diff --git a/poetry.lock b/poetry.lock
index 94d24ca..035f42b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,149 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand.
+
+[[package]]
+name = "aiobotocore"
+version = "2.5.4"
+description = "Async client for aws services using botocore and aiohttp"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.dependencies]
+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 (>=1.29.17,<1.29.18)"]
+boto3 = ["boto3 (>=1.28.17,<1.28.18)"]
+
+[[package]]
+name = "aiohttp"
+version = "3.9.3"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.8"
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+
+[package.dependencies]
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+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
+attrs = ">=17.3.0"
+frozenlist = ">=1.1.1"
+multidict = ">=4.5,<7.0"
+yarl = ">=1.0,<2.0"
+
+[package.extras]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
+
+[[package]]
+name = "aioitertools"
+version = "0.11.0"
+description = "itertools and builtins for AsyncIO and mixed iterables"
+optional = false
+python-versions = ">=3.6"
+files = [
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+
+[package.dependencies]
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+
+[[package]]
+name = "aiosignal"
+version = "1.3.1"
+description = "aiosignal: a list of registered asynchronous callbacks"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.dependencies]
+frozenlist = ">=1.1.0"
 
 [[package]]
 name = "alabaster"
@@ -11,6 +156,33 @@ files = [
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 ]
 
+[[package]]
+name = "anndata"
+version = "0.10.5.post1"
+description = "Annotated data."
+optional = false
+python-versions = ">=3.9"
+files = [
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+[package.dependencies]
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+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
+h5py = ">=3"
+natsort = "*"
+numpy = ">=1.16.5"
+packaging = ">=20"
+pandas = ">=1.1.1,<2.1.0rc0 || >2.1.0rc0,<2.1.2 || >2.1.2"
+scipy = ">1.4"
+
+[package.extras]
+dev = ["pytest-xdist", "setuptools-scm"]
+doc = ["awkward (>=2.0.7)", "ipython", "myst-parser", "nbsphinx", "readthedocs-sphinx-search", "scanpydoc[theme,typehints] (>=0.13.4)", "sphinx (>=4.4)", "sphinx-autodoc-typehints (>=1.11.0)", "sphinx-book-theme (>=1.1.0)", "sphinx-copybutton", "sphinx-design (>=0.5.0)", "sphinx-issues", "sphinxext-opengraph", "zarr"]
+gpu = ["cupy"]
+test = ["awkward (>=2.3)", "boltons", "dask[array,distributed]", "httpx", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow", "pytest (>=6.0)", "pytest-cov (>=2.10)", "pytest-memray", "scanpy", "scikit-learn", "zarr"]
+
 [[package]]
 name = "annotated-types"
 version = "0.6.0"
@@ -24,13 +196,13 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.2.0"
+version = "4.3.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"},
 ]
 
 [package.dependencies]
@@ -112,6 +284,21 @@ cffi = ">=1.0.1"
 dev = ["cogapp", "pre-commit", "pytest", "wheel"]
 tests = ["pytest"]
 
+[[package]]
+name = "array-api-compat"
+version = "1.4.1"
+description = "A wrapper around NumPy and other array libraries to make them compatible with the Array API standard"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "array_api_compat-1.4.1.tar.gz", hash = "sha256:053103b7c0ba73626bff7380abf27a29dc80de144394137bc7455b7eba23d8c0"},
+]
+
+[package.extras]
+cupy = ["cupy"]
+numpy = ["numpy"]
+
 [[package]]
 name = "arrow"
 version = "1.3.0"
@@ -173,6 +360,17 @@ files = [
 [package.dependencies]
 typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
+[[package]]
+name = "async-timeout"
+version = "4.0.3"
+description = "Timeout context manager for asyncio programs"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"},
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+]
+
 [[package]]
 name = "attrs"
 version = "23.2.0"
@@ -229,33 +427,33 @@ lxml = ["lxml"]
 
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 name = "black"
-version = "24.1.1"
+version = "24.2.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
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+    {file = "black-24.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ca610d29415ee1a30a3f30fab7a8f4144e9d34c89a235d81292a1edb2b55f540"},
+    {file = "black-24.2.0-cp39-cp39-win_amd64.whl", hash = "sha256:4dd76e9468d5536abd40ffbc7a247f83b2324f0c050556d9c371c2b9a9a95e31"},
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+    {file = "black-24.2.0.tar.gz", hash = "sha256:bce4f25c27c3435e4dace4815bcb2008b87e167e3bf4ee47ccdc5ce906eb4894"},
 ]
 
 [package.dependencies]
@@ -291,6 +489,25 @@ webencodings = "*"
 [package.extras]
 css = ["tinycss2 (>=1.1.0,<1.3)"]
 
