diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
index 15dd208e..e4a9d43e 100644
--- a/.github/workflows/integration-test.yml
+++ b/.github/workflows/integration-test.yml
@@ -56,6 +56,28 @@ jobs:
         uses: pre-commit/action@v3.0.0
         with:
           extra_args: --all-files
+  python-type-checks:
+    # This job is used to check Python types
+    name: Python type checks
+    # Avoid fail-fast to retain output
+    strategy:
+      fail-fast: false
+    runs-on: ubuntu-22.04
+    if: github.event_name != 'schedule'
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Setup python, and check pre-commit cache
+        uses: ./.github/actions/setup-env
+        with:
+          python-version: ${{ env.TARGET_PYTHON_VERSION }}
+          cache-pre-commit: false
+          cache-venv: true
+          setup-poetry: true
+          install-deps: true
+      - name: Run mypy
+        run: |
+          poetry run mypy .
   integration-test:
     name: Pytest (Python ${{ matrix.python-version }} on ${{ matrix.os }})
     # Runs pytest on all tested versions of python and OSes
diff --git a/poetry.lock b/poetry.lock
index f0c84d28..3bfac446 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -104,7 +104,7 @@ boto3 = ["boto3 (>=1.34.41,<1.34.52)"]
 name = "aiohappyeyeballs"
 version = "2.3.5"
 description = "Happy Eyeballs for asyncio"
-optional = false
+optional = true
 python-versions = ">=3.8"
 files = [
     {file = "aiohappyeyeballs-2.3.5-py3-none-any.whl", hash = "sha256:4d6dea59215537dbc746e93e779caea8178c866856a721c9c660d7a5a7b8be03"},
@@ -115,7 +115,7 @@ files = [
 name = "aiohttp"
 version = "3.10.2"
 description = "Async http client/server framework (asyncio)"
-optional = false
+optional = true
 python-versions = ">=3.8"
 files = [
     {file = "aiohttp-3.10.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:95213b3d79c7e387144e9cb7b9d2809092d6ff2c044cb59033aedc612f38fb6d"},
@@ -226,7 +226,7 @@ typing_extensions = {version = ">=4.0", markers = "python_version < \"3.10\""}
 name = "aiosignal"
 version = "1.3.1"
 description = "aiosignal: a list of registered asynchronous callbacks"
-optional = false
+optional = true
 python-versions = ">=3.7"
 files = [
     {file = "aiosignal-1.3.1-py3-none-any.whl", hash = "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17"},
@@ -319,7 +319,7 @@ test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 name = "async-timeout"
 version = "4.0.3"
 description = "Timeout context manager for asyncio programs"
-optional = false
+optional = true
 python-versions = ">=3.7"
 files = [
     {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"},
@@ -1044,7 +1044,7 @@ termcolor = "*"
 name = "frozenlist"
 version = "1.4.1"
 description = "A list-like structure which implements collections.abc.MutableSequence"
-optional = false
+optional = true
 python-versions = ">=3.8"
 files = [
     {file = "frozenlist-1.4.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f9aa1878d1083b276b0196f2dfbe00c9b7e752475ed3b682025ff20c1c1f51ac"},
@@ -1873,7 +1873,7 @@ test = ["pytest", "pytest-cov"]
 name = "multidict"
 version = "6.0.5"
 description = "multidict implementation"
-optional = false
+optional = true
 python-versions = ">=3.7"
 files = [
     {file = "multidict-6.0.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:228b644ae063c10e7f324ab1ab6b548bdf6f8b47f3ec234fef1093bc2735e5f9"},
@@ -1968,6 +1968,64 @@ files = [
     {file = "multidict-6.0.5.tar.gz", hash = "sha256:f7e301075edaf50500f0b341543c41194d8df3ae5caf4702f2095f3ca73dd8da"},
 ]
 
