diff --git a/REQUIREMENTS.txt b/REQUIREMENTS.txt
index 5056135fa..8a0a13a0c 100644
--- a/REQUIREMENTS.txt
+++ b/REQUIREMENTS.txt
@@ -8,8 +8,8 @@ jsonschema<4.18
 matplotlib<3.8
 # pinning mistune for m2r2 in CI requirements
 mistune==0.8.4
-# numpy 1.25 slightly changes values in three tests causing them to fail
-numpy<1.25
+# numpy 2.0 breaks code and migration requires additional work
+numpy<2
 read_roi
 regional
 # scikit-image is temporarily pinned as newer versions require updating module imports
diff --git a/requirements/REQUIREMENTS-CI.txt b/requirements/REQUIREMENTS-CI.txt
index 2c5905e59..b1fb00718 100644
--- a/requirements/REQUIREMENTS-CI.txt
+++ b/requirements/REQUIREMENTS-CI.txt
@@ -6,15 +6,15 @@ babel==2.16.0
 backports.tarfile==1.2.0
 beautifulsoup4==4.12.3
 bleach==6.1.0
-boto3==1.35.13
-botocore==1.35.13
+boto3==1.35.38
+botocore==1.35.38
 certifi==2024.8.30
 cffi==1.17.1
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
 commonmark==0.9.1
 contourpy==1.3.0
-coverage==7.6.1
+coverage==7.6.2
 cryptography==43.0.1
 cycler==0.12.1
 decorator==5.1.1
@@ -28,36 +28,36 @@ executing==2.1.0
 fastjsonschema==2.20.0
 flake8==7.1.1
 flake8-import-order==0.18.2
-fonttools==4.53.1
-h5py==3.11.0
-idna==3.8
+fonttools==4.54.1
+h5py==3.12.1
+idna==3.10
 imageio==2.35.1
 imagesize==1.4.1
-importlib_metadata==8.4.0
-importlib_resources==6.4.4
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 iniconfig==2.0.0
 ipython==8.18.1
 jaraco.classes==3.4.0
 jaraco.context==6.0.1
-jaraco.functools==4.0.2
+jaraco.functools==4.1.0
 jedi==0.19.1
 jeepney==0.8.0
 Jinja2==3.1.4
 jmespath==1.0.1
 joblib==1.4.2
 jsonschema==4.17.3
-jupyter_client==8.6.2
+jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyterlab_pygments==0.3.0
-keyring==25.3.0
+keyring==25.4.1
 kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-lxml_html_clean==0.2.2
+lxml_html_clean==0.3.1
 m2r2==0.3.3.post2
 markdown-it-py==3.0.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.1
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mccabe==0.7.0
@@ -73,18 +73,18 @@ nbencdec==0.0.10
 nbformat==5.10.4
 networkx==3.2.1
 nh3==0.2.18
-numpy==1.24.4
+numpy==1.26.4
 numpydoc==1.8.0
 packaging==24.1
-pandas==2.2.2
+pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
 pillow==10.4.0
 pkginfo==1.10.0
-platformdirs==4.2.2
+platformdirs==4.3.6
 pluggy==1.5.0
-prompt_toolkit==3.0.47
+prompt_toolkit==3.0.48
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pycodestyle==2.12.1
@@ -93,11 +93,11 @@ pyflakes==3.2.0
 Pygments==2.18.0
 pyparsing==3.1.4
 pyrsistent==0.20.0
-pytest==8.3.2
+pytest==8.3.3
 pytest-cov==5.0.0
 pytest-xdist==3.6.1
 python-dateutil==2.9.0.post0
-pytz==2024.1
+pytz==2024.2
 PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
@@ -108,15 +108,15 @@ regional==1.1.2
 requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
-rich==13.8.0
-s3transfer==0.10.2
+rich==13.9.2
+s3transfer==0.10.3
 scikit-image==0.21.0
-scikit-learn==1.5.1
+scikit-learn==1.5.2
 scipy==1.13.1
 seaborn==0.13.2
 SecretStorage==3.3.3
 semantic-version==2.10.0
-setuptools==74.1.2
+setuptools==75.1.0
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
@@ -125,8 +125,8 @@ soupsieve==2.6
 Sphinx==7.4.7