+[[package]]
+name = "botocore"
+version = "1.31.17"
+description = "Low-level, data-driven core of boto 3."
+optional = false
+python-versions = ">= 3.7"
+files = [
+    {file = "botocore-1.31.17-py3-none-any.whl", hash = "sha256:6ac34a1d34aa3750e78b77b8596617e2bab938964694d651939dba2cbde2c12b"},
+    {file = "botocore-1.31.17.tar.gz", hash = "sha256:396459065dba4339eb4da4ec8b4e6599728eb89b7caaceea199e26f7d824a41c"},
+]
+
+[package.dependencies]
+jmespath = ">=0.7.1,<2.0.0"
+python-dateutil = ">=2.1,<3.0.0"
+urllib3 = ">=1.25.4,<1.27"
+
+[package.extras]
+crt = ["awscrt (==0.16.26)"]
+
 [[package]]
 name = "certifi"
 version = "2024.2.2"
@@ -479,6 +696,51 @@ files = [
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
+[[package]]
+name = "click-plugins"
+version = "1.1.1"
+description = "An extension module for click to enable registering CLI commands via setuptools entry-points."
+optional = false
+python-versions = "*"
+files = [
+    {file = "click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"},
+    {file = "click_plugins-1.1.1-py2.py3-none-any.whl", hash = "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"},
+]
+
+[package.dependencies]
+click = ">=4.0"
+
+[package.extras]
+dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"]
+
+[[package]]
+name = "cligj"
+version = "0.7.2"
+description = "Click params for commmand line interfaces to GeoJSON"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4"
+files = [
+    {file = "cligj-0.7.2-py3-none-any.whl", hash = "sha256:c1ca117dbce1fe20a5809dc96f01e1c2840f6dcc939b3ddbb1111bf330ba82df"},
+    {file = "cligj-0.7.2.tar.gz", hash = "sha256:a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27"},
+]
+
+[package.dependencies]
+click = ">=4.0"
+
+[package.extras]
+test = ["pytest-cov"]
+
+[[package]]
+name = "cloudpickle"
+version = "3.0.0"
+description = "Pickler class to extend the standard pickle.Pickler functionality"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "cloudpickle-3.0.0-py3-none-any.whl", hash = "sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"},
+    {file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"},
+]
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -490,6 +752,28 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "colorcet"
+version = "3.0.1"
+description = "Collection of perceptually uniform colormaps"
+optional = false
+python-versions = ">=2.7"
+files = [
+    {file = "colorcet-3.0.1-py2.py3-none-any.whl", hash = "sha256:8daff01824ee9935fdf762d15c444a67d3e361ad4f8b738ad59ac9bf38f30600"},
+    {file = "colorcet-3.0.1.tar.gz", hash = "sha256:51455a20353d12fac91f953772d8409f2474e6a0db1af3fa4f7005f405a2480b"},
+]
+
+[package.dependencies]
+pyct = ">=0.4.4"
+
+[package.extras]
+all = ["bokeh", "flake8", "holoviews", "matplotlib", "nbsite (>=0.7.2rc10)", "nbsmoke (>=0.2.6)", "numpy", "pyct (>=0.4.4)", "pydata-sphinx-theme (<0.9.0)", "pytest (>=2.8.5)", "pytest-cov", "pytest-mpl", "setuptools (>=30.3.0)", "sphinx-copybutton", "wheel"]
+build = ["pyct (>=0.4.4)", "setuptools (>=30.3.0)", "wheel"]
+doc = ["bokeh", "holoviews", "matplotlib", "nbsite (>=0.7.2rc10)", "numpy", "pydata-sphinx-theme (<0.9.0)", "sphinx-copybutton"]
+examples = ["bokeh", "holoviews", "matplotlib", "numpy"]
+tests = ["flake8", "nbsmoke (>=0.2.6)", "pytest (>=2.8.5)", "pytest-cov"]
+tests-extra = ["flake8", "nbsmoke (>=0.2.6)", "pytest (>=2.8.5)", "pytest-cov", "pytest-mpl"]
+
 [[package]]
 name = "comm"
 version = "0.2.1"
@@ -531,31 +815,123 @@ pandas = ["pandas"]
 rdflib = ["rdflib"]
 tests = ["coverage", "pytest"]
 
+[[package]]
+name = "dask"
+version = "2024.2.1"
+description = "Parallel PyData with Task Scheduling"
+optional = false
+python-versions = ">=3.9"
+files = [
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+    {file = "dask-2024.2.1.tar.gz", hash = "sha256:9504a1e9f5d8e5403fae931f9f1660d41f510f48895ccefce856ec6a4c2198d8"},
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+
+[package.dependencies]
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+cloudpickle = ">=1.5.0"
+fsspec = ">=2021.09.0"
+importlib-metadata = ">=4.13.0"
+numpy = {version = ">=1.21", optional = true, markers = "extra == \"array\""}
+packaging = ">=20.0"
+pandas = {version = ">=1.3", optional = true, markers = "extra == \"dataframe\""}
+partd = ">=1.2.0"
+pyyaml = ">=5.3.1"
+toolz = ">=0.10.0"
+
+[package.extras]
+array = ["numpy (>=1.21)"]
+complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)", "pyarrow-hotfix"]
+dataframe = ["dask[array]", "pandas (>=1.3)"]
+diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
+distributed = ["distributed (==2024.2.1)"]
+test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
+
+[[package]]
+name = "dask-image"
+version = "2023.8.1"
+description = "Distributed image processing"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "dask-image-2023.8.1.tar.gz", hash = "sha256:5e9a8985b0527a1b5942c6a7e744e0e57d264e222c7058f05baeb81c374d04b6"},
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+
+[package.dependencies]
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 typing = ["typing-extensions (>=4.8)"]
 
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 [[package]]
 name = "fqdn"
 version = "1.5.1"
@@ -700,77 +1153,146 @@ files = [
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+description = "File-system specification"
+optional = false
+python-versions = ">=3.8"
+files = [
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+
+[package.extras]
+abfs = ["adlfs"]
+adl = ["adlfs"]
+arrow = ["pyarrow (>=1)"]
+dask = ["dask", "distributed"]
+devel = ["pytest", "pytest-cov"]
+dropbox = ["dropbox", "dropboxdrivefs", "requests"]
+full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"]
+fuse = ["fusepy"]
+gcs = ["gcsfs"]
+git = ["pygit2"]
+github = ["requests"]
+gs = ["gcsfs"]
+gui = ["panel"]
+hdfs = ["pyarrow (>=1)"]
+http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"]
+libarchive = ["libarchive-c"]
+oci = ["ocifs"]
+s3 = ["s3fs"]
+sftp = ["paramiko"]
+smb = ["smbprotocol"]
+ssh = ["paramiko"]
+tqdm = ["tqdm"]
+
+[[package]]
+name = "geopandas"
+version = "0.14.3"
+description = "Geographic pandas extensions"
+optional = false
+python-versions = ">=3.9"
+files = [
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+    {file = "geopandas-0.14.3.tar.gz", hash = "sha256:748af035d4a068a4ae00cab384acb61d387685c833b0022e0729aa45216b23ac"},
+]
+
+[package.dependencies]
+fiona = ">=1.8.21"
+packaging = "*"
+pandas = ">=1.4.0"
+pyproj = ">=3.3.0"
+shapely = ">=1.8.0"
 
