diff --git a/starfish/core/intensity_table/intensity_table.py b/starfish/core/intensity_table/intensity_table.py
index 8f6ab949..01427ba8 100644
--- a/starfish/core/intensity_table/intensity_table.py
+++ b/starfish/core/intensity_table/intensity_table.py
@@ -522,10 +522,11 @@ class IntensityTable(xr.DataArray):
         counts = grouped.count().iloc[:, 0].unstack().fillna(0)
         if self.has_physical_coords:
             grouped = self.to_features_dataframe().groupby([Features.CELL_ID])[[
-                Axes.X, Axes.Y, Axes.ZPLANE, Coordinates.X, Coordinates.Y, Coordinates.Z]]
+                Axes.X.value, Axes.Y.value, Axes.ZPLANE.value, Coordinates.X.value,
+                Coordinates.Y.value, Coordinates.Z.value]]
         else:
             grouped = self.to_features_dataframe().groupby([Features.CELL_ID])[[
-                Axes.X, Axes.Y, Axes.ZPLANE]]
+                Axes.X.value, Axes.Y.value, Axes.ZPLANE.value]]
         min_ = grouped.min()
         max_ = grouped.max()
         coordinate_df = min_ + (max_ - min_) / 2

ExpressionMatrix methods
After target assignment I created an expression matrix (a 2-dimensional cells x genes tensor). 

<img width="589" alt="Screenshot 2019-06-18 at 19 23 41" src="https://user-images.githubusercontent.com/50377927/59705626-0e0e0a80-91ff-11e9-83cd-04fe9d0f25d2.png">

I need to save it for the following usage with single-cell analysis software packages but ExpressionMatrix methods return these kinds of errors.

matrix.save('expression_matrix')

DataArray.name or Dataset key must be either a string or None for serialization to netCDF files

matrix.save_loom('expression_matrix1')

invalid indexer array, does not have integer dtype: array(<Axes.X: 'x'>, dtype=object)

matrix.save_anndata('expression_matrix2')

invalid indexer array, does not have integer dtype: array(<Axes.X: 'x'>, dtype=object)
diff --git a/starfish/core/expression_matrix/test/test_serialization.py b/starfish/core/expression_matrix/test/test_serialization.py
index e69de29b..4f712444 100644
--- a/starfish/core/expression_matrix/test/test_serialization.py
+++ b/starfish/core/expression_matrix/test/test_serialization.py
@@ -0,0 +1,28 @@
+import random
+
+from starfish import IntensityTable
+from starfish.core.codebook.test.factories import codebook_array_factory
+from starfish.core.types import Features
+
+NUMBER_SPOTS = 10
+
+
+def test_save_expression_matrix():
+
+    codebook = codebook_array_factory()
+
+    intensities = IntensityTable.synthetic_intensities(
+        codebook,
+        num_z=3,
+        height=100,
+        width=100,
+        n_spots=10
+    )
+    # mock out come cell_ids
+    cell_ids = random.sample(range(1, 20), NUMBER_SPOTS)
+    intensities[Features.CELL_ID] = (Features.AXIS, cell_ids)
+
+    expression_matrix = intensities.to_expression_matrix()
+
+    # test all saving methods
+    expression_matrix.save("expression")