+[[package]]
+name = "mypy"
+version = "1.11.2"
+description = "Optional static typing for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "mypy-1.11.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d42a6dd818ffce7be66cce644f1dff482f1d97c53ca70908dff0b9ddc120b77a"},
+    {file = "mypy-1.11.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:801780c56d1cdb896eacd5619a83e427ce436d86a3bdf9112527f24a66618fef"},
+    {file = "mypy-1.11.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:41ea707d036a5307ac674ea172875f40c9d55c5394f888b168033177fce47383"},
+    {file = "mypy-1.11.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:6e658bd2d20565ea86da7d91331b0eed6d2eee22dc031579e6297f3e12c758c8"},
+    {file = "mypy-1.11.2-cp310-cp310-win_amd64.whl", hash = "sha256:478db5f5036817fe45adb7332d927daa62417159d49783041338921dcf646fc7"},
+    {file = "mypy-1.11.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:75746e06d5fa1e91bfd5432448d00d34593b52e7e91a187d981d08d1f33d4385"},
+    {file = "mypy-1.11.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:a976775ab2256aadc6add633d44f100a2517d2388906ec4f13231fafbb0eccca"},
+    {file = "mypy-1.11.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:cd953f221ac1379050a8a646585a29574488974f79d8082cedef62744f0a0104"},
+    {file = "mypy-1.11.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:57555a7715c0a34421013144a33d280e73c08df70f3a18a552938587ce9274f4"},
+    {file = "mypy-1.11.2-cp311-cp311-win_amd64.whl", hash = "sha256:36383a4fcbad95f2657642a07ba22ff797de26277158f1cc7bd234821468b1b6"},
+    {file = "mypy-1.11.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:e8960dbbbf36906c5c0b7f4fbf2f0c7ffb20f4898e6a879fcf56a41a08b0d318"},
+    {file = "mypy-1.11.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:06d26c277962f3fb50e13044674aa10553981ae514288cb7d0a738f495550b36"},
+    {file = "mypy-1.11.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:6e7184632d89d677973a14d00ae4d03214c8bc301ceefcdaf5c474866814c987"},
+    {file = "mypy-1.11.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:3a66169b92452f72117e2da3a576087025449018afc2d8e9bfe5ffab865709ca"},
+    {file = "mypy-1.11.2-cp312-cp312-win_amd64.whl", hash = "sha256:969ea3ef09617aff826885a22ece0ddef69d95852cdad2f60c8bb06bf1f71f70"},
+    {file = "mypy-1.11.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:37c7fa6121c1cdfcaac97ce3d3b5588e847aa79b580c1e922bb5d5d2902df19b"},
+    {file = "mypy-1.11.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4a8a53bc3ffbd161b5b2a4fff2f0f1e23a33b0168f1c0778ec70e1a3d66deb86"},
+    {file = "mypy-1.11.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:2ff93107f01968ed834f4256bc1fc4475e2fecf6c661260066a985b52741ddce"},
+    {file = "mypy-1.11.2-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:edb91dded4df17eae4537668b23f0ff6baf3707683734b6a818d5b9d0c0c31a1"},
+    {file = "mypy-1.11.2-cp38-cp38-win_amd64.whl", hash = "sha256:ee23de8530d99b6db0573c4ef4bd8f39a2a6f9b60655bf7a1357e585a3486f2b"},
+    {file = "mypy-1.11.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:801ca29f43d5acce85f8e999b1e431fb479cb02d0e11deb7d2abb56bdaf24fd6"},
+    {file = "mypy-1.11.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:af8d155170fcf87a2afb55b35dc1a0ac21df4431e7d96717621962e4b9192e70"},
+    {file = "mypy-1.11.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:f7821776e5c4286b6a13138cc935e2e9b6fde05e081bdebf5cdb2bb97c9df81d"},
+    {file = "mypy-1.11.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:539c570477a96a4e6fb718b8d5c3e0c0eba1f485df13f86d2970c91f0673148d"},
+    {file = "mypy-1.11.2-cp39-cp39-win_amd64.whl", hash = "sha256:3f14cd3d386ac4d05c5a39a51b84387403dadbd936e17cb35882134d4f8f0d24"},
+    {file = "mypy-1.11.2-py3-none-any.whl", hash = "sha256:b499bc07dbdcd3de92b0a8b29fdf592c111276f6a12fe29c30f6c417dd546d12"},
+    {file = "mypy-1.11.2.tar.gz", hash = "sha256:7f9993ad3e0ffdc95c2a14b66dee63729f021968bff8ad911867579c65d13a79"},
+]
+
+[package.dependencies]
+mypy-extensions = ">=1.0.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = ">=4.6.0"
+
+[package.extras]
+dmypy = ["psutil (>=4.0)"]
+install-types = ["pip"]
+mypyc = ["setuptools (>=50)"]
+reports = ["lxml"]
+
+[[package]]
+name = "mypy-extensions"
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
+]
+
 [[package]]
 name = "nbclient"
 version = "0.10.0"
@@ -2224,6 +2282,50 @@ 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)"]
 