 [[package]]
 name = "h11"
@@ -833,13 +1355,13 @@ files = [
 
 [[package]]
 name = "httpcore"
-version = "1.0.2"
+version = "1.0.4"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-1.0.2-py3-none-any.whl", hash = "sha256:096cc05bca73b8e459a1fc3dcf585148f63e534eae4339559c9b8a8d6399acc7"},
-    {file = "httpcore-1.0.2.tar.gz", hash = "sha256:9fc092e4799b26174648e54b74ed5f683132a464e95643b226e00c2ed2fa6535"},
+    {file = "httpcore-1.0.4-py3-none-any.whl", hash = "sha256:ac418c1db41bade2ad53ae2f3834a3a0f5ae76b56cf5aa497d2d033384fc7d73"},
+    {file = "httpcore-1.0.4.tar.gz", hash = "sha256:cb2839ccfcba0d2d3c1131d3c3e26dfc327326fbe7a5dc0dbfe9f6c9151bb022"},
 ]
 
 [package.dependencies]
@@ -850,17 +1372,17 @@ h11 = ">=0.13,<0.15"
 asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
-trio = ["trio (>=0.22.0,<0.23.0)"]
+trio = ["trio (>=0.22.0,<0.25.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.26.0"
+version = "0.27.0"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.26.0-py3-none-any.whl", hash = "sha256:8915f5a3627c4d47b73e8202457cb28f1266982d1159bd5779d86a80c0eab1cd"},
-    {file = "httpx-0.26.0.tar.gz", hash = "sha256:451b55c30d5185ea6b23c2c793abf9bb237d2a7dfb901ced6ff69ad37ec1dfaf"},
+    {file = "httpx-0.27.0-py3-none-any.whl", hash = "sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5"},
+    {file = "httpx-0.27.0.tar.gz", hash = "sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5"},
 ]
 
 [package.dependencies]
@@ -887,6 +1409,38 @@ files = [
     {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
+[[package]]
+name = "imageio"
+version = "2.34.0"
+description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "imageio-2.34.0-py3-none-any.whl", hash = "sha256:08082bf47ccb54843d9c73fe9fc8f3a88c72452ab676b58aca74f36167e8ccba"},
+    {file = "imageio-2.34.0.tar.gz", hash = "sha256:ae9732e10acf807a22c389aef193f42215718e16bd06eed0c5bb57e1034a4d53"},
+]
+
+[package.dependencies]
+numpy = "*"
+pillow = ">=8.3.2"
+
+[package.extras]
+all-plugins = ["astropy", "av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
+all-plugins-pypy = ["av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
+build = ["wheel"]
+dev = ["black", "flake8", "fsspec[github]", "pytest", "pytest-cov"]
+docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"]
+ffmpeg = ["imageio-ffmpeg", "psutil"]
+fits = ["astropy"]
+full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpydoc", "pillow-heif", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
+gdal = ["gdal"]
+itk = ["itk"]
+linting = ["black", "flake8"]
+pillow-heif = ["pillow-heif"]
+pyav = ["av"]
+test = ["fsspec[github]", "pytest", "pytest-cov"]
+tifffile = ["tifffile"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
@@ -930,13 +1484,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.29.2"
+version = "6.29.3"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.29.2-py3-none-any.whl", hash = "sha256:50384f5c577a260a1d53f1f59a828c7266d321c9b7d00d345693783f66616055"},
-    {file = "ipykernel-6.29.2.tar.gz", hash = "sha256:3bade28004e3ff624ed57974948116670604ac5f676d12339693f3142176d3f0"},
+    {file = "ipykernel-6.29.3-py3-none-any.whl", hash = "sha256:5aa086a4175b0229d4eca211e181fb473ea78ffd9869af36ba7694c947302a21"},
+    {file = "ipykernel-6.29.3.tar.gz", hash = "sha256:e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2"},
 ]
 
 [package.dependencies]
@@ -959,7 +1513,7 @@ cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (==0.23.4)", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
@@ -1083,6 +1637,17 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "jmespath"
+version = "1.0.1"
+description = "JSON Matching Expressions"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"},
+    {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
+]
+
 [[package]]
 name = "json-flattener"
 version = "0.1.9"
@@ -1100,13 +1665,13 @@ pyyaml = "*"
 
 [[package]]
 name = "json5"
-version = "0.9.14"
+version = "0.9.17"
 description = "A Python implementation of the JSON5 data format."
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "json5-0.9.14-py2.py3-none-any.whl", hash = "sha256:740c7f1b9e584a468dbb2939d8d458db3427f2c93ae2139d05f47e453eae964f"},
-    {file = "json5-0.9.14.tar.gz", hash = "sha256:9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02"},
+    {file = "json5-0.9.17-py2.py3-none-any.whl", hash = "sha256:f8ec1ecf985951d70f780f6f877c4baca6a47b6e61e02c4cd190138d10a7805a"},
+    {file = "json5-0.9.17.tar.gz", hash = "sha256:717d99d657fa71b7094877b1d921b1cce40ab444389f6d770302563bb7dfd9ae"},
 ]
 
 [package.extras]
@@ -1294,13 +1859,13 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 
 [[package]]
 name = "jupyter-lsp"
-version = "2.2.2"
+version = "2.2.3"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter-lsp-2.2.2.tar.gz", hash = "sha256:256d24620542ae4bba04a50fc1f6ffe208093a07d8e697fea0a8d1b8ca1b7e5b"},
-    {file = "jupyter_lsp-2.2.2-py3-none-any.whl", hash = "sha256:3b95229e4168355a8c91928057c1621ac3510ba98b2a925e82ebd77f078b1aa5"},
+    {file = "jupyter-lsp-2.2.3.tar.gz", hash = "sha256:33dbcbc5df24237ff5c8b696b04ff4689fcd316cb8d4957d620fe5504d7d2c3f"},
+    {file = "jupyter_lsp-2.2.3-py3-none-any.whl", hash = "sha256:57dd90d0a2e2530831793550846168c81c952b49e187aa339e455027a5f0fd2e"},
 ]
 
