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1685,36 +1940,65 @@ files = [
 [package.extras]
 plugins = ["importlib-metadata"]
 
+[[package]]
+name = "pymdown-extensions"
+version = "10.1"
+description = "Extension pack for Python Markdown."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pymdown_extensions-10.1-py3-none-any.whl", hash = "sha256:ef25dbbae530e8f67575d222b75ff0649b1e841e22c2ae9a20bad9472c2207dc"},
+    {file = "pymdown_extensions-10.1.tar.gz", hash = "sha256:508009b211373058debb8247e168de4cbcb91b1bff7b5e961b2c3e864e00b195"},
+]
+
+[package.dependencies]
+markdown = ">=3.2"
+pyyaml = "*"
+
+[[package]]
+name = "pyquery"
+version = "2.0.0"
+description = "A jquery-like library for python"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pyquery-2.0.0-py3-none-any.whl", hash = "sha256:8dfc9b4b7c5f877d619bbae74b1898d5743f6ca248cfd5d72b504dd614da312f"},
+    {file = "pyquery-2.0.0.tar.gz", hash = "sha256:963e8d4e90262ff6d8dec072ea97285dc374a2f69cad7776f4082abcf6a1d8ae"},
+]
+
+[package.dependencies]
+cssselect = ">=1.2.0"
+lxml = ">=2.1"
+
+[package.extras]
+test = ["pytest", "pytest-cov", "requests", "webob", "webtest"]
+
 [[package]]
 name = "pytest"
-version = "6.2.5"
+version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"},
-    {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
+    {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
+    {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
 ]
 
 [package.dependencies]
-atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
-attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
+exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<2.0"
-py = ">=1.8.2"
-toml = "*"
+tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
 version = "3.0.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1729,11 +2013,26 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
+[[package]]
+name = "pytest-examples"
+version = "0.0.9"
+description = "Pytest plugin for testing examples in docstrings and markdown files."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pytest_examples-0.0.9-py3-none-any.whl", hash = "sha256:a37c798289580bd8fce47582a67cf821e6dda0d45b63fa8e9cbbd4713ed2bf08"},
+    {file = "pytest_examples-0.0.9.tar.gz", hash = "sha256:d5f9d670d4ae16f55f3e4ef79949e1133ee5e52856cc482fb9e305f2cdf4016a"},
+]
+
+[package.dependencies]
+black = ">=23"
+pytest = ">=7"
+ruff = ">=0.0.258"
+
 [[package]]
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1748,7 +2047,6 @@ six = ">=1.5"
 name = "pytz"
 version = "2023.3"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1760,7 +2058,6 @@ files = [
 name = "pyyaml"
 version = "6.0.1"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1810,7 +2107,6 @@ files = [
 name = "pyyaml-env-tag"
 version = "0.1"
 description = "A custom YAML tag for referencing environment variables in YAML files. "
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1821,11 +2117,122 @@ files = [
 [package.dependencies]
 pyyaml = "*"
 
+[[package]]
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+description = "Calculates the time some text takes the average human to read, based on Medium's read time forumula"
+optional = false
+python-versions = "*"
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+pyquery = ">=1.2"
+
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+    {file = "regex-2023.8.8-cp39-cp39-win_amd64.whl", hash = "sha256:5543c055d8ec7801901e1193a51570643d6a6ab8751b1f7dd9af71af467538bb"},
+    {file = "regex-2023.8.8.tar.gz", hash = "sha256:fcbdc5f2b0f1cd0f6a56cdb46fe41d2cce1e644e3b68832f3eeebc5fb0f7712e"},
+]
+
 [[package]]
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1847,7 +2254,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "rich"
 version = "13.5.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1862,11 +2268,36 @@ pygments = ">=2.13.0,<3.0.0"
 [package.extras]
 jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
+[[package]]
+name = "ruff"
+version = "0.0.285"
+description = "An extremely fast Python linter, written in Rust."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "ruff-0.0.285-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:72a3a0936369b986b0e959f9090206ed3c18f9e5e439ea5b8e6867c6707aded5"},
+    {file = "ruff-0.0.285-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:0d9ab6ad16742eb78919e0fba09f914f042409df40ad63423c34bb20d350162a"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6c48926156288b8ac005eb1db5e77c15e8a37309ae49d9fb6771d5cf5f777590"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:1d2a60c102e7a5e147b58fc2cbea12a563c565383effc527c987ea2086a05742"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:b02aae62f922d088bb01943e1dbd861688ada13d735b78b8348a7d90121fd292"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:f572c4296d8c7ddd22c3204de4031965be524fdd1fdaaef273945932912b28c5"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:80effdf4fe69763d69eb4ab9443e186fd09e668b59fe70ba4b49f4c077d15a1b"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:5977ce304da35c263f5e082901bd7ac0bd2be845a8fcfd1a29e4d6680cddb307"},
+    {file = "ruff-0.0.285-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:72a087712d474fa17b915d7cb9ef807e1256182b12ddfafb105eb00aeee48d1a"},
+    {file = "ruff-0.0.285-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:7ce67736cd8dfe97162d1e7adfc2d9a1bac0efb9aaaff32e4042c7cde079f54b"},
+    {file = "ruff-0.0.285-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:5473a4c6cac34f583bff08c5f63b8def5599a0ea4dc96c0302fbd2cc0b3ecbad"},
+    {file = "ruff-0.0.285-py3-none-musllinux_1_2_i686.whl", hash = "sha256:e6b1c961d608d373a032f047a20bf3c55ad05f56c32e7b96dcca0830a2a72348"},
+    {file = "ruff-0.0.285-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:2933cc9631f453305399c7b8fb72b113ad76b49ae1d7103cc4afd3a423bed164"},
+    {file = "ruff-0.0.285-py3-none-win32.whl", hash = "sha256:770c5eb6376de024111443022cda534fb28980a9dd3b4abc83992a8770167ba6"},
+    {file = "ruff-0.0.285-py3-none-win_amd64.whl", hash = "sha256:a8c6ad6b9cd77489bf6d1510950cbbe47a843aa234adff0960bae64bd06c3b6d"},
+    {file = "ruff-0.0.285-py3-none-win_arm64.whl", hash = "sha256:de44fbc6c3b25fccee473ddf851416fd4e246fc6027b2197c395b1b3b3897921"},
+    {file = "ruff-0.0.285.tar.gz", hash = "sha256:45866048d1dcdcc80855998cb26c4b2b05881f9e043d2e3bfe1aa36d9a2e8f28"},
+]
+
 [[package]]
 name = "s3fs"
 version = "2023.6.0"
 description = "Convenient Filesystem interface over S3"
-category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -1887,7 +2318,6 @@ boto3 = ["aiobotocore[boto3] (>=2.5.0,<2.6.0)"]
 name = "scipy"
 version = "1.9.3"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1926,7 +2356,6 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 name = "setuptools"
 version = "68.1.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1943,7 +2372,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1955,7 +2383,6 @@ files = [
 name = "sortedcontainers"
 version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1963,11 +2390,21 @@ files = [
     {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"},
 ]
 
