diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 30c2c1741..4413211c8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,23 +15,22 @@ repos:
     hooks:
       - id: isort
         files: ^python/cucim/src/.*
-        args: ["--settings-path=python/cucim/pyproject_.toml"]
+        args: ["--settings-path=python/cucim/pyproject.toml"]
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
       - id: black
         files: (python|legate)/.*
-        args: ["--config", "python/cucim/pyproject_.toml"]
+        args: ["--config", "python/cucim/pyproject.toml"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.0.278
     hooks:
       - id: ruff
         files: python/.*$
-        args: ["--exclude", "__init__.py"]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4
     hooks:
       - id: codespell
-        args: ["--toml", "python/cucim/pyproject_.toml"]
+        args: ["--toml", "python/cucim/pyproject.toml"]
         additional_dependencies:
           - tomli
diff --git a/conda/recipes/cucim/build.sh b/conda/recipes/cucim/build.sh
index 28b1112c2..cd484ce48 100644
--- a/conda/recipes/cucim/build.sh
+++ b/conda/recipes/cucim/build.sh
@@ -18,6 +18,6 @@ cp -P python/install/lib/* python/cucim/src/cucim/clara/
 pushd python/cucim
 
 echo "PYTHON: ${PYTHON}"
-$PYTHON setup.py install
+$PYTHON -m pip install .
 
 popd
diff --git a/python/cucim/pyproject.toml b/python/cucim/pyproject.toml
new file mode 100644
index 000000000..6534906ba
--- /dev/null
+++ b/python/cucim/pyproject.toml
@@ -0,0 +1,241 @@
+# Copyright (c) 2023, NVIDIA CORPORATION. All rights reserved.
+# See file LICENSE for terms.
+
+[build-system]
+build-backend = "setuptools.build_meta"
+# TODO: generate this list with `rapids-dependency-file-generator`
+requires = [
+    "setuptools>=24.2.0",
+    "wheel",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+
+[project]
+name = "cucim"
+version = "23.12.00"
+description = "cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image processing primitives for N-Dimensional images with a focus on biomedical imaging."
+# TODO: tried also adding CHANGELOG.md as in setup.py's long_description, but ruff complained about it
+readme = { file = "README.md", content-type = "text/markdown" }
+# readme = [
+#     { file = "README.md", content-type = "text/markdown" },
+#     { file = "CHANGELOG.md", content-type = "text/markdown" },
+# ]
+authors = [
+    { name = "NVIDIA Corporation" },
+]
+license = { text = "Apache 2.0" }
+requires-python = ">=3.8"
+#TODO: add dependencies.yaml and generate this by `rapids-dependency-file-generator` instead
+dependencies = [
+    "click",
+    "numpy",
+    "lazy_loader>=0.1",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Healthcare Industry",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: POSIX :: Linux",
+    "Environment :: Console",
+    "Environment :: GPU :: NVIDIA CUDA :: 11.0",
+    "Environment :: GPU :: NVIDIA CUDA :: 12.0",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: C++",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+
+[project.urls]
+Homepage = "https://developer.nvidia.com/multidimensional-image-processing"
+Documentation = "https://docs.rapids.ai/api/cucim/stable/"
+Changelog = "https://github.com/rapidsai/cucim/blob/branch-23.12/CHANGELOG.md"
+Source = "https://github.com/rapidsai/cucim"
+Tracker = "https://github.com/rapidsai/cucim/issues"
+
+[project.optional-dependencies]
+test = [
+    "cupy-cuda11x>=12.0.0",
+    "scipy",
+    "scikit-image>=0.19",
+    "pytest",
+    "pytest-lazy-fixture",
+    "gputil",
+    "openslide-python",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+developer = [
+    "black",
+    "isort",
+    "pre-commit",
+    "ruff",
+]
+docs = [
+    "Sphinx==4.5.0",
+    "sphinx-autobuild",
+    "sphinx-book-theme",
+    "sphinxcontrib-bibtex<2.0.0",  # https://github.com/executablebooks/jupyter-book/issues/1137
+    "sphinx-copybutton",
+    "sphinx-panels",
+    "sphinx-thebe",
+    "sphinx-togglebutton",
+    "sphinxemoji",
+    "ablog",
+    "docutils==0.16", # 0.17 causes error. https://github.com/executablebooks/MyST-Parser/issues/343
+    "pydata_sphinx_theme",
+    "myst-parser",
+    "myst-nb",
+    "ipywidgets",
+    "nbclient",
+    "plotly<5",
+    "pandas",
+    "matplotlib",
+    "cupy-cuda110",
+    "numpy",
+    "scipy",
+    "scikit-image",
+]
+
+[project.entry-points."console_scripts"]
+cucim = "cucim.clara.cli:main"
+
+[tool.setuptools]
+license-files = ["LICENSE"]
+# By default, include-package-data is true in pyproject.toml, so you do
+# NOT have to specify this line.