 [package.dependencies]
@@ -1364,13 +1929,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.1.0"
+version = "4.1.2"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1390,7 +1955,7 @@ tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.1.15)"]
+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.2.0)"]
 docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<7.3.0)", "sphinx-copybutton"]
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@@ -1408,13 +1973,13 @@ files = [
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.25.2"
+version = "2.25.3"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1443,15 +2008,30 @@ files = [
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 ]
 
+[[package]]
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+version = "0.3"
+description = "lazy_loader"
+optional = false
+python-versions = ">=3.7"
+files = [
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+
+[package.extras]
+lint = ["pre-commit (>=3.3)"]
+test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"]
+
 [[package]]
 name = "linkml-runtime"
-version = "1.7.0"
+version = "1.7.2"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8,<4.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1469,6 +2049,47 @@ pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = "*"
 
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+[[package]]
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+version = "1.0.0"
+description = "File-based locks for Python on Linux and Windows"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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 [[package]]
 name = "markdown-it-py"
 version = "2.2.0"
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 ]
 
+[[package]]
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+description = "MessagePack serializer"
+optional = false
+python-versions = ">=3.8"
+files = [
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+[[package]]
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+description = "Generate a multiscale, chunked, multi-dimensional spatial image data structure that can be serialized to OME-NGFF."
+optional = false
+python-versions = ">=3.8"
+files = [
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+xarray-datatree = ">=0.0.5"
+
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+itk = ["itk-filtering (>=5.3.0)"]
+test = ["dask-image", "fsspec", "ipfsspec", "itk-filtering (>=5.3.0)", "jsonschema", "nbmake", "pooch", "pytest", "pytest-mypy", "urllib3", "zarr"]
+
 [[package]]
 name = "mypy"
 version = "1.8.0"
@@ -1701,6 +2520,21 @@ linkify = ["linkify-it-py (>=1.0,<2.0)"]
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+[[package]]
+name = "natsort"
+version = "8.4.0"
+description = "Simple yet flexible natural sorting in Python."
+optional = false
+python-versions = ">=3.7"
+files = [
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+icu = ["PyICU (>=1.0.0)"]
+
 [[package]]
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 version = "0.9.0"
@@ -1725,13 +2559,13 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
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-description = "Converting Jupyter Notebooks"
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+description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
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-    {file = "nbconvert-7.16.0.tar.gz", hash = "sha256:813e6553796362489ae572e39ba1bff978536192fb518e10826b0e8cadf03ec8"},
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 ]
 
 [package.dependencies]
@@ -1794,19 +2628,37 @@ files = [
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 [[package]]
-name = "notebook"
-version = "7.0.7"
-description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
+name = "networkx"
+version = "3.2.1"
+description = "Python package for creating and manipulating graphs and networks"
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-python-versions = ">=3.8"
+python-versions = ">=3.9"
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-[package.dependencies]
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+test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
+
+[[package]]
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+description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
+optional = false
+python-versions = ">=3.8"
+files = [
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 jupyterlab-server = ">=2.22.1,<3"
 notebook-shim = ">=0.2,<0.3"
 tornado = ">=6.2.0"
@@ -1818,13 +2670,13 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4
 
 [[package]]
 name = "notebook-shim"
-version = "0.2.3"
+version = "0.2.4"
 description = "A shim layer for notebook traits and config"
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -1855,6 +2707,40 @@ dev = ["autoflake", "beartype (<0.10.0)", "beartype (>=0.10.0)", "black", "codec
 pandas = ["pandas", "pandas-stubs-fork"]
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+description = "compiling Python code using LLVM"
+optional = false
+python-versions = ">=3.9"
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+numpy = ">=1.22,<1.27"
+
 [[package]]
 name = "numcodecs"
 version = "0.12.1"
@@ -1895,6 +2781,43 @@ test = ["coverage", "flake8", "pytest", "pytest-cov"]
 test-extras = ["importlib-metadata"]
 zfpy = ["zfpy (>=1.0.0)"]
 
+[[package]]
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+description = "NumPy is the fundamental package for array computing with Python."
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@@ -2029,6 +2974,7 @@ parquet = ["pyarrow (>=10.0.1)"]
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 postgresql = ["SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "psycopg2 (>=2.9.6)"]
+pyarrow = ["pyarrow (>=10.0.1)"]
 spss = ["pyreadstat (>=1.2.0)"]
 sql-other = ["SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "adbc-driver-sqlite (>=0.8.0)"]
 test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
@@ -2045,6 +2991,27 @@ files = [
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 ]
 
+[[package]]
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+description = "Make your Python code clearer and more reliable by declaring Parameters."
+optional = false
+python-versions = ">=3.8"
+files = [
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+
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+examples = ["aiohttp", "pandas", "panel"]
+lint = ["flake8", "pre-commit"]
+tests = ["coverage[toml]", "pytest", "pytest-asyncio"]
+tests-deser = ["odfpy", "openpyxl", "pyarrow", "tables", "xlrd"]
+tests-examples = ["nbval", "param[examples]", "pytest", "pytest-asyncio", "pytest-xdist"]
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+
 [[package]]
 name = "parso"
 version = "0.8.3"
@@ -2060,6 +3027,24 @@ files = [
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
 testing = ["docopt", "pytest (<6.0.0)"]
 
+[[package]]
+name = "partd"
+version = "1.4.1"
+description = "Appendable key-value storage"
+optional = false
+python-versions = ">=3.7"
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+toolz = "*"
+
+[package.extras]
+complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
+
 [[package]]
 name = "pathspec"
 version = "0.12.1"
@@ -2085,6 +3070,106 @@ files = [
 [package.dependencies]
 ptyprocess = ">=0.5"
 