+[[package]]
+name = "pandas-stubs"
+version = "2.0.2.230605"
+description = "Type annotations for pandas"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pandas_stubs-2.0.2.230605-py3-none-any.whl", hash = "sha256:39106b602f3cb6dc5f728b84e1b32bde6ecf41ee34ee714c66228009609fbada"},
+    {file = "pandas_stubs-2.0.2.230605.tar.gz", hash = "sha256:624c7bb06d38145a44b61be459ccd19b038e0bf20364a025ecaab78fea65e858"},
+]
+
+[package.dependencies]
+numpy = ">=1.24.3"
+types-pytz = ">=2022.1.1"
+
+[[package]]
+name = "pandas-stubs"
+version = "2.0.3.230814"
+description = "Type annotations for pandas"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pandas_stubs-2.0.3.230814-py3-none-any.whl", hash = "sha256:4b3dfc027d49779176b7daa031a3405f7b839bcb6e312f4b9f29fea5feec5b4f"},
+    {file = "pandas_stubs-2.0.3.230814.tar.gz", hash = "sha256:1d5cc09e36e3d9f9a1ed9dceae4e03eeb26d1b898dd769996925f784365c8769"},
+]
+
+[package.dependencies]
+types-pytz = ">=2022.1.1"
+
+[[package]]
+name = "pandas-stubs"
+version = "2.2.2.240909"
+description = "Type annotations for pandas"
+optional = false
+python-versions = ">=3.10"
+files = [
+    {file = "pandas_stubs-2.2.2.240909-py3-none-any.whl", hash = "sha256:e230f5fa4065f9417804f4d65cd98f86c002efcc07933e8abcd48c3fad9c30a2"},
+    {file = "pandas_stubs-2.2.2.240909.tar.gz", hash = "sha256:3c0951a2c3e45e3475aed9d80b7147ae82f176b9e42e9fb321cfdebf3d411b3d"},
+]
+
+[package.dependencies]
+numpy = ">=1.23.5"
+types-pytz = ">=2022.1.1"
+
 [[package]]
 name = "pandocfilters"
 version = "1.5.1"
@@ -3529,6 +3631,39 @@ files = [
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.1)", "pytest-mock", "pytest-mypy-testing"]
 