 sphinx-autodoc-typehints==2.3.0
 sphinx-bootstrap-theme==0.8.1
-sphinx-gallery==0.17.1
-sphinx-rtd-theme==2.0.0
+sphinx-gallery==0.18.0
+sphinx-rtd-theme==3.0.1
 sphinxcontrib-applehelp==2.0.0
 sphinxcontrib-devhelp==2.0.0
 sphinxcontrib-htmlhelp==2.1.0
@@ -136,26 +136,26 @@ sphinxcontrib-programoutput==0.17
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
-sympy==1.13.2
+sympy==1.13.3
 tabulate==0.9.0
 threadpoolctl==3.5.0
 tifffile==2024.8.30
 tinycss2==1.3.0
-tomli==2.0.1
+tomli==2.0.2
 tornado==6.4.1
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3
 twine==5.1.1
-types-PyYAML==6.0.12.20240808
+types-PyYAML==6.0.12.20240917
 types-requests==2.31.0.6
-types-setuptools==74.1.0.20240906
+types-setuptools==75.1.0.20240917
 types-urllib3==1.26.25.14
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2024.2
 urllib3==1.26.20
 validators==0.34.0
 wcwidth==0.2.13
 webencodings==0.5.1
 xarray==2023.8.0
-zipp==3.20.1
+zipp==3.20.2
diff --git a/requirements/REQUIREMENTS-JUPYTER.txt b/requirements/REQUIREMENTS-JUPYTER.txt
index bfa50197f..e9283f010 100644
--- a/requirements/REQUIREMENTS-JUPYTER.txt
+++ b/requirements/REQUIREMENTS-JUPYTER.txt
@@ -1,5 +1,5 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-JUPYTER.txt.in) and run make requirements/REQUIREMENTS-JUPYTER.txt
-anyio==4.4.0
+anyio==4.6.0
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
@@ -9,16 +9,16 @@ attrs==24.2.0
 babel==2.16.0
 beautifulsoup4==4.12.3
 bleach==6.1.0
-boto3==1.35.13
-botocore==1.35.13
+boto3==1.35.38
+botocore==1.35.38
 certifi==2024.8.30
 cffi==1.17.1
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
 comm==0.2.2
 contourpy==1.3.0
 cycler==0.12.1
-debugpy==1.8.5
+debugpy==1.8.7
 decorator==5.1.1
 defusedxml==0.7.1
 diskcache==5.6.3
@@ -27,16 +27,16 @@ entrypoints==0.4
 exceptiongroup==1.2.2
 executing==2.1.0
 fastjsonschema==2.20.0
-fonttools==4.53.1
+fonttools==4.54.1
 fqdn==1.5.1
 h11==0.14.0
-h5py==3.11.0
-httpcore==1.0.5
+h5py==3.12.1
+httpcore==1.0.6
 httpx==0.27.2
-idna==3.8
+idna==3.10
 imageio==2.35.1
-importlib_metadata==8.4.0
-importlib_resources==6.4.4
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 ipykernel==6.29.5
 ipython==8.18.1
 ipywidgets==8.1.5
@@ -52,7 +52,7 @@ jupyter==1.1.1
 jupyter-console==6.6.3
 jupyter-events==0.6.3
 jupyter-lsp==2.2.5
-jupyter_client==8.6.2
+jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyter_server==2.10.0
 jupyter_server_terminals==0.5.3
@@ -64,7 +64,7 @@ kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.1
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mistune==0.8.4
@@ -76,17 +76,17 @@ nest-asyncio==1.6.0
 networkx==3.2.1
 notebook==7.1.3
 notebook_shim==0.2.4
-numpy==1.24.4
+numpy==1.26.4
 overrides==7.7.0
 packaging==24.1
-pandas==2.2.2
+pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
 pillow==10.4.0
-platformdirs==4.2.2
-prometheus_client==0.20.0
-prompt_toolkit==3.0.47
+platformdirs==4.3.6
+prometheus_client==0.21.0
+prompt_toolkit==3.0.48
 psutil==6.0.0
 ptyprocess==0.7.0
 pure_eval==0.2.3
@@ -96,7 +96,7 @@ pyparsing==3.1.4
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
-pytz==2024.1
+pytz==2024.2
 PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