+[[package]]
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+description = "Python Imaging Library (Fork)"
+optional = false
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+xmp = ["defusedxml"]
+
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 win32 = ["pywin32"]
 
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 [[package]]
@@ -2975,6 +4432,64 @@ files = [
     {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
 ]
 
+[[package]]
+name = "spatial-image"
+version = "0.3.0"
+description = "spatial-image"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "spatial_image-0.3.0-py3-none-any.whl", hash = "sha256:aa4bd9a6c538146c00ac7f27fa05cad1070174df8522f88db10e680622dd8211"},
+    {file = "spatial_image-0.3.0.tar.gz", hash = "sha256:508ed434d1cdba5147c1dd358aea0ea41a0f913b02a73e0fd36fcbdbee14b40d"},
+]
+
+[package.dependencies]
+numpy = "*"
+xarray = "*"
+xarray-dataclasses = ">=1.1.0"
+
+[package.extras]
+test = ["pytest", "pytest-mypy"]
+
+[[package]]
+name = "spatialdata"
+version = "0.0.15"
+description = "Spatial data format."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "spatialdata-0.0.15-py3-none-any.whl", hash = "sha256:4660d77694018bf772ddc26845aae797fde5b07ef8bebd2fdf9063f560a6232a"},
+    {file = "spatialdata-0.0.15.tar.gz", hash = "sha256:7372b13b9fa84c0eadcbfca2f2cd354a9ae8dd370401745d55d572864eb4dc75"},
+]
+
+[package.dependencies]
+anndata = ">=0.9.1"
+dask-image = "*"
+fsspec = "<=2023.6"
+geopandas = "*"
+multiscale-spatial-image = "0.11.2"
+networkx = "*"
+numpy = "*"
+ome-zarr = ">=0.7.0"
+pyarrow = "*"
+pygeos = "*"
+rich = "*"
+shapely = ">=2.0.1"
+spatial-image = "0.3.0"
+tqdm = "*"
+typing-extensions = ">=4.8.0"
+xarray = "*"
+xarray-schema = "*"
+xarray-spatial = ">=0.3.5"
+zarr = "*"
+
+[package.extras]
+dev = ["bump2version"]
+docs = ["ipython (>=8.6.0)", "myst-nb", "sphinx (>=4.5)", "sphinx-autodoc-typehints", "sphinx-book-theme (>=1.0.0)", "sphinx-copybutton", "sphinx-design", "sphinx-rtd-theme", "sphinxcontrib-bibtex (>=1.0.0)"]
+extra = ["napari-spatialdata (>=0.2.4)", "spatialdata-io", "spatialdata-plot"]
+test = ["pytest", "pytest-cov"]
+torch = ["torch"]
+
 [[package]]
 name = "sphinx"
 version = "5.3.0"
@@ -3194,6 +4709,17 @@ pure-eval = "*"
 [package.extras]
 tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
+[[package]]
+name = "tblib"
+version = "3.0.0"
+description = "Traceback serialization library."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "tblib-3.0.0-py3-none-any.whl", hash = "sha256:80a6c77e59b55e83911e1e607c649836a69c103963c5f28a46cbeef44acf8129"},
+    {file = "tblib-3.0.0.tar.gz", hash = "sha256:93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6"},
+]
+
 [[package]]
 name = "terminado"
 version = "0.18.0"
@@ -3215,6 +4741,23 @@ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
 typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
+[[package]]
+name = "tifffile"
+version = "2024.2.12"
+description = "Read and write TIFF files"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "tifffile-2024.2.12-py3-none-any.whl", hash = "sha256:870998f82fbc94ff7c3528884c1b0ae54863504ff51dbebea431ac3fa8fb7c21"},
+    {file = "tifffile-2024.2.12.tar.gz", hash = "sha256:4920a3ec8e8e003e673d3c6531863c99eedd570d1b8b7e141c072ed78ff8030d"},
+]
+
+[package.dependencies]
+numpy = "*"
+
+[package.extras]
+all = ["defusedxml", "fsspec", "imagecodecs (>=2023.8.12)", "lxml", "matplotlib", "zarr"]
+
 [[package]]
 name = "tinycss2"
 version = "1.2.1"
@@ -3244,6 +4787,17 @@ files = [
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
+[[package]]
+name = "toolz"
+version = "0.12.1"
+description = "List processing tools and functional utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
+    {file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
+]
+
 [[package]]
 name = "tornado"
 version = "6.4"
@@ -3289,6 +4843,26 @@ virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,
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 testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psutil (>=5.6.1)", "pytest (>=4.0.0)", "pytest-cov (>=2.5.1)", "pytest-mock (>=1.10.0)", "pytest-randomly (>=1.0.0)"]
 
+[[package]]
+name = "tqdm"
+version = "4.66.2"
+description = "Fast, Extensible Progress Meter"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tqdm-4.66.2-py3-none-any.whl", hash = "sha256:1ee4f8a893eb9bef51c6e35730cebf234d5d0b6bd112b0271e10ed7c24a02bd9"},
+    {file = "tqdm-4.66.2.tar.gz", hash = "sha256:6cd52cdf0fef0e0f543299cfc96fec90d7b8a7e88745f411ec33eb44d5ed3531"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
+[package.extras]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
+telegram = ["requests"]
+
 [[package]]
 name = "traitlets"
 version = "5.14.1"
@@ -3317,24 +4891,24 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.9.0"
+version = "4.10.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
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+    {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"},
+    {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
 ]
 
 [[package]]
 name = "tzdata"
-version = "2023.4"
+version = "2024.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2023.4-py2.py3-none-any.whl", hash = "sha256:aa3ace4329eeacda5b7beb7ea08ece826c28d761cda36e747cfbf97996d39bf3"},
-    {file = "tzdata-2023.4.tar.gz", hash = "sha256:dd54c94f294765522c77399649b4fefd95522479a664a0cec87f41bebc6148c9"},
+    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
+    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
 ]
 