+[[package]]
+name = "types-openpyxl"
+version = "3.1.5.20240918"
+description = "Typing stubs for openpyxl"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "types-openpyxl-3.1.5.20240918.tar.gz", hash = "sha256:22a71a1b601ed8194e356e33e2bebb93dddc47915b410db14ace5a6b7b856955"},
+    {file = "types_openpyxl-3.1.5.20240918-py3-none-any.whl", hash = "sha256:e9bf3c6f7966d347a2514b48f889f272d58e9b22a762244f778a5d66aee2101e"},
+]
+
+[[package]]
+name = "types-pytz"
+version = "2024.2.0.20240913"
+description = "Typing stubs for pytz"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "types-pytz-2024.2.0.20240913.tar.gz", hash = "sha256:4433b5df4a6fc587bbed41716d86a5ba5d832b4378e506f40d34bc9c81df2c24"},
+    {file = "types_pytz-2024.2.0.20240913-py3-none-any.whl", hash = "sha256:a1eebf57ebc6e127a99d2fa2ba0a88d2b173784ef9b3defcc2004ab6855a44df"},
+]
+
+[[package]]
+name = "types-sqlalchemy"
+version = "1.4.53.38"
+description = "Typing stubs for SQLAlchemy"
+optional = false
+python-versions = "*"
+files = [
+    {file = "types-SQLAlchemy-1.4.53.38.tar.gz", hash = "sha256:5bb7463537e04e1aa5a3557eb725930df99226dcfd3c9bf93008025bfe5c169e"},
+    {file = "types_SQLAlchemy-1.4.53.38-py3-none-any.whl", hash = "sha256:7e60e74f823931cc9a9e8adb0a4c05e5533e6708b8a266807893a739faf4eaaa"},
+]
+
 [[package]]
 name = "typing-extensions"
 version = "4.10.0"
@@ -3799,7 +3934,7 @@ test = ["pytest", "pytest-cov"]
 name = "yarl"
 version = "1.9.4"
 description = "Yet another URL library"
-optional = false
+optional = true
 python-versions = ">=3.7"
 files = [
     {file = "yarl-1.9.4-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a8c1df72eb746f4136fe9a2e72b0c9dc1da1cbd23b5372f94b5820ff8ae30e0e"},
@@ -3920,4 +4055,4 @@ collate = ["cytominer-database"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<4.0"
-content-hash = "8cd2e790b6c426bf02ddd240f8cd3d34bc72aa79d23cb012ab51bd48bff15a38"
+content-hash = "fc4eaf105cbba065f88e875c38b39b5f9542b1d6b6984f491bf9f779137f4469"
diff --git a/pycytominer/aggregate.py b/pycytominer/aggregate.py
index bf8403ba..707f4329 100644
--- a/pycytominer/aggregate.py
+++ b/pycytominer/aggregate.py
@@ -83,7 +83,7 @@ def aggregate(
     # Only extract single object column in preparation for count
     if compute_object_count:
         count_object_df = (
-            population_df.loc[:, np.union1d(strata, [object_feature])]
+            population_df.loc[:, list(np.union1d(strata, [object_feature]))]
             .groupby(strata)[object_feature]
             .count()
             .reset_index()
@@ -92,7 +92,9 @@ def aggregate(
 
     if features == "infer":
         features = infer_cp_features(population_df)
-    population_df = population_df[features]
+
+    # recast as dataframe to protect against scenarios where a series may be returned
+    population_df = pd.DataFrame(population_df[features])
 
     # Fix dtype of input features (they should all be floats!)
     population_df = population_df.astype(float)
@@ -101,7 +103,9 @@ def aggregate(
     population_df = pd.concat([strata_df, population_df], axis="columns")
 
     # Perform aggregating function
-    population_df = population_df.groupby(strata, dropna=False)
+    # Note: type ignore added below to address the change in variable types for
+    # label `population_df`.
+    population_df = population_df.groupby(strata, dropna=False)  # type: ignore[assignment]
 
     if operation == "median":
         population_df = population_df.median().reset_index()
@@ -118,10 +122,10 @@ def aggregate(
         for column in population_df.columns
         if column in ["ImageNumber", "ObjectNumber"]
     ]:
-        population_df = population_df.drop([columns_to_drop], axis="columns")
+        population_df = population_df.drop(columns=columns_to_drop, axis="columns")
 
     if output_file is not None:
-        output(
+        return output(
             df=population_df,
             output_filename=output_file,
             output_type=output_type,
diff --git a/pycytominer/cyto_utils/DeepProfiler_processing.py b/pycytominer/cyto_utils/DeepProfiler_processing.py
index e33f1036..cc2117d3 100644
--- a/pycytominer/cyto_utils/DeepProfiler_processing.py
+++ b/pycytominer/cyto_utils/DeepProfiler_processing.py
@@ -7,8 +7,9 @@
 import pandas as pd
 import warnings
 
-from pycytominer import aggregate, normalize
-from pycytominer.cyto_utils import (
+# use mypy ignores below to avoid duplicate import warnings
+from pycytominer import aggregate, normalize  # type: ignore[no-redef]
+from pycytominer.cyto_utils import (  # type: ignore[no-redef]
     load_npz_features,
     load_npz_locations,
     infer_cp_features,
diff --git a/pycytominer/cyto_utils/cell_locations.py b/pycytominer/cyto_utils/cell_locations.py
index 612ae873..5c4edeb7 100644
--- a/pycytominer/cyto_utils/cell_locations.py
+++ b/pycytominer/cyto_utils/cell_locations.py
@@ -106,7 +106,9 @@ def __init__(
             "s3", config=botocore.config.Config(signature_version=botocore.UNSIGNED)
         )
 