@@ -105,33 +105,33 @@ regional==1.1.2
 requests==2.32.3
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
-s3transfer==0.10.2
+s3transfer==0.10.3
 scikit-image==0.21.0
-scikit-learn==1.5.1
+scikit-learn==1.5.2
 scipy==1.13.1
 seaborn==0.13.2
 semantic-version==2.10.0
 Send2Trash==1.8.3
-setuptools==74.1.2
+setuptools==75.1.0
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
 sniffio==1.3.1
 soupsieve==2.6
 stack-data==0.6.3
-sympy==1.13.2
+sympy==1.13.3
 terminado==0.18.1
 threadpoolctl==3.5.0
 tifffile==2024.8.30
 tinycss2==1.3.0
-tomli==2.0.1
+tomli==2.0.2
 tornado==6.4.1
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3
-types-python-dateutil==2.9.0.20240906
+types-python-dateutil==2.9.0.20241003
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2024.2
 uri-template==1.3.0
 urllib3==1.26.20
 validators==0.34.0
@@ -141,4 +141,4 @@ webencodings==0.5.1
 websocket-client==1.8.0
 widgetsnbextension==4.0.13
 xarray==2023.8.0
-zipp==3.20.1
+zipp==3.20.2
diff --git a/requirements/REQUIREMENTS-NAPARI-CI.txt b/requirements/REQUIREMENTS-NAPARI-CI.txt
index 901b3b016..7c497392d 100644
--- a/requirements/REQUIREMENTS-NAPARI-CI.txt
+++ b/requirements/REQUIREMENTS-NAPARI-CI.txt
@@ -1,25 +1,25 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-NAPARI-CI.txt.in) and run make requirements/REQUIREMENTS-NAPARI-CI.txt
 alabaster==0.7.16
 annotated-types==0.7.0
-app-model==0.2.8
+app-model==0.3.0
 appdirs==1.4.4
 asciitree==0.3.3
 asttokens==2.4.1
 attrs==24.2.0
 babel==2.16.0
-boto3==1.35.13
-botocore==1.35.13
-build==1.2.1
+boto3==1.35.38
+botocore==1.35.38
+build==1.2.2.post1
 cachey==0.2.1
 certifi==2024.8.30
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
 cloudpickle==3.0.0
 comm==0.2.2
 contourpy==1.3.0
 cycler==0.12.1
 dask==2024.8.0
-debugpy==1.8.5
+debugpy==1.8.7
 decorator==5.1.1
 diskcache==5.6.3
 docstring_parser==0.16
@@ -29,17 +29,17 @@ executing==2.1.0
 fasteners==0.19
 flexcache==0.3
 flexparser==0.3.1
-fonttools==4.53.1
+fonttools==4.54.1
 freetype-py==2.5.1
 fsspec==2024.9.0
-h5py==3.11.0
+h5py==3.12.1
 HeapDict==1.0.1
 hsluv==5.0.4
-idna==3.8
+idna==3.10
 imageio==2.35.1
 imagesize==1.4.1
-importlib_metadata==8.4.0
-importlib_resources==6.4.4
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 in-n-out==0.2.1
 iniconfig==2.0.0
 ipykernel==6.29.5
@@ -49,7 +49,7 @@ Jinja2==3.1.4
 jmespath==1.0.1
 joblib==1.4.2
 jsonschema==4.17.3
-jupyter_client==8.6.2
+jupyter_client==8.6.3
 jupyter_core==5.7.2
 kiwisolver==1.4.7
 lazy_loader==0.4
@@ -58,55 +58,55 @@ locket==1.0.0
 looseversion==1.3.0
 magicgui==0.9.1
 markdown-it-py==3.0.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.1
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mdurl==0.1.2
 mistune==0.8.4
 mpmath==1.3.0
-napari==0.5.3
-napari-console==0.0.9
+napari==0.5.4
+napari-console==0.1.0
 napari-plugin-engine==0.2.0
-napari-plugin-manager==0.1.0
+napari-plugin-manager==0.1.3
 napari-svg==0.2.0
 nest-asyncio==1.6.0
 networkx==3.2.1
 npe2==0.7.7
 numba==0.60.0
 numcodecs==0.12.1
-numpy==1.24.4
+numpy==1.26.4
 numpydoc==1.8.0
 packaging==24.1
-pandas==2.2.2
+pandas==2.2.3
 parso==0.8.4
 partd==1.4.2
 pexpect==4.9.0
 pillow==10.4.0
 Pint==0.24.3
-platformdirs==4.2.2