 [[package]]
@@ -3353,30 +4927,29 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.2.0"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
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+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
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 [package.extras]
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-h2 = ["h2 (>=4,<5)"]
-socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
+brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
+socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.25.0"
+version = "20.25.1"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
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+    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
+    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
 ]
 
 [package.dependencies]
@@ -3533,19 +5106,19 @@ files = [
 
 [[package]]
 name = "xarray"
-version = "2024.1.1"
+version = "2023.12.0"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "xarray-2024.1.1-py3-none-any.whl", hash = "sha256:0bec81303b088c8df4f075e1579c00cfd7e5069688e4434007f0b8d7df17fc1c"},
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+    {file = "xarray-2023.12.0-py3-none-any.whl", hash = "sha256:3c22b6824681762b6c3fcad86dfd18960a617bccbc7f456ce21b43a20e455fb9"},
+    {file = "xarray-2023.12.0.tar.gz", hash = "sha256:4565dbc890de47e278346c44d6b33bb07d3427383e077a7ca8ab6606196fd433"},
 ]
 
 [package.dependencies]
-numpy = ">=1.23"
-packaging = ">=22"
-pandas = ">=1.5"
+numpy = ">=1.22"
+packaging = ">=21.3"
+pandas = ">=1.4"
 
 [package.extras]
 accel = ["bottleneck", "flox", "numbagg", "opt-einsum", "scipy"]
@@ -3554,27 +5127,230 @@ io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zar
 parallel = ["dask[complete]"]
 viz = ["matplotlib", "nc-time-axis", "seaborn"]
 
+[[package]]
+name = "xarray-dataclasses"
+version = "1.7.0"
+description = "xarray data creation made easy by dataclass"
+optional = false
+python-versions = ">=3.8,<3.13"
+files = [
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+    {file = "xarray_dataclasses-1.7.0.tar.gz", hash = "sha256:b82b454c5800bf9d488c188d6362428e6bc310d2fc35f96fa4063efa40d33267"},
+]
+
+[package.dependencies]
+numpy = {version = ">=1.22,<2.0", markers = "python_version >= \"3.9\" and python_version < \"3.13\""}
+typing-extensions = ">=4.0,<5.0"
+xarray = {version = ">=2022.3,<2024.0", markers = "python_version >= \"3.9\" and python_version < \"3.13\""}
+
+[[package]]
+name = "xarray-datatree"
+version = "0.0.14"
+description = "Hierarchical tree-like data structures for xarray"
+optional = false
+python-versions = ">=3.9"
+files = [
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+
+[package.dependencies]
+packaging = "*"
+xarray = ">=2023.12.0"
+
+[[package]]
+name = "xarray-schema"
+version = "0.0.3"
+description = "Schema validation for Xarray objects"
+optional = false
+python-versions = ">=3.8"
+files = [
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+[package.dependencies]
+numpy = ">=1.21"
+xarray = ">=0.16"
+
+[[package]]
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+version = "0.3.5"
+description = "xarray-based spatial analysis tools"
+optional = false
+python-versions = ">=3.7"
+files = [
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+optional = ["awkward (>=1.4)", "geopandas", "rtxpy", "shapely", "spatialpandas"]
+tests = ["flake8", "isort", "noise (>=1.2.2)", "pytest", "pytest-cov"]
+
+[[package]]
+name = "xarray-spatial"
+version = "0.3.7"
+description = "xarray-based spatial analysis tools"
+optional = false
+python-versions = ">=3.7"
+files = [
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+tests = ["flake8", "isort", "noise (>=1.2.2)", "pytest", "pytest-cov"]
+
+[[package]]
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+optional = false
+python-versions = ">=3.7"
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+    {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
+
 [[package]]
 name = "zarr"
-version = "2.16.1"
+version = "2.17.0"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
-    {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"},
+    {file = "zarr-2.17.0-py3-none-any.whl", hash = "sha256:d287cb61019c4a0a0f386f76eeaa7f0b1160b1cb90cf96173a4b6cbc135df6e1"},
+    {file = "zarr-2.17.0.tar.gz", hash = "sha256:6390a2b8af31babaab4c963efc45bf1da7f9500c9aafac193f84cf019a7c66b0"},
 ]
 
 [package.dependencies]
 asciitree = "*"
-fasteners = "*"
+fasteners = {version = "*", markers = "sys_platform != \"emscripten\""}
 numcodecs = ">=0.10.0"
-numpy = ">=1.20,<1.21.0 || >1.21.0"
+numpy = ">=1.21.1"
 
 [package.extras]
-docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"]
+docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-automodapi", "sphinx-copybutton", "sphinx-design", "sphinx-issues"]
 jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
+[[package]]
+name = "zict"
+version = "3.0.0"
+description = "Mutable mapping tools"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zict-3.0.0-py2.py3-none-any.whl", hash = "sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae"},
+    {file = "zict-3.0.0.tar.gz", hash = "sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5"},
+]
+
 [[package]]
 name = "zipp"
 version = "3.17.0"
@@ -3596,5 +5372,5 @@ jupyter = []
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.9"
-content-hash = "367b60c6639a725f4bd9a2ef837dbca12ee3a32cf0fe8a71f5684e5515981d93"
+python-versions = ">=3.9,<3.13"
+content-hash = "693c62b4a731ddfe85c358ca47c04bbf3a688a446583ec14aee26777382118b1"
diff --git a/pyproject.toml b/pyproject.toml
index a314337..d882061 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,13 +7,11 @@ license = "BSD-3"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = ">=3.9,<3.13"
+botocore = "1.31.17" # Setting this version is not a hard requirement but reduces resolving time to less than 1 min.
+spatialdata = "^0.0.15" # includes numpy, zarr, h5py etc..
 linkml-runtime = ">=1.7.0"
-numpy = ">=1.24.3"
-h5py = ">=3.9.0"
-zarr = ">=2.16.1"
 nptyping = ">=2.5.0"
-xarray = "^2024.1.1"
 tox = "^3.25.1"  # TODO move out of main deps
 