+[[package]]
+name = "soupsieve"
+version = "2.4.1"
+description = "A modern CSS selector implementation for Beautiful Soup."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
+    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
+]
+
 [[package]]
 name = "tblib"
 version = "2.0.0"
 description = "Traceback serialization library."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1979,7 +2416,6 @@ files = [
 name = "textual"
 version = "0.16.0"
 description = "Modern Text User Interface framework"
-category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -2001,7 +2437,6 @@ dev = ["aiohttp (>=3.8.1)", "click (>=8.1.2)", "msgpack (>=1.0.3)"]
 name = "tifffile"
 version = "2023.8.12"
 description = "Read and write TIFF files"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2015,23 +2450,10 @@ numpy = "*"
 [package.extras]
 all = ["defusedxml", "fsspec", "imagecodecs (>=2023.8.12)", "lxml", "matplotlib", "zarr"]
 
-[[package]]
-name = "toml"
-version = "0.10.2"
-description = "Python Library for Tom's Obvious, Minimal Language"
-category = "dev"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-files = [
-    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
-    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
-]
-
 [[package]]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2043,7 +2465,6 @@ files = [
 name = "toolz"
 version = "0.12.0"
 description = "List processing tools and functional utilities"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2055,7 +2476,6 @@ files = [
 name = "tornado"
 version = "6.3.3"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
-category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -2076,7 +2496,6 @@ files = [
 name = "typing-extensions"
 version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2088,7 +2507,6 @@ files = [
 name = "tzdata"
 version = "2023.3"
 description = "Provider of IANA time zone data"
-category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -2100,7 +2518,6 @@ files = [
 name = "uc-micro-py"
 version = "1.0.2"
 description = "Micro subset of unicode data files for linkify-it-py projects."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2115,7 +2532,6 @@ test = ["coverage", "pytest", "pytest-cov"]
 name = "urllib3"
 version = "1.26.16"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -2132,7 +2548,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "virtualenv"
 version = "20.24.3"
 description = "Virtual Python Environment builder"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2153,7 +2568,6 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 name = "watchdog"
 version = "3.0.0"
 description = "Filesystem events monitoring"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2193,7 +2607,6 @@ watchmedo = ["PyYAML (>=3.10)"]
 name = "wrapt"
 version = "1.15.0"
 description = "Module for decorators, wrappers and monkey patching."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 files = [
@@ -2278,7 +2691,6 @@ files = [
 name = "xarray"
 version = "2023.8.0"
 description = "N-D labeled arrays and datasets in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2303,7 +2715,6 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"]
 name = "xarray-datatree"
 version = "0.0.12"
 description = "Hierarchical tree-like data structures for xarray"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2318,7 +2729,6 @@ xarray = ">=2022.6.0"
 name = "xarray-multiscale"
 version = "2.1.0"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
@@ -2334,14 +2744,13 @@ xarray = ">=2022.03.0"
 
 [[package]]
 name = "xarray-ome-ngff"
-version = "1.2.1"
+version = "1.2.3"
 description = "xarray and ome-ngff"
-category = "main"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "xarray_ome_ngff-1.2.1-py3-none-any.whl", hash = "sha256:938d853cedbc64383c20368a1c0dd2ebb576adff7a5b31cf2d69c62e485958ad"},
-    {file = "xarray_ome_ngff-1.2.1.tar.gz", hash = "sha256:5f1701cfc1f2cfb15906e1b3c4532c24707a4972b360a40c0efd7c9169eb17bd"},
+    {file = "xarray_ome_ngff-1.2.3-py3-none-any.whl", hash = "sha256:2a999cfede8af688a4813816e261d2f9c1a7bc7f3e5ec48d1d66a31ede70008d"},
+    {file = "xarray_ome_ngff-1.2.3.tar.gz", hash = "sha256:56461b24e6dacf833350f7b04def9e7b141d21fb8aa091e63f27b030790fae89"},
 ]
 
 [package.dependencies]
@@ -2354,7 +2763,6 @@ xarray = ">=2023.2.0,<2024.0.0"
 name = "yarl"
 version = "1.9.2"
 description = "Yet another URL library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2442,7 +2850,6 @@ multidict = ">=4.0"
 name = "zarr"
 version = "2.16.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2464,7 +2871,6 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 name = "zict"
 version = "3.0.0"
 description = "Mutable mapping tools"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2476,7 +2882,6 @@ files = [
 name = "zipp"
 version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2491,4 +2896,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "a9859268b74e57c2a73d7ad777478d43cbe9757f47eeeba4dd3394988dee0edf"
+content-hash = "e947da904c27edd5a42b7e4df65ffe192da1e359a9cd35bdcf5d0a5e1c597a55"
diff --git a/pyproject.toml b/pyproject.toml
index 8819f90..1720dc5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,12 +31,19 @@ pydantic-zarr = "^0.5.0"
 
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^6.1.2"
+pytest = "^7.4.0"
 pytest-cov = "^3.0.0"
 pre-commit = "2.21.0"
 mypy = "^1.1.1"
 requests = "^2.28.2"
 