+platformdirs==4.3.6
 pluggy==1.5.0
 pooch==1.8.2
-prompt_toolkit==3.0.47
+prompt_toolkit==3.0.48
 psutil==6.0.0
 psygnal==0.11.1
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pyconify==0.1.6
-pydantic==2.9.0
+pydantic==2.9.2
 pydantic-compat==0.1.2
-pydantic_core==2.23.2
+pydantic_core==2.23.4
 Pygments==2.18.0
 PyOpenGL==3.1.7
 pyparsing==3.1.4
-pyproject_hooks==1.1.0
+pyproject_hooks==1.2.0
 PyQt5==5.15.11
-PyQt5-Qt5==5.15.14
+PyQt5-Qt5==5.15.15
 PyQt5_sip==12.15.0
 pyrsistent==0.20.0
-pytest==8.3.2
+pytest==8.3.3
 pytest-qt==4.4.0
 python-dateutil==2.9.0.post0
-pytz==2024.1
+pytz==2024.2
 PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
@@ -115,14 +115,14 @@ QtPy==2.4.1
 read-roi==1.6.0
 regional==1.1.2
 requests==2.32.3
-rich==13.8.0
-s3transfer==0.10.2
+rich==13.9.2
+s3transfer==0.10.3
 scikit-image==0.21.0
-scikit-learn==1.5.1
+scikit-learn==1.5.2
 scipy==1.13.1
 seaborn==0.13.2
 semantic-version==2.10.0
-setuptools==74.1.2
+setuptools==75.1.0
 shellingham==1.5.4
 showit==1.1.4
 six==1.16.0
@@ -137,13 +137,13 @@ sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
 superqt==0.6.7
-sympy==1.13.2
+sympy==1.13.3
 tabulate==0.9.0
 threadpoolctl==3.5.0
 tifffile==2024.8.30
-tomli==2.0.1
-tomli_w==1.0.0
-toolz==0.12.1
+tomli==2.0.2
+tomli_w==1.1.0
+toolz==1.0.0
 tornado==6.4.1
 tqdm==4.66.5
 trackpy==0.6.4
@@ -151,7 +151,7 @@ traitlets==5.14.3
 triangle==20230923
 typer==0.12.5
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2024.2
 urllib3==1.26.20
 validators==0.34.0
 vispy==0.14.3
@@ -159,4 +159,4 @@ wcwidth==0.2.13
 wrapt==1.16.0
 xarray==2023.8.0
 zarr==2.18.2
-zipp==3.20.1
+zipp==3.20.2
diff --git a/starfish/REQUIREMENTS-STRICT.txt b/starfish/REQUIREMENTS-STRICT.txt
index 1044ae28a..1e3a4d041 100644
--- a/starfish/REQUIREMENTS-STRICT.txt
+++ b/starfish/REQUIREMENTS-STRICT.txt
@@ -1,19 +1,19 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (REQUIREMENTS.txt) and run make starfish/REQUIREMENTS-STRICT.txt
 attrs==24.2.0
-boto3==1.35.13
-botocore==1.35.13
+boto3==1.35.38
+botocore==1.35.38
 certifi==2024.8.30
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
 contourpy==1.3.0
 cycler==0.12.1
 diskcache==5.6.3
 docutils==0.20.1
-fonttools==4.53.1
-h5py==3.11.0
-idna==3.8
+fonttools==4.54.1
+h5py==3.12.1
+idna==3.10
 imageio==2.35.1
-importlib_resources==6.4.4
+importlib_resources==6.4.5
 jmespath==1.0.1
 joblib==1.4.2
 jsonschema==4.17.3
@@ -24,36 +24,36 @@ matplotlib==3.7.5
 mistune==0.8.4
 mpmath==1.3.0
 networkx==3.2.1
-numpy==1.24.4
+numpy==1.26.4
 packaging==24.1
-pandas==2.2.2
+pandas==2.2.3
 pillow==10.4.0
 pyparsing==3.1.4
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
-pytz==2024.1
+pytz==2024.2
 PyWavelets==1.6.0
 PyYAML==6.0.2
 read-roi==1.6.0
 regional==1.1.2
 requests==2.32.3
-s3transfer==0.10.2
+s3transfer==0.10.3
 scikit-image==0.21.0
-scikit-learn==1.5.1
+scikit-learn==1.5.2
 scipy==1.13.1
 seaborn==0.13.2
 semantic-version==2.10.0
-setuptools==74.1.2
+setuptools==75.1.0
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
-sympy==1.13.2
+sympy==1.13.3
 threadpoolctl==3.5.0
 tifffile==2024.8.30
 tqdm==4.66.5
 trackpy==0.6.4
-tzdata==2024.1
+tzdata==2024.2
 urllib3==1.26.20
 validators==0.34.0