-    def _expanduser(self, obj: Union[str, None]):
+    def _expanduser(
+        self, obj: Union[str, pd.DataFrame, sqlalchemy.engine.Engine, None]
+    ):
         """Expand the user home directory in a path"""
         if obj is not None and isinstance(obj, str) and not obj.startswith("s3://"):
             return pathlib.Path(obj).expanduser().as_posix()
diff --git a/pycytominer/cyto_utils/cells.py b/pycytominer/cyto_utils/cells.py
index 4e0a80f9..a2f6062f 100644
--- a/pycytominer/cyto_utils/cells.py
+++ b/pycytominer/cyto_utils/cells.py
@@ -714,7 +714,7 @@ def merge_single_cells(
         """
 
         # Load the single cell dataframe by merging on the specific linking columns
-        sc_df = ""
+        left_compartment_loaded = False
         linking_check_cols = []
         merge_suffix_rename = []
         for left_compartment in self.compartment_linking_cols:
@@ -737,7 +737,7 @@ def merge_single_cells(
                     left_compartment
                 ]
 
-                if isinstance(sc_df, str):
+                if not left_compartment_loaded:
                     sc_df = self.load_compartment(compartment=left_compartment)
 
                     if compute_subsample:
@@ -752,6 +752,8 @@ def merge_single_cells(
                             sc_df, how="left", on=subset_logic_df.columns.tolist()
                         ).reindex(sc_df.columns, axis="columns")
 
+                    left_compartment_loaded = True
+
                 sc_df = sc_df.merge(
                     self.load_compartment(compartment=right_compartment),
                     left_on=[*self.merge_cols, left_link_col],
@@ -804,11 +806,13 @@ def merge_single_cells(
 
             normalize_args["features"] = features
 
-            sc_df = normalize(profiles=sc_df, **normalize_args)
+            # ignore mypy warnings below as these reference root package imports
+            sc_df = normalize(profiles=sc_df, **normalize_args)  # type: ignore[operator]
 
         # In case platemap metadata is provided, use pycytominer.annotate for metadata
         if platemap is not None:
-            sc_df = annotate(
+            # ignore mypy warnings below as these reference root package imports
+            sc_df = annotate(  # type: ignore[operator]
                 profiles=sc_df, platemap=platemap, output_file=None, **kwargs
             )
 
diff --git a/pycytominer/cyto_utils/collate.py b/pycytominer/cyto_utils/collate.py
index a21752fd..4d51b249 100644
--- a/pycytominer/cyto_utils/collate.py
+++ b/pycytominer/cyto_utils/collate.py
@@ -131,7 +131,7 @@ def collate(
         with sqlite3.connect(cache_backend_file, isolation_level=None) as connection:
             cursor = connection.cursor()
             if column:
-                if print:
+                if printtoscreen:
                     print(f"Adding a Metadata_Plate column based on column {column}")
                 cursor.execute("ALTER TABLE Image ADD COLUMN Metadata_Plate TEXT;")
                 cursor.execute(f"UPDATE image SET Metadata_Plate ={column};")
diff --git a/pycytominer/cyto_utils/output.py b/pycytominer/cyto_utils/output.py
index aa5290a0..62716508 100644
--- a/pycytominer/cyto_utils/output.py
+++ b/pycytominer/cyto_utils/output.py
@@ -2,7 +2,7 @@
 Utility function to compress output data
 """
 