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src/cucim"]
+
+[tool.setuptools.package-data]
+mypkg = ["*.pyi", "*.h", "*.cu"]
+
+[tool.isort]
+profile = "black"
+force_single_line = false
+line_length = 80
+forced_separate = "test_cucim"
+force_grid_wrap = 0
+multi_line_output = 3
+order_by_type = true
+combine_as_imports = true
+include_trailing_comma = true
+known_first_party = [
+    "cucim",
+]
+default_section = "THIRDPARTY"
+sections = [
+    "FUTURE",
+    "STDLIB",
+    "THIRDPARTY",
+    "FIRSTPARTY",
+    "LOCALFOLDER",
+]
+skip = [
+    "3rdparty",
+    "thirdparty",
+    ".eggs",
+    ".git",
+    ".hg",
+    ".mypy_cache",
+    ".tox",
+    ".venv",
+    "ci",
+    "cpp",
+    "_build",
+    "build",
+    "build-debug",
+    "build-release",
+    "_deps",
+    "dist",
+]
+
+[tool.pytest.ini_options]
+# If a pytest section is found in one of the possible config files
+# (pytest.ini, tox.ini or setup.cfg), then pytest will not look for any others,
+# so if you add a pytest config section elsewhere,
+# you will need to delete this section from setup.cfg.
+norecursedirs = "migrations"
+python_files = [
+    "test_*.py",
+    "*_test.py",
+    "tests.py",
+]
+addopts = [
+    "-ra",
+    "--strict-markers",
+    # --doctest-modules",
+    # --doctest-glob=\*.rst",
+    "--tb=short",
+    "--ignore-glob=build*",
+]
+testpaths = [
+    "src",
+    "tests",
+]
+
+[tool.ruff]
+# see: https://docs.astral.sh/ruff/rules/
+select = ["E", "F", "W"]
+fixable = ["ALL"]
+exclude = [
+    # TODO: Remove this in a follow-up where we fix __all__.
+    ".tox",
+    ".eggs",
+    "ci/templates",
+    "build",
+    "dist",
+    ".git",
+    "__pycache__",
+    "doc/conf.py",
+    "doc/sphinxext",
+    "__init__.py",
+]
+line-length = 80
+
+[tool.ruff.per-file-ignores]
+# "src/cucim/skimage/util/tests/test_shape.py" = ["E201", "E202"]
+
+[tool.black]
+line-length = 80
+target-version = ["py39"]
+include = '\.py?$'
+exclude = '''
+/(
+    3rdparty |
+    thirdparty |
+    \.eggs |
+    \.git |
+    \.hg |
+    \.mypy_cache |
+    \.tox |
+    \.venv |
+    _build |
+    _deps |
+    cpp |
+    ci |
+    build |
+    build-debug |
+    build-release |
+    dist |
+    docker |
+    docs |
+)/
+'''
+
+[tool.codespell]
+# note: pre-commit passes explicit lists of files here, which this skip file list doesn't override -
+# this is only to allow you to run codespell interactively
+# e.g. via
+#   codespell --toml python/cucim/pyproject.toml . -i 3 -w
+skip = "build*,dist,.cache,html,_build,_deps,3rdparty,_static,generated,latex,.git,*.ipynb,test_data/input/LICENSE-3rdparty,jitify_testing"
+# ignore-regex = ""
+ignore-words-list = "ans,coo,boun,bui,gool,hart,lond,nd,paeth,unser,wronly"
+quiet-level = 3
+
+# to undo: ./test_data/input/LICENSE-3rdparty
diff --git a/python/cucim/pyproject_.toml b/python/cucim/pyproject_.toml
deleted file mode 100644
index c5351f058..000000000
--- a/python/cucim/pyproject_.toml
+++ /dev/null
@@ -1,129 +0,0 @@
-# Copyright (c) 2023, NVIDIA CORPORATION. All rights reserved.
-# See file LICENSE for terms.