+
+[tool.poetry.group.docs.dependencies]
+mkdocs = "^1.4.3"
+mkdocs-material = "^9.1.18"
+mkdocstrings = {extras = ["python"], version = "^0.22.0"}
+pytest-examples = "^0.0.9"
+
 [tool.poetry.scripts]
 tiff2zarr = 'fibsem_tools.cli.tiff2zarr:run'
 zarr-scan = 'fibsem_tools.cli.zarr_scan:cli'
diff --git a/src/fibsem_tools/cli/tiff2zarr.py b/src/fibsem_tools/cli/tiff2zarr.py
index 9148b5d..37431a9 100644
--- a/src/fibsem_tools/cli/tiff2zarr.py
+++ b/src/fibsem_tools/cli/tiff2zarr.py
@@ -48,7 +48,10 @@ class ArrayMoveStrict(BaseModel):
     chunks: List[int]
 
 
-def represents_int(s):
+def represents_int(s: Any) -> bool:
+    """
+    Returns `True` if the value can be parsed as an int, and `False` otherwise.
+    """
     try:
         int(s)
     except ValueError:
diff --git a/src/fibsem_tools/cli/zarr2json.py b/src/fibsem_tools/cli/zarr2json.py
index 333b190..e33c575 100644
--- a/src/fibsem_tools/cli/zarr2json.py
+++ b/src/fibsem_tools/cli/zarr2json.py
@@ -5,11 +5,16 @@
 from fibsem_tools import read
 from fibsem_tools.io.util import split_by_suffix
 from rich import print
+import os
 
 
 def parse_zarr_path(path: str) -> Union[ArraySpec, GroupSpec]:
+    """
+    Resolve a path to a zarr group or zarr array, and parse that array or group to an
+    instance of ArraySpec or GroupSpec, respectively.
+    """
     pre, post, suffix = split_by_suffix(path, (".n5", ".zarr"))
-    obj = read(path)
+    obj = read(os.path.join(pre, post, suffix))
     if isinstance(obj, zarr.Array):
         result = ArraySpec.from_zarr(obj)
     elif isinstance(obj, zarr.Group):
@@ -22,6 +27,9 @@ def parse_zarr_path(path: str) -> Union[ArraySpec, GroupSpec]:
 @click.command()
 @click.argument("path", type=click.STRING)
 def cli(path: str):
+    """
+    Generate a JSON representation of the structure of a zarr array or group.
+    """
     result = parse_zarr_path(path)
     print(result.json(indent=2))
 
diff --git a/src/fibsem_tools/cli/zarr_scan.py b/src/fibsem_tools/cli/zarr_scan.py
index 53cf3eb..74bc0eb 100644
--- a/src/fibsem_tools/cli/zarr_scan.py
+++ b/src/fibsem_tools/cli/zarr_scan.py
@@ -13,17 +13,29 @@
 
 @dataclass
 class Missing:
+    """
+    This class represents a chunk that was missing.
+    """
+
     variant = "missing"
 
 
 @dataclass
 class Invalid:
+    """
+    This class represents a chunk that raised an exception upon loading / decompression.
+    """
+
     variant = "invalid"
     exception: BaseException
 
 
 @dataclass
 class Valid:
+    """
+    This class represents a chunk that was valid.
+    """
+
     variant = "valid"
 
 
@@ -32,6 +44,26 @@ class ChunkSetResults(dict[ChunkState, dict[str, Union[Missing, Valid, Invalid]]
 
 
 def check_zarray(array: zarr.Array) -> dict[str, Union[Missing, Invalid, Valid]]:
+    """
+    Check the state of each chunk of a zarr array. This function iterates over the
+    chunks of an array, attempts to access each chunk, and records whether that chunk
+    is valid (the chunk was fetched + decompressed without incident), invalid (
+    an exception was raised when loading + decompressing the chunk) or missing (the
+    chunk was not found in storage).
+
+    Parameters
+    ----------
+
+    array: Zarr.Array
+        The zarr array to check.
+
+    Returns
+    -------
+
+    A dict with string keys and  where each key is the location of a chunk in the key
+    space of the store object associated with the array, and each value is either a
+    Valid, Missing, or Invalid object.
+    """
     ckeys = tuple(get_chunk_keys(array))
     results = {}
     for ckey in track(ckeys, description="Checking chunks..."):
@@ -76,7 +108,38 @@ def check_zarray(array: zarr.Array) -> dict[str, Union[Missing, Invalid, Valid]]
     default=False,
     help="delete invalid chunks",
 )
-def cli(array_path, valid, missing, invalid, delete_invalid):
+def cli(
+    array_path: str, valid: bool, missing: bool, invalid: bool, delete_invalid: bool
+):
+    """
+    Checks the chunks of a zarr array, prints the results as JSON, and optionally
+    deletes invalid chunks.
+
+    Parameters
+    ----------
+
+    array_path: string
+        The path to the array.
+
+    valid: bool
+        Whether to report valid chunks. Default is False, which results in no output if
+        a chunk is valid.
+
+    missing: bool
+        Whether to report missing chunks. Default is False, which results in no output
+        if a chunk is missing.
+
+    invalid: bool
+        Whether to report invalid chunks. Default is True. An invalid chunk is defined
+        as one which raises an OSError upon loading + decompression. This definition may
+        change to include more exception types, but the basic idea is that a chunk is
+        invalid if it has been corrupted or cannot be read with the compressor as
+        defined in the array metadata.
+
+    delete_invalid: bool
+        Whether to delete invalid chunks. Default is False.
+
+    """
     start = time.time()
     array = access(array_path, mode="r")
     all_results = check_zarray(array)
diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index b708f97..ec972c9 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -110,6 +110,27 @@ class LabelList(StrictBase):
 
 
 class SemanticSegmentation(StrictBase):
+    """
+    Metadata for a semantic segmentation, i.e. a segmentation where numerical values
+    represent different semantic classes.
+
+    Attributes
+    ----------
+
+    type: string
+        Must be the literal 'semantic_segmentation'.
+
+    encoding: dict with string keys and numeric values
+        This dict represents the mapping from possibilities to numeric values. The keys
+        must be strings in the set {'unknown', 'absent', 'present'}, and the values
+        must be numeric values contained in the array described by this metadata.
+
+        For example, if an annotator produces an array where 0 represents 'unknown' and
+        1 represents the presence of class X then `encoding` would take the value
+        {'unknown': 0, 'present': 1}
+
+    """
+
     type: Literal["semantic_segmentation"] = "semantic_segmentation"
     encoding: Dict[Union[Possibility, Literal["present"]], int]
 