 [tool.poetry.dev-dependencies]
@@ -45,6 +43,10 @@ black = "^24.1.1"
 pytest = "^7.1.2"
 mypy = "^1.8.0"
 
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+xfail_strict = true
+
 [tool.poetry-dynamic-versioning]
 enable = true
 vcs = "git"
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..6d5c79d
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,248 @@
+"""Pytest fixture and helper functions to create a SpatialData object during test time."""
+
+from typing import Union
+
+import numpy as np
+import pandas as pd
+import pyarrow as pa
+import pytest
+from anndata import AnnData
+from geopandas import GeoDataFrame
+from multiscale_spatial_image import MultiscaleSpatialImage
+from numpy.random import default_rng
+from shapely.geometry import MultiPolygon, Point, Polygon
+from spatial_image import SpatialImage
+from spatialdata import SpatialData
+from spatialdata.models import (
+    Image2DModel,
+    Image3DModel,
+    Labels2DModel,
+    Labels3DModel,
+    PointsModel,
+    ShapesModel,
+    TableModel,
+)
+from xarray import DataArray
+
+# Added from https://github.com/scverse/spatialdata-plot
+
+RNG = default_rng()
+
+
+@pytest.fixture()
+def full_sdata() -> SpatialData:
+    """Create SpatialData object."""
+    return SpatialData(
+        images=_get_images(),
+        labels=_get_labels(),
+        shapes=_get_shapes(),
+        points=_get_points(),
+        table=_get_table(region="sample1"),
+    )
+
+
+def _get_images() -> dict[str, Union[SpatialImage, MultiscaleSpatialImage]]:
+    out = {}
+    dims_2d = ("c", "y", "x")
+    dims_3d = ("z", "y", "x", "c")
+    out["image2d"] = Image2DModel.parse(
+        RNG.normal(size=(3, 64, 64)), dims=dims_2d, c_coords=["r", "g", "b"]
+    )
+    out["image2d_multiscale"] = Image2DModel.parse(
+        RNG.normal(size=(3, 64, 64)), scale_factors=[2, 2], dims=dims_2d, c_coords=["r", "g", "b"]
+    )
+    out["image2d_xarray"] = Image2DModel.parse(
+        DataArray(RNG.normal(size=(3, 64, 64)), dims=dims_2d), dims=None
+    )
+    out["image2d_multiscale_xarray"] = Image2DModel.parse(
+        DataArray(RNG.normal(size=(3, 64, 64)), dims=dims_2d),
+        scale_factors=[2, 4],
+        dims=None,
+    )
+    out["image3d_numpy"] = Image3DModel.parse(RNG.normal(size=(2, 64, 64, 3)), dims=dims_3d)
+    out["image3d_multiscale_numpy"] = Image3DModel.parse(
+        RNG.normal(size=(2, 64, 64, 3)), scale_factors=[2], dims=dims_3d
+    )
+    out["image3d_xarray"] = Image3DModel.parse(
+        DataArray(RNG.normal(size=(2, 64, 64, 3)), dims=dims_3d), dims=None
+    )
+    out["image3d_multiscale_xarray"] = Image3DModel.parse(
+        DataArray(RNG.normal(size=(2, 64, 64, 3)), dims=dims_3d),
+        scale_factors=[2],
+        dims=None,
+    )
+    return out
+
+
+def _get_labels() -> dict[str, Union[SpatialImage, MultiscaleSpatialImage]]:
+    out = {}
+    dims_2d = ("y", "x")
+    dims_3d = ("z", "y", "x")
+
+    out["labels2d"] = Labels2DModel.parse(RNG.integers(0, 100, size=(64, 64)), dims=dims_2d)
+    out["labels2d_multiscale"] = Labels2DModel.parse(
+        RNG.integers(0, 100, size=(64, 64)), scale_factors=[2, 4], dims=dims_2d
+    )
+    out["labels2d_xarray"] = Labels2DModel.parse(
+        DataArray(RNG.integers(0, 100, size=(64, 64)), dims=dims_2d), dims=None
+    )
+    out["labels2d_multiscale_xarray"] = Labels2DModel.parse(
+        DataArray(RNG.integers(0, 100, size=(64, 64)), dims=dims_2d),
+        scale_factors=[2, 4],
+        dims=None,
+    )
+    out["labels3d_numpy"] = Labels3DModel.parse(
+        RNG.integers(0, 100, size=(10, 64, 64)), dims=dims_3d
+    )
+    out["labels3d_multiscale_numpy"] = Labels3DModel.parse(
+        RNG.integers(0, 100, size=(10, 64, 64)), scale_factors=[2, 4], dims=dims_3d
+    )
+    out["labels3d_xarray"] = Labels3DModel.parse(
+        DataArray(RNG.integers(0, 100, size=(10, 64, 64)), dims=dims_3d), dims=None
+    )
+    out["labels3d_multiscale_xarray"] = Labels3DModel.parse(
+        DataArray(RNG.integers(0, 100, size=(10, 64, 64)), dims=dims_3d),
+        scale_factors=[2, 4],
+        dims=None,
+    )
+    return out
+
+
+def _get_polygons() -> dict[str, GeoDataFrame]:
+    out = {}
+    poly = GeoDataFrame(
+        {
+            "geometry": [
+                Polygon(((0, 0), (0, 1), (1, 1), (1, 0))),
+                Polygon(((0, 0), (0, -1), (-1, -1), (-1, 0))),
+                Polygon(((0, 0), (0, 1), (1, 10))),
+                Polygon(((0, 0), (0, 1), (1, 1))),
+                Polygon(((0, 0), (0, 1), (1, 1), (1, 0), (1, 0))),
+            ]
+        }
+    )
+
+    multipoly = GeoDataFrame(
+        {
+            "geometry": [
+                MultiPolygon(
+                    [
+                        Polygon(((0, 0), (0, 1), (1, 1), (1, 0))),
+                        Polygon(((0, 0), (0, -1), (-1, -1), (-1, 0))),
+                    ]
+                ),
+                MultiPolygon(
+                    [
+                        Polygon(((0, 0), (0, 1), (1, 10))),
+                        Polygon(((0, 0), (0, 1), (1, 1))),
+                        Polygon(((0, 0), (0, 1), (1, 1), (1, 0), (1, 0))),
+                    ]
+                ),
+            ]
+        }
+    )
+
+    out["poly"] = ShapesModel.parse(poly, name="poly")
+    out["multipoly"] = ShapesModel.parse(multipoly, name="multipoly")
+
+    return out
+
+
+def _get_shapes() -> dict[str, AnnData]:
+    out = {}
+    poly = GeoDataFrame(
+        {
+            "geometry": [
+                Polygon(((0, 0), (0, 1), (1, 1), (1, 0))),
+                Polygon(((0, 0), (0, -1), (-1, -1), (-1, 0))),
+                Polygon(((0, 0), (0, 1), (1, 10))),
+                Polygon(((10, 10), (10, 20), (20, 20))),
+                Polygon(((0, 0), (0, 1), (1, 1), (1, 0), (1, 0))),
+            ]
+        }
+    )
+
+    multipoly = GeoDataFrame(
+        {
+            "geometry": [
+                MultiPolygon(
+                    [
+                        Polygon(((0, 0), (0, 1), (1, 1), (1, 0))),
+                        Polygon(((0, 0), (0, -1), (-1, -1), (-1, 0))),
+                    ]
+                ),
+                MultiPolygon(
+                    [
+                        Polygon(((0, 0), (0, 1), (1, 10))),
+                        Polygon(((0, 0), (1, 0), (1, 1))),
+                    ]
+                ),
+            ]
+        }
+    )
+
+    points = GeoDataFrame(
+        {
+            "geometry": [
+                Point((0, 1)),
+                Point((1, 1)),
+                Point((3, 4)),
+                Point((4, 2)),
+                Point((5, 6)),
+            ]
+        }
+    )
+    rng = np.random.default_rng(seed=0)
+    points["radius"] = np.abs(rng.normal(size=(len(points), 1)))
+
+    out["poly"] = ShapesModel.parse(poly)
+    out["poly"].index = [0, 1, 2, 3, 4]
+    out["multipoly"] = ShapesModel.parse(multipoly)
+    out["circles"] = ShapesModel.parse(points)
+
+    return out
+
+
+def _get_points() -> dict[str, pa.Table]:
+    name = "points"
+    out = {}
+    for i in range(2):
+        name = f"{name}_{i}"
+        arr = RNG.normal(size=(300, 2))
+        # randomly assign some values from v to the points
+        points_assignment0 = RNG.integers(0, 10, size=arr.shape[0]).astype(np.int_)
+        if i == 0:
+            genes = RNG.choice(["a", "b"], size=arr.shape[0])
+        else:
+            genes = np.tile(np.array(list(map(str, range(280)))), 2)[:300]
+        annotation = pd.DataFrame(
+            {
+                "genes": genes,
+                "instance_id": points_assignment0,
+            },
+        )
+        out[name] = PointsModel.parse(
+            arr, annotation=annotation, feature_key="genes", instance_key="instance_id"
+        )
+    return out
+
+
+def _get_table(
+    region: None | str | list[str] = "sample1",
+    region_key: None | str = "region",
+    instance_key: None | str = "instance_id",
+) -> AnnData:
+    adata = AnnData(
+        RNG.normal(size=(100, 10)),
+        obs=pd.DataFrame(RNG.normal(size=(100, 3)), columns=["a", "b", "c"]),
+    )
+    if not all(var for var in (region, region_key, instance_key)):
+        return TableModel.parse(adata=adata)
+    adata.obs[instance_key] = np.arange(adata.n_obs)
+    if isinstance(region, str):
+        adata.obs[region_key] = region
+    elif isinstance(region, list):
+        adata.obs[region_key] = RNG.choice(region, size=adata.n_obs)
+    return TableModel.parse(
+        adata=adata, region=region, region_key=region_key, instance_key=instance_key
+    )
diff --git a/tests/test_dumpers/array_classes.py b/tests/test_dumpers/array_classes.py
index 1656a5c..8944597 100644
--- a/tests/test_dumpers/array_classes.py
+++ b/tests/test_dumpers/array_classes.py
@@ -1,7 +1,8 @@
 from __future__ import annotations
-import numpy as np
-from pydantic import BaseModel as BaseModel, ConfigDict, Field
 