-
-[tool.isort]
-profile = "black"
-force_single_line = false
-line_length = 80
-forced_separate = "test_cucim"
-force_grid_wrap = 0
-multi_line_output = 3
-order_by_type = true
-combine_as_imports = true
-include_trailing_comma = true
-known_first_party = [
-    "cucim",
-]
-default_section = "THIRDPARTY"
-sections = [
-    "FUTURE",
-    "STDLIB",
-    "THIRDPARTY",
-    "FIRSTPARTY",
-    "LOCALFOLDER",
-]
-skip = [
-    "3rdparty",
-    "thirdparty",
-    ".eggs",
-    ".git",
-    ".hg",
-    ".mypy_cache",
-    ".tox",
-    ".venv",
-    "ci",
-    "cpp",
-    "_build",
-    "build",
-    "build-debug",
-    "build-release",
-    "_deps",
-    "dist",
-]
-
-[tool.pytest.ini_options]
-# If a pytest section is found in one of the possible config files
-# (pytest.ini, tox.ini or setup.cfg), then pytest will not look for any others,
-# so if you add a pytest config section elsewhere,
-# you will need to delete this section from setup.cfg.
-norecursedirs = "migrations"
-python_files = [
-    "test_*.py",
-    "*_test.py",
-    "tests.py",
-]
-addopts = [
-    "-ra",
-    "--strict-markers",
-    # --doctest-modules",
-    # --doctest-glob=\*.rst",
-    "--tb=short",
-    "--ignore-glob=build*",
-]
-testpaths = [
-    "src",
-    "tests",
-]
-
-[tool.ruff]
-select = ["E", "F", "W"]
-fixable = ["ALL"]
-exclude = [
-    # TODO: Remove this in a follow-up where we fix __all__.
-    ".tox",
-    ".eggs",
-    "ci/templates",
-    "build",
-    "dist",
-    ".git",
-    "__pycache__",
-    "doc/conf.py",
-    "doc/sphinxext",
-    "__init__.py",
-]
-line-length = 80
-
-[tool.ruff.per-file-ignores]
-# "src/cucim/skimage/util/tests/test_shape.py" = ["E201", "E202"]
-
-[tool.black]
-line-length = 80
-target-version = ["py39"]
-include = '\.py?$'
-exclude = '''
-/(
-    3rdparty |
-    thirdparty |
-    \.eggs |
-    \.git |
-    \.hg |
-    \.mypy_cache |
-    \.tox |
-    \.venv |
-    _build |
-    _deps |
-    cpp |
-    ci |
-    build |
-    build-debug |
-    build-release |
-    dist |
-    docker |
-    docs |
-)/
-'''
-
-[tool.setuptools]
-license-files = ["LICENSE"]
-
-[tool.codespell]
-# note: pre-commit passes explicit lists of files here, which this skip file list doesn't override -
-# this is only to allow you to run codespell interactively
-# e.g. via
-#   codespell --toml python/cucim/pyproject.toml . -i 3 -w
-skip = "build*,dist,.cache,html,_build,_deps,3rdparty,_static,generated,latex,.git,*.ipynb,test_data/input/LICENSE-3rdparty,jitify_testing"
-# ignore-regex = ""
-ignore-words-list = "ans,coo,boun,bui,gool,hart,lond,nd,paeth,unser,wronly"
-quiet-level = 3
-
-# to undo: ./test_data/input/LICENSE-3rdparty
diff --git a/python/cucim/setup.py b/python/cucim/setup.py
deleted file mode 100755
index ad6b05600..000000000
--- a/python/cucim/setup.py
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/usr/bin/env python
-# -*- encoding: utf-8 -*-
-
-import io
-import sys
-from os.path import dirname, join
-
-from setuptools import find_packages, setup
-
-# Give setuptools a hint to complain if it's too old a version
-# 24.2.0 added the python_requires option
-# Should match pyproject.toml
-SETUP_REQUIRES = ["setuptools >= 24.2.0"]
-# This enables setuptools to install wheel on-the-fly
-SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else []
-
-
-def read(*names, **kwargs):
-    with io.open(
-        join(dirname(__file__), *names), encoding=kwargs.get("encoding", "utf8")
-    ) as fh:
-        return fh.read()
-
-
-opts = dict(
-    name="cucim",
-    version=read("VERSION").strip(),
-    license="Apache-2.0",
-    description="cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image processing primitives for N-Dimensional images with a focus on biomedical imaging.",  # noqa
-    long_description="%s\n%s" % (read("README.md"), read("CHANGELOG.md")),
-    long_description_content_type="text/markdown",