@@ -127,6 +148,24 @@ class InstanceSegmentation(StrictBase):
 class AnnotationArrayAttrs(GenericModel, Generic[TName]):
     """
     The metadata for an array of annotated values.
+
+    Attributes
+    ----------
+
+    class_name: string
+        The name of the semantic class annotated in this array.
+
+    histogram: dict with string keys and integer values, or None
+        The frequency of 'absent' and / or 'missing' values in the array data.
+
+        The total number of elements in the array that represent "positive" examples can
+        be calculated from this histogram -- take the number of elements in the array
+        minus the sum of the values in the histogram.
+
+    annotation_type: SemanticSegmentation or InstanceSegmentation
+        The type of the annotation. Must be either an instance of SemanticSegmentation
+        or an instance of InstanceSegmentation.
+
     """
 
     class_name: TName
@@ -153,6 +192,15 @@ class AnnotationGroupAttrs(GenericModel, Generic[TName]):
     In a storage hierarchy like zarr or hdf5, this metadata is associated with a
     group-like container that contains a collection of arrays that contain the
     annotation data in a multiscale representation.
+
+    Attributes
+    ----------
+
+    class_name: string
+        The name of the semantic class annotated by the data in this group.
+
+    annotation_type: AnnotationType
+        The type of annotation represented by the data in this group.
     """
 
     class_name: TName
@@ -161,7 +209,43 @@ class AnnotationGroupAttrs(GenericModel, Generic[TName]):
 
 class CropGroupAttrs(GenericModel, Generic[TName]):
     """
-    The metadata for all annotations in a single crop.
+    The metadata for all annotations in zarr group representing a single crop.
+
+    Attributes
+    ----------
+    name: string or None
+        The name of the crop. Optional.
+
+    description: string or None.
+        A description of the crop. Optional.
+
+    created_by: list of strings
+        The people or entities responsible for creating the annotations in the crop.
+
+    created_with: list of strings
+        The tool(s) used to create the annotations in the crop. Optional.
+
+    start_date: datetime.date or None
+        The calendar date when the crop was started. Optional.
+
+    end_date: datetime.date or None
+        The calendar date when the crop was completed. None may be used here if the date
+        of completion is unknown, for example if the crop is not yet finished.
+
+    duration_days: int or None
+        The number of days spent annotating the crop. Optional.
+
+    protocol_uri: string or None
+        A URI pointing to a description of the annotation protocol used to produce the
+        annotations. Optional.
+
+    class_names: list of strings
+        The names of the semantic classes that **could** be annotated in this crop.
+
+    index: dict with string keys and string values
+        Each key of this dict is an element of the `class_names` attribute. Each
+        value is the relative path to the zarr group containing the label data for that
+        class name.
     """
 
     name: Optional[str]
@@ -171,10 +255,9 @@ class CropGroupAttrs(GenericModel, Generic[TName]):
     start_date: Optional[date]
     end_date: Optional[date]
     duration_days: Optional[int]
-    protocol_url: Optional[str]
+    protocol_uri: Optional[str]
     class_names: list[TName]
     index: dict[TName, str]
-    doi: Optional[str]
 
 
 AnnotationArray = ArraySpec[AnnotationArrayAttrs]

From 2ebe8f432dc226f64201e5387bc367f738b99b13 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 13 Sep 2023 17:15:30 -0400
Subject: [PATCH 8/9] docs: more documentation

---
 docs/api/metadata/neuroglancer.md         |   1 +
 docs/api/metadata/transform.md            |   1 +
 mkdocs.yml                                |  10 +-
 poetry.lock                               | 624 ++++++++--------------
 src/fibsem_tools/cli/zarr_scan.py         |   2 +-
 src/fibsem_tools/io/multiscale.py         |  13 +
 src/fibsem_tools/metadata/groundtruth.py  |  32 +-
 src/fibsem_tools/metadata/neuroglancer.py |  51 +-
 src/fibsem_tools/metadata/transform.py    |  62 ++-
 9 files changed, 348 insertions(+), 448 deletions(-)
 create mode 100644 docs/api/metadata/neuroglancer.md
 create mode 100644 docs/api/metadata/transform.md

diff --git a/docs/api/metadata/neuroglancer.md b/docs/api/metadata/neuroglancer.md
new file mode 100644
index 0000000..566f3b6
--- /dev/null
+++ b/docs/api/metadata/neuroglancer.md
@@ -0,0 +1 @@
+::: fibsem_tools.metadata.neuroglancer
\ No newline at end of file
diff --git a/docs/api/metadata/transform.md b/docs/api/metadata/transform.md
new file mode 100644
index 0000000..56bc1ba
--- /dev/null
+++ b/docs/api/metadata/transform.md
@@ -0,0 +1 @@
+::: fibsem_tools.metadata.transform
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index a4fecc5..484ca24 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -44,6 +44,8 @@ nav:
         - zarr: api/io/zarr.md
       - metadata:
         - groundtruth: api/metadata/groundtruth.md
+        - transform: api/metadata/transform.md
+        - neuroglancer: api/metadata/neuroglancer.md
       - cli:
         - tiff2zarr: api/cli/tiff2zarr.md
         - zarr_scan: api/cli/zarr_scan.md
@@ -54,7 +56,13 @@ plugins:
     handlers:
         python:
           options:
-            show_signature_annotations: true
+            docstring_style: numpy
+            members_order: source
+            separate_signature: true
+            filters: ["!^_"]
+            docstring_options:
+              ignore_init_summary: true
+            merge_init_into_class: true
 
 markdown_extensions:
   - pymdownx.highlight:
diff --git a/poetry.lock b/poetry.lock
index dc9747e..0078bd9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -218,53 +218,35 @@ files = [
     {file = "backoff-1.11.1.tar.gz", hash = "sha256:ccb962a2378418c667b3c979b504fdeb7d9e0d29c0579e3b13b86467177728cb"},
 ]
 