+import numpy as np
+from pydantic import BaseModel as BaseModel
+from pydantic import ConfigDict, Field
 
 metamodel_version = "None"
 version = "None"
diff --git a/tests/test_spatialdata/__init__.py b/tests/test_spatialdata/__init__.py
new file mode 100644
index 0000000..403afe5
--- /dev/null
+++ b/tests/test_spatialdata/__init__.py
@@ -0,0 +1 @@
+"""Test for writing and reading SpatialData using pytest fixture."""
diff --git a/tests/test_spatialdata/test_spatialdata_temp.py b/tests/test_spatialdata/test_spatialdata_temp.py
new file mode 100644
index 0000000..6a43cf0
--- /dev/null
+++ b/tests/test_spatialdata/test_spatialdata_temp.py
@@ -0,0 +1,19 @@
+"""Test writing and reading of SpatialData using fixture."""
+
+from pathlib import Path
+
+from spatialdata import SpatialData
+
+
+class TestWriteRead:
+    """Test writing and reading using pytest fixture."""
+
+    def test_write_read(
+        self,
+        tmp_path: str,
+        full_sdata: SpatialData,
+    ) -> None:
+        """Test writing and reading a SpatialData object with all elements present."""
+        tmpdir = Path(tmp_path) / "tmp.zarr"
+        full_sdata.write(tmpdir)
+        SpatialData.read(tmpdir)