 xarray==2023.8.0
-zipp==3.20.1
+zipp==3.20.2
diff --git a/starfish/core/_display.py b/starfish/core/_display.py
index 991a57cf8..e14e20839 100644
--- a/starfish/core/_display.py
+++ b/starfish/core/_display.py
@@ -95,7 +95,7 @@ def _spots_to_markers(intensity_table: IntensityTable) -> Tuple[np.ndarray, np.n
     code_length = n_rounds * n_channels
 
     # create 5-d coordinates for plotting in (x, y, round. channel, z)
-    n_markers = np.product(intensity_table.shape)
+    n_markers = np.prod(intensity_table.shape)
     coords = np.zeros((n_markers, 5), dtype=np.uint16)
 
     # create the coordinates.
diff --git a/starfish/core/spots/AssignTargets/label.py b/starfish/core/spots/AssignTargets/label.py
index cc6fc54c5..0a837c9bf 100644
--- a/starfish/core/spots/AssignTargets/label.py
+++ b/starfish/core/spots/AssignTargets/label.py
@@ -42,7 +42,7 @@ def _assign(
             else:
                 warnings.warn(
                     "AssignTargets will require 3D masks in the future.", DeprecationWarning)
-                z_min, z_max = np.NINF, np.inf
+                z_min, z_max = -np.inf, np.inf
             y_min, y_max = float(mask.y.min()), float(mask.y.max())
             x_min, x_max = float(mask.x.min()), float(mask.x.max())
 
diff --git a/starfish/test/full_pipelines/api/test_dartfish.py b/starfish/test/full_pipelines/api/test_dartfish.py
index aa4cf0a03..6234d0fc4 100644
--- a/starfish/test/full_pipelines/api/test_dartfish.py
+++ b/starfish/test/full_pipelines/api/test_dartfish.py
@@ -179,7 +179,8 @@ def test_dartfish_pipeline_cropped_data(tmpdir):
     cnts_starfish.rename(columns={'target': 'gene', 'area': 'cnt_starfish'}, inplace=True)
 
     # get top 5 genes and verify they are correct
-    high_expression_genes = cnts_starfish.sort_values('cnt_starfish', ascending=False).head(5)
+    high_expression_genes = cnts_starfish.sort_values('cnt_starfish', ascending=False,
+                                                      kind='stable').head(5)
 
     assert np.array_equal(
         high_expression_genes['cnt_starfish'].values,
@@ -187,7 +188,7 @@ def test_dartfish_pipeline_cropped_data(tmpdir):
     )
     assert np.array_equal(
         high_expression_genes['gene'].values,
-        ['MBP', 'MOBP', 'ADCY8', 'TRIM66', 'SYT6']
+        ['MBP', 'MOBP', 'ADCY8', 'SYT6', 'TRIM66']
     )
 
     # verify correlation is accurate for this subset of the image
diff --git a/starfish/test/full_pipelines/api/test_merfish.py b/starfish/test/full_pipelines/api/test_merfish.py
index f6d2362e9..0e57b1054 100644
--- a/starfish/test/full_pipelines/api/test_merfish.py
+++ b/starfish/test/full_pipelines/api/test_merfish.py
@@ -236,7 +236,7 @@ def test_merfish_pipeline_cropped_data():
         spot_intensities[Features.PASSES_THRESHOLDS], drop=True
     )
     genes, counts = np.unique(spot_intensities_passing_filters[Features.TARGET], return_counts=True)
-    result_counts = pd.Series(counts, index=genes).sort_values(ascending=False)[:5]
+    result_counts = pd.Series(counts, index=genes).sort_values(ascending=False, kind='stable')[:5]
 
     # assert that number of high-expression detected genes are correct
     expected_counts = pd.Series(