-[[package]]
-name = "beautifulsoup4"
-version = "4.12.2"
-description = "Screen-scraping library"
-optional = false
-python-versions = ">=3.6.0"
-files = [
-    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
-    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
-]
-
-[package.dependencies]
-soupsieve = ">1.2"
-
-[package.extras]
-html5lib = ["html5lib"]
-lxml = ["lxml"]
-
 [[package]]
 name = "black"
-version = "23.7.0"
+version = "23.9.1"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -274,7 +256,7 @@ packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
@@ -445,63 +427,63 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.3.0"
+version = "7.3.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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@@ -510,26 +492,15 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
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 [[package]]
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 [[package]]
 name = "distlib"
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+version = "2023.9.1"
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 python-versions = ">=3.9"
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 [package.dependencies]
 click = ">=8.0"
 cloudpickle = ">=1.5.0"
-dask = "2023.8.1"
+dask = "2023.9.1"
 jinja2 = ">=2.10.3"
 locket = ">=1.0.0"
 msgpack = ">=1.0.0"
@@ -587,7 +558,7 @@ tblib = ">=1.6.0"
 toolz = ">=0.10.0"
 tornado = ">=6.0.4"
 urllib3 = ">=1.24.3"
-zict = ">=2.2.0"
+zict = ">=3.0.0"
 
 [[package]]
 name = "entrypoints"
@@ -627,18 +598,21 @@ files = [
 
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 name = "filelock"
-version = "3.12.2"
+version = "3.12.3"
 description = "A platform independent file lock."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.7.1", markers = "python_version < \"3.11\""}
+
 [package.extras]
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 [[package]]
 name = "frozenlist"
@@ -712,13 +686,13 @@ files = [
 
 [[package]]
 name = "fsspec"
-version = "2023.6.0"
+version = "2023.9.0"
 description = "File-system specification"
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 python-versions = ">=3.8"
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 [package.extras]
@@ -764,13 +738,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "0.35.0"
+version = "0.36.2"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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-htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=0.29.35)"]
-
 [[package]]
 name = "markdown"
 version = "3.4.4"
@@ -1074,22 +941,6 @@ profiling = ["gprof2dot"]
 rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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-description = "A fast and complete Python implementation of Markdown"
-optional = false
-python-versions = ">=3.5, <4"
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-wavedrom = ["wavedrom"]
-
 [[package]]
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@@ -1251,29 +1102,27 @@ mkdocs = "*"
 
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 name = "mkdocs-material"
-version = "9.2.3"
+version = "9.3.1"
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 name = "mkdocs-material-extensions"
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 [[package]]
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 [package.dependencies]
 numpy = [
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-    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
+    {version = ">=1.22.4", markers = "python_version < \"3.11\""},
     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
@@ -1700,27 +1542,28 @@ pytz = ">=2020.1"
 tzdata = ">=2022.1"
 
 [package.extras]
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+clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"]
+compression = ["zstandard (>=0.17.0)"]
+computation = ["scipy (>=1.8.1)", "xarray (>=2022.03.0)"]
+consortium-standard = ["dataframe-api-compat (>=0.1.7)"]
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-hdf5 = ["tables (>=3.6.1)"]
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-mysql = ["SQLAlchemy (>=1.4.16)", "pymysql (>=1.0.2)"]
-output-formatting = ["jinja2 (>=3.0.0)", "tabulate (>=0.8.9)"]
+fss = ["fsspec (>=2022.05.0)"]
+gcp = ["gcsfs (>=2022.05.0)", "pandas-gbq (>=0.17.5)"]
+hdf5 = ["tables (>=3.7.0)"]
+html = ["beautifulsoup4 (>=4.11.1)", "html5lib (>=1.1)", "lxml (>=4.8.0)"]
+mysql = ["SQLAlchemy (>=1.4.36)", "pymysql (>=1.0.2)"]
+output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.8.10)"]
 parquet = ["pyarrow (>=7.0.0)"]
-performance = ["bottleneck (>=1.3.2)", "numba (>=0.53.1)", "numexpr (>=2.7.1)"]
+performance = ["bottleneck (>=1.3.4)", "numba (>=0.55.2)", "numexpr (>=2.8.0)"]
 plot = ["matplotlib (>=3.6.1)"]
-postgresql = ["SQLAlchemy (>=1.4.16)", "psycopg2 (>=2.8.6)"]
-spss = ["pyreadstat (>=1.1.2)"]
-sql-other = ["SQLAlchemy (>=1.4.16)"]
-test = ["hypothesis (>=6.34.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
-xml = ["lxml (>=4.6.3)"]
+postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"]
+spss = ["pyreadstat (>=1.1.5)"]
+sql-other = ["SQLAlchemy (>=1.4.36)"]
+test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
+xml = ["lxml (>=4.8.0)"]
 
 [[package]]
 name = "partd"
@@ -1788,13 +1631,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
@@ -1942,46 +1785,31 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.1"
+version = "10.3"
 description = "Extension pack for Python Markdown."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 markdown = ">=3.2"
 pyyaml = "*"
 
-[[package]]
-name = "pyquery"
-version = "2.0.0"
-description = "A jquery-like library for python"
-optional = false
-python-versions = "*"
-files = [
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-
-[package.dependencies]
-cssselect = ">=1.2.0"
-lxml = ">=2.1"
-
 [package.extras]
-test = ["pytest", "pytest-cov", "requests", "webob", "webtest"]
+extra = ["pygments (>=2.12)"]
 
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
+    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
 ]
 
 [package.dependencies]
@@ -2045,13 +1873,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
 ]
 
 [[package]]
@@ -2117,21 +1945,6 @@ files = [
 [package.dependencies]
 pyyaml = "*"
 