pip install -e .[dev]
parse_log_pytest
requirements.txt
pytest pytest-cov pytest-xdist
3.6
REQUIREMENTS.txt REQUIREMENTS-CI.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
alabaster==0.7.13
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
async-generator==1.10
attrs==22.2.0
Babel==2.11.0
backcall==0.2.0
bleach==4.1.0
certifi==2021.5.30
cffi==1.15.1
charset-normalizer==2.0.12
click==8.0.4
colorama==0.4.5
comm==0.1.4
commonmark==0.9.1
coverage==6.2
cryptography==40.0.2
cycler==0.11.0
dataclasses==0.8
decorator==4.4.2
defusedxml==0.7.1
diskcache==5.6.3
docutils==0.18.1
entrypoints==0.3
execnet==1.9.0
flake8==3.7.9
flake8-import-order==0.18.2
idna==3.10
imageio==2.15.0
imagesize==1.4.1
importlib-metadata==4.8.3
importlib-resources==5.4.0
iniconfig==1.1.1
ipykernel==5.5.6
ipython==7.16.3
ipython-genutils==0.2.0
ipywidgets==7.8.5
jedi==0.17.2
jeepney==0.7.1
Jinja2==3.0.3
joblib==1.1.1
jsonschema==3.2.0
jupyter-client==7.1.2
jupyter-core==4.9.2
jupyterlab-pygments==0.1.2
jupyterlab_widgets==1.1.11
keyring==23.4.1
kiwisolver==1.3.1
m2r==0.3.1
MarkupSafe==2.0.1
matplotlib==3.3.4
mccabe==0.6.1
mistune==0.8.4
mpmath==1.3.0
mypy==0.971
mypy-extensions==1.0.0
nbclient==0.5.9
nbconvert==6.0.7
nbencdec==0.0.10
nbformat==5.1.3
nest-asyncio==1.6.0
networkx==2.5.1
notebook==6.4.10
numpy==1.19.5
numpydoc==1.1.0
packaging==21.3
pandas==1.1.5
pandocfilters==1.5.1
parso==0.7.1
pexpect==4.9.0
pickleshare==0.7.5
Pillow==8.4.0
pkginfo==1.10.0
pluggy==1.0.0
prometheus-client==0.17.1
prompt-toolkit==3.0.36
ptyprocess==0.7.0
py==1.11.0
pycodestyle==2.5.0
pycparser==2.21
pyflakes==2.1.1
Pygments==2.14.0
pyparsing==3.1.4
pyrsistent==0.18.0
pytest==7.0.1
pytest-cov==4.0.0
pytest-xdist==3.0.2
python-dateutil==2.9.0.post0
pytz==2025.2
PyWavelets==1.1.1
PyYAML==6.0.1
pyzmq==25.1.2
readme-renderer==34.0
recommonmark==0.7.1
regional==1.1.2
requests==2.27.1
requests-toolbelt==1.0.0
rfc3986==1.5.0
scikit-image==0.17.2
scikit-learn==0.24.2
scipy==1.5.4
seaborn==0.11.2
SecretStorage==3.3.3
semantic-version==2.10.0
Send2Trash==1.8.3
showit==1.1.4
six==1.17.0
slicedimage==3.1.1
snowballstemmer==2.2.0
Sphinx==5.3.0
sphinx-autodoc-typehints==1.12.0
sphinx-bootstrap-theme==0.8.1
sphinx-gallery==0.10.0
sphinx-rtd-theme==2.0.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jquery==4.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-programoutput==0.17
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
-e git+https://github.com/spacetx/starfish.git@30ec15749c1a59c7922289ea63e8d2d22989cb60#egg=starfish
sympy==1.9
terminado==0.12.1
testpath==0.6.0
threadpoolctl==3.1.0
tifffile==2020.9.3
tomli==1.2.3
tornado==6.1
tqdm==4.64.1
trackpy==0.5.0
traitlets==4.3.3
twine==3.8.0
typed-ast==1.5.5
typing_extensions==4.1.1
urllib3==1.26.20
validators==0.20.0
wcwidth==0.2.13
webencodings==0.5.1
widgetsnbextension==3.6.10
xarray==0.16.2
zipp==3.6.0