-from typing import Dict, Union, Optional
+from typing import Dict, Union, Optional, Any
 
 import pandas as pd
 
@@ -12,10 +12,13 @@
 def output(
     df: pd.DataFrame,
     output_filename: str,
-    output_type: str = "csv",
+    output_type: Optional[str] = "csv",
     sep: str = ",",
     float_format: Optional[str] = None,
-    compression_options: Union[str, Dict] = {"method": "gzip", "mtime": 1},
+    compression_options: Optional[Union[str, Dict[str, Any]]] = {
+        "method": "gzip",
+        "mtime": 1,
+    },
     **kwargs,
 ):
     """Given an output file and compression options, write file to disk
@@ -79,6 +82,10 @@ def output(
     )
     """
 
+    # ensure a default output type
+    if output_type is None:
+        output_type = "csv"
+
     if output_type == "csv":
         compression_options = set_compression_method(compression=compression_options)
 
@@ -98,7 +105,7 @@ def output(
     return output_filename
 
 
-def set_compression_method(compression: Union[str, Dict]):
+def set_compression_method(compression: Optional[Union[str, Dict]]) -> Dict[str, Any]:
     """Set the compression options
 
     Parameters
diff --git a/pyproject.toml b/pyproject.toml
index a8ea5428..cd5ce0ad 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,6 +73,13 @@ pytest-cov = "^4.1.0"
 pre-commit = ">=3.3.2"
 commitizen = "^3.12.0"
 ruff = "^0.3.4"
+mypy = "^1.11.2"
+types-openpyxl = "^3.1.5.20240918"
+pandas-stubs = [
+  {version = "<2.2.2.240909", python = "<3.10"},
+  {version = "^2.2.2.240909", python = ">=3.10"}
+]
+types-sqlalchemy = "^1.4.53.38"
 
 [tool.poetry.group.docs]
 optional = true
@@ -177,6 +184,29 @@ preview = true
 [tool.pytest.ini_options]
 testpaths = "tests"
 
+[tool.mypy]
+exclude = [
+    # ignore notebook-based walkthroughs
+    "walkthroughs",
+    # ignore tests dir
+    "tests"
+]
+
+
+[[tool.mypy.overrides]]
+# ignore missing import errors for the following
+# packages which do not have standard type stubs
+# or experience issues with imported types.
+module = [
+    "sklearn.*",
+    "scipy.*",
+    "cytominer_database.*",
+    "fire.*",
+    "boto3.*",
+    "botocore.*"
+]
+ignore_missing_imports = true
+
 [build-system]
 requires = ["poetry-core>=1.7.0", "poetry-dynamic-versioning>=1.1.0"]
 build-backend = "poetry_dynamic_versioning.backend"
diff --git a/tests/test_aggregate.py b/tests/test_aggregate.py
index d1a08889..7765ec31 100644
--- a/tests/test_aggregate.py
+++ b/tests/test_aggregate.py
@@ -64,6 +64,19 @@ def test_aggregate_median_allvar():
 
     assert aggregate_result.equals(expected_result)
 
+    # Test that ImageNumber column would be dropped before return
+    data_df_with_imagenumber = data_df.copy()
+    data_df_with_imagenumber["ImageNumber"] = "1"
+
+    aggregate_result = aggregate(
+        population_df=data_df_with_imagenumber,
+        strata=["g"],
+        features="infer",
+        operation="median",
+    )
+
+    assert aggregate_result.equals(expected_result)
+
     # Test output
     aggregate(
         population_df=data_df,
diff --git a/tests/test_cyto_utils/test_output.py b/tests/test_cyto_utils/test_output.py
index 72d5a9cf..0aeefd06 100644
--- a/tests/test_cyto_utils/test_output.py
+++ b/tests/test_cyto_utils/test_output.py
@@ -56,6 +56,20 @@ def test_output_default():
         result, DATA_DF, check_names=False, check_exact=False, atol=1e-3
     )
 
+    # test with an output_type of None
+    output_result = output(
+        df=DATA_DF,
+        output_filename=output_filename,
+        compression_options=TEST_COMPRESSION_OPTIONS,
+        float_format=None,
+        output_type=None,
+    )
+    result = pd.read_csv(output_result)
+
+    pd.testing.assert_frame_equal(
+        result, DATA_DF, check_names=False, check_exact=False, atol=1e-3
+    )
+
 
 def test_output_tsv():
     # Test input filename of writing a tab separated file