-[[package]]
-name = "readtime"
-version = "3.0.0"
-description = "Calculates the time some text takes the average human to read, based on Medium's read time forumula"
-optional = false
-python-versions = "*"
-files = [
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-]
-
-[package.dependencies]
-beautifulsoup4 = ">=4.0.1"
-markdown2 = ">=2.4.3"
-pyquery = ">=1.2"
-
 [[package]]
 name = "regex"
 version = "2023.8.8"
@@ -2270,49 +2083,49 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "ruff"
-version = "0.0.285"
+version = "0.0.288"
 description = "An extremely fast Python linter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "s3fs"
-version = "2023.6.0"
+version = "2023.9.0"
 description = "Convenient Filesystem interface over S3"
 optional = false
 python-versions = ">= 3.8"
 files = [
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 ]
 
 [package.dependencies]
-aiobotocore = ">=2.5.0,<2.6.0"
+aiobotocore = ">=2.5.4,<2.6.0"
 aiohttp = "<4.0.0a0 || >4.0.0a0,<4.0.0a1 || >4.0.0a1"
-fsspec = "2023.6.0"
+fsspec = "2023.9.0"
 
 [package.extras]
-awscli = ["aiobotocore[awscli] (>=2.5.0,<2.6.0)"]
-boto3 = ["aiobotocore[boto3] (>=2.5.0,<2.6.0)"]
+awscli = ["aiobotocore[awscli] (>=2.5.4,<2.6.0)"]
+boto3 = ["aiobotocore[boto3] (>=2.5.4,<2.6.0)"]
 
 [[package]]
 name = "scipy"
@@ -2354,19 +2167,19 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "68.1.2"
+version = "68.2.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-68.1.2-py3-none-any.whl", hash = "sha256:3d8083eed2d13afc9426f227b24fd1659489ec107c0e86cec2ffdde5c92e790b"},
-    {file = "setuptools-68.1.2.tar.gz", hash = "sha256:3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d"},
+    {file = "setuptools-68.2.1-py3-none-any.whl", hash = "sha256:eff96148eb336377ab11beee0c73ed84f1709a40c0b870298b0d058828761bae"},
+    {file = "setuptools-68.2.1.tar.gz", hash = "sha256:56ee14884fd8d0cd015411f4a13f40b4356775a0aefd9ebc1d3bfb9a1acb32f1"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5,<=7.1.2)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
 testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -2390,17 +2203,6 @@ files = [
     {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"},
 ]
 
-[[package]]
-name = "soupsieve"
-version = "2.4.1"
-description = "A modern CSS selector implementation for Beautiful Soup."
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
-    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
-]
-
 [[package]]
 name = "tblib"
 version = "2.0.0"
@@ -2435,13 +2237,13 @@ dev = ["aiohttp (>=3.8.1)", "click (>=8.1.2)", "msgpack (>=1.0.3)"]
 
 [[package]]
 name = "tifffile"
-version = "2023.8.12"
+version = "2023.8.30"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "tifffile-2023.8.12-py3-none-any.whl", hash = "sha256:d1ef06461a947a6800ba6121b330b54a57fb9cbf7e5bc0adab8307081297d66b"},
-    {file = "tifffile-2023.8.12.tar.gz", hash = "sha256:824956b6d974b9d346aae59932bea862a2ad18fcc2b1a820b6941b7f6ddb2bca"},
+    {file = "tifffile-2023.8.30-py3-none-any.whl", hash = "sha256:62364eef35a6fdcc7bc2ad6f97dd270f577efb01b31260ff800af76a66c1e145"},
+    {file = "tifffile-2023.8.30.tar.gz", hash = "sha256:6a8c53b012a286b75d09a1498ab32f202f24cc6270a105b5d5911dc4426f162a"},
 ]
 
 [package.dependencies]
@@ -2546,13 +2348,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.24.3"
+version = "20.24.5"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.24.3-py3-none-any.whl", hash = "sha256:95a6e9398b4967fbcb5fef2acec5efaf9aa4972049d9ae41f95e0972a683fd02"},
-    {file = "virtualenv-20.24.3.tar.gz", hash = "sha256:e5c3b4ce817b0b328af041506a2a299418c98747c4b1e68cb7527e74ced23efc"},
+    {file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"},
+    {file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"},
 ]
 
 [package.dependencies]
@@ -2561,7 +2363,7 @@ filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<4"
 
 [package.extras]
-docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
 test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
diff --git a/src/fibsem_tools/cli/zarr_scan.py b/src/fibsem_tools/cli/zarr_scan.py
index 74bc0eb..a65a3e6 100644
--- a/src/fibsem_tools/cli/zarr_scan.py
+++ b/src/fibsem_tools/cli/zarr_scan.py
@@ -60,7 +60,7 @@ def check_zarray(array: zarr.Array) -> dict[str, Union[Missing, Invalid, Valid]]
     Returns
     -------
 
-    A dict with string keys and  where each key is the location of a chunk in the key
+    A dict with string keys, where each key is the location of a chunk in the key
     space of the store object associated with the array, and each value is either a
     Valid, Missing, or Invalid object.
     """
diff --git a/src/fibsem_tools/io/multiscale.py b/src/fibsem_tools/io/multiscale.py
index 8dbf79d..ee7e750 100644
--- a/src/fibsem_tools/io/multiscale.py
+++ b/src/fibsem_tools/io/multiscale.py
@@ -56,6 +56,19 @@ def multiscale_group(
     """
     Generate multiscale metadata of the desired flavor from a list of DataArrays
 
+    Arguments
+    ---------
+
+    arrays : Sequence[DataArray]
+        The arrays to store.
+    metadata_types : List[str]
+        The metadata flavor(s) to use.
+    array_paths : Sequence[str]
+        The path for each array in storage, relative to the parent group.
+    name : Optional[str]
+        The name for the multiscale group. Only relevant for metadata flavors that
+        support this field, e.g. ome-ngff
+
     Returns
     -------
 
diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index ec972c9..4ac1577 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -119,7 +119,6 @@ class SemanticSegmentation(StrictBase):
 
     type: string
         Must be the literal 'semantic_segmentation'.
-
     encoding: dict with string keys and numeric values
         This dict represents the mapping from possibilities to numeric values. The keys
         must be strings in the set {'unknown', 'absent', 'present'}, and the values
@@ -152,20 +151,17 @@ class AnnotationArrayAttrs(GenericModel, Generic[TName]):
     Attributes
     ----------
 
-    class_name: string
+    class_name: str
         The name of the semantic class annotated in this array.
-
-    histogram: dict with string keys and integer values, or None
+    histogram: Optional[Dict[str, int]]
         The frequency of 'absent' and / or 'missing' values in the array data.
-
         The total number of elements in the array that represent "positive" examples can
         be calculated from this histogram -- take the number of elements in the array
         minus the sum of the values in the histogram.
 