-    author="NVIDIA Corporation",
-    url="https://developer.nvidia.com/multidimensional-image-processing",
-    packages=find_packages("src"),
-    package_dir={"cucim": "src/cucim"},
-    package_data={"": ["*.pyi", "*.h", "*.cu"]},
-    include_package_data=True,
-    zip_safe=False,
-    classifiers=[
-        # complete classifier list:
-        #   http://pypi.python.org/pypi?%3Aaction=list_classifiers
-        "Development Status :: 4 - Beta",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Education",
-        "Intended Audience :: Science/Research",
-        "Intended Audience :: Healthcare Industry",
-        "Operating System :: POSIX :: Linux",
-        "Environment :: Console",
-        "Environment :: GPU :: NVIDIA CUDA :: 11.0",
-        "License :: OSI Approved :: Apache Software License",
-        "Programming Language :: C++",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        # 'Operating System :: OS Independent',
-        # 'Operating System :: Unix',
-        # 'Operating System :: POSIX',
-        # 'Operating System :: Microsoft :: Windows',
-        # 'Programming Language :: Python :: Implementation :: CPython',
-        # uncomment if you test on these interpreters:
-        # 'Programming Language :: Python :: Implementation :: PyPy',
-        # 'Programming Language :: Python :: Implementation :: IronPython',
-        # 'Programming Language :: Python :: Implementation :: Jython',
-        # 'Programming Language :: Python :: Implementation :: Stackless',
-        "Topic :: Scientific/Engineering :: Image Processing",
-    ],
-    project_urls={
-        "Source": "https://github.com/rapidsai/cucim",
-        "Documentation": "https://docs.rapids.ai/api/cucim/stable/",
-        "Changelog": "https://github.com/rapidsai/cucim/blob/main/CHANGELOG.md",
-        "Issue Tracker": "https://github.com/rapidsai/cucim/issues",
-    },
-    keywords=[
-        # eg: 'keyword1', 'keyword2', 'keyword3',
-    ],
-    python_requires=">= 3.6",
-    platforms=["manylinux2014_x86_64"],
-    setup_requires=SETUP_REQUIRES,
-    install_requires=[
-        # TODO: Check cupy dependency based on cuda version
-        "click",
-        "numpy",
-        "lazy_loader>=0.1",  # 'scipy', 'scikit-image'
-        # eg: 'aspectlib==1.1.1', 'six>=1.7',
-    ],
-    extras_require={
-        # eg:
-        #   'rst': ['docutils>=0.11'],
-        #   ':python_version=="2.6"': ['argparse'],
-    },
-    entry_points={
-        "console_scripts": [
-            "cucim = cucim.clara.cli:main",
-        ]
-    },
-)
-
-if __name__ == "__main__":
-    setup(**opts)
diff --git a/run b/run
index a70dfe891..862dd74f5 100755
--- a/run
+++ b/run
@@ -744,17 +744,19 @@ build_python_package_() {
     rm -rf ${SRC_ROOT}/python/cucim/build
     # Compile wheels (one python binary is enough)
     pybins="$(echo /opt/python/*/bin)"
-    [ ! -e /opt/python/cp36-cp36m/bin ] && pybins="$(dirname $(which python3))" # for building at host
+    [ ! -e /opt/python/cp39-cp39/bin ] && pybins="$(dirname $(which python3))" # for building at host
 
     pybins="$(echo /opt/python/*/bin)"
     if [ "${pybins}" = "/opt/python/*/bin" ]; then # if multiple python binaries not found
         pybins="$(dirname $(which python3))" # for building at host
     else
-        pybins=/opt/python/cp36-cp36m/bin # use Python 3.6 for executing setup.py
+        pybins=/opt/python/cp39-cp39/bin # use Python 3.9 for executing `pip wheel`
     fi
 
     for PYBIN in ${pybins}; do # /opt/python/*/bin
-        run_command "${PYBIN}/python3" setup.py bdist_wheel -p $PLAT -d ${TEMP_PYPKG_DIR}
+        # run_command "${PYBIN}/python3" setup.py bdist_wheel -p $PLAT -d ${TEMP_PYPKG_DIR}
+        # no pip equivalent of -p for platform?
+        run_command "${PYBIN}/python3" -m pip wheel . --wheel-dir ${TEMP_PYPKG_DIR}
     done
 
     # Do not bundle external shared libraries for now.