name: starfish
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2021.5.30=py36h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.3=he6710b0_2
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - pip=21.2.2=py36h06a4308_0
  - python=3.6.13=h12debd9_1
  - readline=8.2=h5eee18b_0
  - setuptools=58.0.4=py36h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - alabaster==0.7.13
      - argon2-cffi==21.3.0
      - argon2-cffi-bindings==21.2.0
      - async-generator==1.10
      - attrs==22.2.0
      - babel==2.11.0
      - backcall==0.2.0
      - bleach==4.1.0
      - cffi==1.15.1
      - charset-normalizer==2.0.12
      - click==8.0.4
      - colorama==0.4.5
      - comm==0.1.4
      - commonmark==0.9.1
      - coverage==6.2
      - cryptography==40.0.2
      - cycler==0.11.0
      - dataclasses==0.8
      - decorator==4.4.2
      - defusedxml==0.7.1
      - diskcache==5.6.3
      - docutils==0.18.1
      - entrypoints==0.3
      - execnet==1.9.0
      - flake8==3.7.9
      - flake8-import-order==0.18.2
      - idna==3.10
      - imageio==2.15.0
      - imagesize==1.4.1
      - importlib-metadata==4.8.3
      - importlib-resources==5.4.0
      - iniconfig==1.1.1
      - ipykernel==5.5.6
      - ipython==7.16.3
      - ipython-genutils==0.2.0
      - ipywidgets==7.8.5
      - jedi==0.17.2
      - jeepney==0.7.1
      - jinja2==3.0.3
      - joblib==1.1.1
      - jsonschema==3.2.0
      - jupyter-client==7.1.2
      - jupyter-core==4.9.2
      - jupyterlab-pygments==0.1.2
      - jupyterlab-widgets==1.1.11
      - keyring==23.4.1
      - kiwisolver==1.3.1
      - m2r==0.3.1
      - markupsafe==2.0.1
      - matplotlib==3.3.4
      - mccabe==0.6.1
      - mistune==0.8.4
      - mpmath==1.3.0
      - mypy==0.971
      - mypy-extensions==1.0.0
      - nbclient==0.5.9
      - nbconvert==6.0.7
      - nbencdec==0.0.10
      - nbformat==5.1.3
      - nest-asyncio==1.6.0
      - networkx==2.5.1
      - notebook==6.4.10
      - numpy==1.19.5
      - numpydoc==1.1.0
      - packaging==21.3
      - pandas==1.1.5
      - pandocfilters==1.5.1
      - parso==0.7.1
      - pexpect==4.9.0
      - pickleshare==0.7.5
      - pillow==8.4.0
      - pkginfo==1.10.0
      - pluggy==1.0.0
      - prometheus-client==0.17.1
      - prompt-toolkit==3.0.36
      - ptyprocess==0.7.0
      - py==1.11.0
      - pycodestyle==2.5.0
      - pycparser==2.21
      - pyflakes==2.1.1
      - pygments==2.14.0
      - pyparsing==3.1.4
      - pyrsistent==0.18.0
      - pytest==7.0.1
      - pytest-cov==4.0.0
      - pytest-xdist==3.0.2
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - pywavelets==1.1.1
      - pyyaml==6.0.1
      - pyzmq==25.1.2
      - readme-renderer==34.0
      - recommonmark==0.7.1
      - regional==1.1.2
      - requests==2.27.1
      - requests-toolbelt==1.0.0
      - rfc3986==1.5.0
      - scikit-image==0.17.2
      - scikit-learn==0.24.2
      - scipy==1.5.4
      - seaborn==0.11.2
      - secretstorage==3.3.3
      - semantic-version==2.10.0
      - send2trash==1.8.3
      - showit==1.1.4
      - six==1.17.0
      - slicedimage==3.1.1
      - snowballstemmer==2.2.0
      - sphinx==5.3.0
      - sphinx-autodoc-typehints==1.12.0
      - sphinx-bootstrap-theme==0.8.1
      - sphinx-gallery==0.10.0
      - sphinx-rtd-theme==2.0.0
      - sphinxcontrib-applehelp==1.0.2
      - sphinxcontrib-devhelp==1.0.2
      - sphinxcontrib-htmlhelp==2.0.0
      - sphinxcontrib-jquery==4.1
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-programoutput==0.17
      - sphinxcontrib-qthelp==1.0.3
      - sphinxcontrib-serializinghtml==1.1.5
      - sympy==1.9
      - terminado==0.12.1
      - testpath==0.6.0
      - threadpoolctl==3.1.0
      - tifffile==2020.9.3
      - tomli==1.2.3
      - tornado==6.1
      - tqdm==4.64.1
      - trackpy==0.5.0
      - traitlets==4.3.3
      - twine==3.8.0
      - typed-ast==1.5.5
      - typing-extensions==4.1.1
      - urllib3==1.26.20
      - validators==0.20.0
      - wcwidth==0.2.13
      - webencodings==0.5.1
      - widgetsnbextension==3.6.10
      - xarray==0.16.2
      - zipp==3.6.0
prefix: /opt/conda/envs/starfish

starfish/core/expression_matrix/test/test_serialization.py::test_save_expression_matrix
starfish/core/intensity_table/intensity_table.py
starfish/core/intensity_table/intensity_table.py