-    annotation_type: SemanticSegmentation or InstanceSegmentation
+    annotation_type: SemanticSegmentation | InstanceSegmentation
         The type of the annotation. Must be either an instance of SemanticSegmentation
         or an instance of InstanceSegmentation.
-
     """
 
     class_name: TName
@@ -196,7 +192,7 @@ class AnnotationGroupAttrs(GenericModel, Generic[TName]):
     Attributes
     ----------
 
-    class_name: string
+    class_name: str
         The name of the semantic class annotated by the data in this group.
 
     annotation_type: AnnotationType
@@ -213,36 +209,36 @@ class CropGroupAttrs(GenericModel, Generic[TName]):
 
     Attributes
     ----------
-    name: string or None
+    name: Optional[str]
         The name of the crop. Optional.
 
-    description: string or None.
+    description: Optional[str]
         A description of the crop. Optional.
 
-    created_by: list of strings
+    created_by: list[str]
         The people or entities responsible for creating the annotations in the crop.
 
-    created_with: list of strings
+    created_with: list[str]
         The tool(s) used to create the annotations in the crop. Optional.
 
-    start_date: datetime.date or None
+    start_date: Optional[datetime.date]
         The calendar date when the crop was started. Optional.
 
-    end_date: datetime.date or None
+    end_date: Optional[datetime.date]
         The calendar date when the crop was completed. None may be used here if the date
         of completion is unknown, for example if the crop is not yet finished.
 
-    duration_days: int or None
+    duration_days: Optional[int]
         The number of days spent annotating the crop. Optional.
 
-    protocol_uri: string or None
+    protocol_uri: Optional[str]
         A URI pointing to a description of the annotation protocol used to produce the
         annotations. Optional.
 
-    class_names: list of strings
+    class_names: list[str]
         The names of the semantic classes that **could** be annotated in this crop.
 
-    index: dict with string keys and string values
+    index: dict[str, str]
         Each key of this dict is an element of the `class_names` attribute. Each
         value is the relative path to the zarr group containing the label data for that
         class name.
diff --git a/src/fibsem_tools/metadata/neuroglancer.py b/src/fibsem_tools/metadata/neuroglancer.py
index 2284e36..4d53610 100644
--- a/src/fibsem_tools/metadata/neuroglancer.py
+++ b/src/fibsem_tools/metadata/neuroglancer.py
@@ -9,8 +9,17 @@
 
 class PixelResolution(BaseModel):
     """
-    PixelResolution attribute used by the Saalfeld lab. The dimensions attribute
+    PixelResolution attribute used by the Saalfeld lab. The `dimensions` attribute
     contains a list of scales that define the grid spacing of the data, in F-order.
+
+    Attributes
+    ----------
+
+    dimensions: Sequence[float]
+        The distance, in units given by the `unit` attribute, between samples per
+        axis
+    unit: str
+        The physical unit for the `dimensions` attribute.
     """
 
     dimensions: Sequence[float]
@@ -21,10 +30,26 @@ class PixelResolution(BaseModel):
 class NeuroglancerN5GroupMetadata(BaseModel):
     """
     Metadata to enable displaying an N5 group containing several datasets
-    as a multiresolution dataset in neuroglancer.
-    see https://github.com/google/neuroglancer/issues/176#issuecomment-553027775
+    as a multiresolution dataset in neuroglancer, based on
+    [this comment](https://github.com/google/neuroglancer/issues/176#issuecomment-553027775).
     Axis properties will be indexed in the opposite order of C-contiguous axis indexing.
-    """
+
+    Attributes
+    ----------
+    axes : Sequence[str]
+        The names of the axes of the data
+    units : Sequence[str]
+        The units for the axes of the data
+    scales : Sequence[Sequence[PositiveInt]]
+        The relative scales of each axis. E.g., if this metadata describes a 3D dataset
+        that was downsampled isotropically by 2 twice, resulting in 3 total arrays,
+          then `scales` would be the list `[[1,1,1], [2,2,2], [4,4,4]]`.
+    pixelResolution: PixelResolution
+        An instance of PixelResolution that specifies the interval, in physical units,
+        between adjacent samples per axis. Note that PixelResolution also defines a
+        `unit` attribute, which is redundant with the `units` attribute defined on this
+        class.
+    """  # noqa: E501
 
     axes: Sequence[str]
     units: Sequence[str]
@@ -39,7 +64,7 @@ def from_xarrays(cls, arrays: Sequence[DataArray]) -> "NeuroglancerN5GroupMetada
         Parameters
         ----------
 
-        arrays : list or tuple of xarray.DataArray
+        arrays : Sequence[xarray.DataArray]
             The collection of arrays from which to generate multiscale metadata. These
             arrays are assumed to share the same `dims` attributes, albeit with varying
             `coords`.
@@ -68,6 +93,22 @@ def from_xarrays(cls, arrays: Sequence[DataArray]) -> "NeuroglancerN5GroupMetada
 
 
 class NeuroglancerN5Group(GroupSpec):
+    """
+    A `GroupSpec` representing the structure of a N5 group with
+    neuroglancer-compatible structure and metadata
+
+    Attributes
+    ----------
+
+    attrs : NeuroglancerN5GroupMetadata
+        The metadata required to convey to neuroglancer that this group represents a
+        multiscale image.
+    members : Dict[str, Union[GroupSpec, ArraySpec]]
+        The members of this group. Arrays must be consistent with the `scales` attribute
+        in `attrs`.
+
+    """
+
     attrs: NeuroglancerN5GroupMetadata
 
     @validator("members")
diff --git a/src/fibsem_tools/metadata/transform.py b/src/fibsem_tools/metadata/transform.py
index 39d1776..58de5dc 100644
--- a/src/fibsem_tools/metadata/transform.py
+++ b/src/fibsem_tools/metadata/transform.py
@@ -4,16 +4,38 @@
 from xarray import DataArray
 import fibsem_tools.io.xr as fsxr
 
-ArrayOrder = Literal["C", "F"]
-
 
 class STTransform(BaseModel):
     """
     Representation of an N-dimensional scaling -> translation transform for labelled
     axes with units.
+
+    Attributes
+    ----------
+
+    axes: Sequence[str]
+        Names for the axes of the data.
+    units: Sequence[str]
+        Units for the axes of the data.
+    translate: Sequence[float]
+        The location of the origin of the data, in units given specified by the `units`
+        attribute.
+    scale: Sequence[float]
+        The difference between adjacent coordinates of the data, in units specified by
+        the `units` attribute. Note that when converting an array index into a
+        coordinate, the scaling should be applied before translation.
+    order:
+        Defines the array indexing convention assumed by the other metadata fields.
+        Must be "C", which denotes C-ordered indexing, or "F", which denotes F-ordered
+        indexing. Tools in the N5 ecosystem express axes in "F" order, contrary to the
+        "C" order that is native to python. This attribute allows an N5-based tool to
+        express a scaling + translation in the axis order that is native to that
+        ecosystem, while retaining compatibility with python-based tools.
+
+        The default is "C".
     """
 
-    order: Optional[ArrayOrder] = "C"
+    order: Optional[Literal["C", "F"]] = "C"
     axes: Sequence[str]
     units: Sequence[str]
     translate: Sequence[float]
@@ -38,9 +60,22 @@ def validate_argument_length(
 
     def to_coords(self, shape: Tuple[int, ...]) -> List[DataArray]:
         """
-        Given an array shape (represented as a dict with dimension names as keys),
-        return a dict of numpy arrays representing a bounded coordinate grid derived
-        from this transform.
+        Given an array shape, return a list of DataArrays representing a
+        bounded coordinate grid derived from this transform. This list can be used as
+        the `coords` argument to construct a DataArray.
+
+        Parameters
+        ----------
+
+        shape: Tuple[int, ...]
+            The shape of the coordinate grid, e.g. the size of the array that will be
+            annotated with coordinates.
+
+        Returns
+        -------
+        List[DataArray]
+            A list of DataArrays, one per axis.
+
         """
         if self.order == "C":
             axes = self.axes
@@ -65,18 +100,21 @@ def from_xarray(cls, array: DataArray, reverse_axes: bool = False) -> "STTransfo
         Parameters
         ----------
 
-        array: DataArray
-
+        array: xarray.DataArray
+            A DataArray with coordinates that can be expressed as scaling + translation
+            applied to a regular grid.
         reverse_axes: boolean, default=False
-            If True, the order of the `axes` in the spatial transform will
-            be reversed relative to the order of the dimensions of `array`.
-
+            If `True`, the order of the `axes` in the spatial transform will
+            be reversed relative to the order of the dimensions of `array`, and the
+            `order` field of the resulting STTransform will be set to "F". This is
+            designed for compatibility with N5 tools.
 
         Returns
         -------
 
         STTransform
-
+            An instance of STTransform that is consistent with the coordinates defined
+            on the input DataArray.
         """
 
         orderer = slice(None)

From 2d80d8b28f8b03c7b6ae8bc197604beae8e6b7d5 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Fri, 15 Sep 2023 12:43:47 -0400
Subject: [PATCH 9/9] docs: update docstrings

---
 src/fibsem_tools/metadata/groundtruth.py | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/src/fibsem_tools/metadata/groundtruth.py b/src/fibsem_tools/metadata/groundtruth.py
index 4ac1577..62b5f4b 100644
--- a/src/fibsem_tools/metadata/groundtruth.py
+++ b/src/fibsem_tools/metadata/groundtruth.py
@@ -158,7 +158,6 @@ class AnnotationArrayAttrs(GenericModel, Generic[TName]):
         The total number of elements in the array that represent "positive" examples can
         be calculated from this histogram -- take the number of elements in the array
         minus the sum of the values in the histogram.
-
     annotation_type: SemanticSegmentation | InstanceSegmentation
         The type of the annotation. Must be either an instance of SemanticSegmentation
         or an instance of InstanceSegmentation.
@@ -194,7 +193,6 @@ class AnnotationGroupAttrs(GenericModel, Generic[TName]):
 
     class_name: str
         The name of the semantic class annotated by the data in this group.
-
     annotation_type: AnnotationType
         The type of annotation represented by the data in this group.
     """
@@ -211,37 +209,29 @@ class CropGroupAttrs(GenericModel, Generic[TName]):
     ----------
     name: Optional[str]
         The name of the crop. Optional.
-
     description: Optional[str]
         A description of the crop. Optional.
-
     created_by: list[str]
         The people or entities responsible for creating the annotations in the crop.
-
     created_with: list[str]
         The tool(s) used to create the annotations in the crop. Optional.
-
     start_date: Optional[datetime.date]
         The calendar date when the crop was started. Optional.
-
     end_date: Optional[datetime.date]
         The calendar date when the crop was completed. None may be used here if the date
         of completion is unknown, for example if the crop is not yet finished.
-
     duration_days: Optional[int]
         The number of days spent annotating the crop. Optional.
-
     protocol_uri: Optional[str]
         A URI pointing to a description of the annotation protocol used to produce the
         annotations. Optional.
-
     class_names: list[str]
         The names of the semantic classes that **could** be annotated in this crop.
-
     index: dict[str, str]
-        Each key of this dict is an element of the `class_names` attribute. Each
-        value is the relative path to the zarr group containing the label data for that
-        class name.
+        A dict that expresses the mapping from class names to relative locations of
+        Zarr Groups. Keys of this dict are elements drawn (nonexhaustively) from the
+        `class_names` attribute. Values are relative paths to the zarr groups containing
+        label data.
     """
 
     name: Optional[str]