Repository: camlab-bioml/starling (language: python)

Issue:
Error when using init_clustering with FlowSom method
Get this error when using init_clustering(initial_clustering_method="FS"):

```
Traceback (most recent call last):
  File "/ddn_exa/campbell/dchan/starling/run_starling.py", line 400, in <module>
    main()
  File "/ddn_exa/campbell/dchan/starling/run_starling.py", line 130, in main
    starling_adata = utility.init_clustering(cluster_type, sc_expr_subset_adata, k=leiden_resolution, seed=seed)
  File "/ddn_exa/campbell/dchan/starling/starling/utility.py", line 105, in init_clustering
    pd.DataFrame(X).to_csv("fs.csv")
NameError: name 'X' is not defined
```

Presumably, the error is that it should be `adata.X` instead of just `X`. 


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8b81995..3227acd 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -7,9 +7,11 @@ on:
     branches: [ "main" ]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        python-version: [ '3.9', '3.10', '3.11', '3.12'  ]
     steps:
     - uses: actions/checkout@v3
     - name: Install Poetry
@@ -19,7 +21,7 @@ jobs:
       uses: snok/install-poetry@v1
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: ${{ matrix.python-version }}
         cache: 'poetry'
     - name: Install project
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
@@ -31,6 +33,23 @@ jobs:
     - name: Pytest
       run: |
         poetry run pytest
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install Poetry
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+      uses: snok/install-poetry@v1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+        cache: 'poetry'
+    - name: Install project
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --with docs,dev --no-interaction
     - name: Build documentation
       run: |
           mkdir gh-pages
diff --git a/Dockerfile b/Dockerfile
index 52d7df5..c4348b3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.10-slim
+FROM python:3.12-slim
 
 WORKDIR /code
 
@@ -25,7 +25,7 @@ ENV POETRY_HOME=/opt/poetry
 
 # install poetry into its own venv
 RUN python3 -m venv $POETRY_HOME && \
-    $POETRY_HOME/bin/pip install poetry==1.7.1
+    $POETRY_HOME/bin/pip install poetry==1.8.0
 
 ENV VIRTUAL_ENV=/poetry-env \
     PATH="/poetry-env/bin:$POETRY_HOME/bin:$PATH"
@@ -39,6 +39,6 @@ USER $USERNAME
 COPY --chown=${USER_UID}:${USER_GID} pyproject.toml poetry.lock README.md /code/
 COPY --chown=${USER_UID}:${USER_GID} starling/__init__.py /code/starling/__init__.py
 
-RUN poetry install --with docs,dev
+RUN poetry install --with docs,dev && poetry self add poetry-plugin-export
 
 COPY --chown=${USER_UID}:${USER_GID} . .
diff --git a/README.md b/README.md
index 11c0864..a70ba5c 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,8 @@
 ![build](https://github.com/camlab-bioml/starling/actions/workflows/main.yml/badge.svg)
 ![](https://img.shields.io/badge/Python-3.9-blue)
 ![](https://img.shields.io/badge/Python-3.10-blue)
+![](https://img.shields.io/badge/Python-3.11-blue)
+![](https://img.shields.io/badge/Python-3.12-blue)
 
 
 STARLING is a probabilistic model for clustering cells measured with spatial expression assays (e.g. IMC, MIBI, etc...) while accounting for segmentation errors.
diff --git a/poetry.lock b/poetry.lock
index 34a8004..4b4d259 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "absl-py"
@@ -11,92 +11,104 @@ files = [
     {file = "absl_py-2.1.0-py3-none-any.whl", hash = "sha256:526a04eadab8b4ee719ce68f204172ead1027549089702d99b9059f129ff1308"},
 ]
 
+[[package]]
+name = "aiohappyeyeballs"
+version = "2.3.5"
+description = "Happy Eyeballs for asyncio"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "aiohappyeyeballs-2.3.5-py3-none-any.whl", hash = "sha256:4d6dea59215537dbc746e93e779caea8178c866856a721c9c660d7a5a7b8be03"},
+    {file = "aiohappyeyeballs-2.3.5.tar.gz", hash = "sha256:6fa48b9f1317254f122a07a131a86b71ca6946ca989ce6326fff54a99a920105"},
+]
+
 [[package]]
 name = "aiohttp"
-version = "3.9.5"
+version = "3.10.3"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
+aiohappyeyeballs = ">=2.3.0"
 aiosignal = ">=1.1.2"
 async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
@@ -105,7 +117,7 @@ multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "brotlicffi"]
+speedups = ["Brotli", "aiodns (>=3.2.0)", "brotlicffi"]
 
 [[package]]
 name = "aiosignal"
@@ -220,22 +232,22 @@ files = [
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
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 [package.dependencies]
@@ -667,43 +694,38 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "cryptography"
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 optional = false
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 [package.dependencies]
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 sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
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 test-randomorder = ["pytest-randomly"]
 
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 [[package]]
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 [package.extras]
@@ -1172,61 +1194,61 @@ test = ["objgraph", "psutil"]
 
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 ]
 
 [package.dependencies]
@@ -1345,13 +1367,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.2.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1513,21 +1535,21 @@ testing = ["portend", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytes
 
 [[package]]
 name = "jaraco-functools"
-version = "4.0.1"
+version = "4.0.2"
 description = "Functools like those found in stdlib"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 more-itertools = "*"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.classes", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["jaraco.classes", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "jedi"
@@ -1593,13 +1615,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
@@ -1610,7 +1632,7 @@ rpds-py = ">=0.7.1"
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
@@ -1698,13 +1720,13 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"
 
 [[package]]
 name = "jupytext"
-version = "1.16.2"
+version = "1.16.4"
 description = "Jupyter notebooks as Markdown documents, Julia, Python or R scripts"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1716,24 +1738,24 @@ pyyaml = "*"
 tomli = {version = "*", markers = "python_version < \"3.11\""}
 
 [package.extras]
-dev = ["autopep8", "black", "flake8", "gitpython", "ipykernel", "isort", "jupyter-fs (<0.4.0)", "jupyter-server (!=2.11)", "nbconvert", "pre-commit", "pytest", "pytest-cov (>=2.6.1)", "pytest-randomly", "pytest-xdist", "sphinx-gallery (<0.8)"]
+dev = ["autopep8", "black", "flake8", "gitpython", "ipykernel", "isort", "jupyter-fs (>=1.0)", "jupyter-server (!=2.11)", "nbconvert", "pre-commit", "pytest", "pytest-cov (>=2.6.1)", "pytest-randomly", "pytest-xdist", "sphinx-gallery (<0.8)"]
 docs = ["myst-parser", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"]
 test = ["pytest", "pytest-randomly", "pytest-xdist"]
 test-cov = ["ipykernel", "jupyter-server (!=2.11)", "nbconvert", "pytest", "pytest-cov (>=2.6.1)", "pytest-randomly", "pytest-xdist"]
-test-external = ["autopep8", "black", "flake8", "gitpython", "ipykernel", "isort", "jupyter-fs (<0.4.0)", "jupyter-server (!=2.11)", "nbconvert", "pre-commit", "pytest", "pytest-randomly", "pytest-xdist", "sphinx-gallery (<0.8)"]
+test-external = ["autopep8", "black", "flake8", "gitpython", "ipykernel", "isort", "jupyter-fs (>=1.0)", "jupyter-server (!=2.11)", "nbconvert", "pre-commit", "pytest", "pytest-randomly", "pytest-xdist", "sphinx-gallery (<0.8)"]
 test-functional = ["pytest", "pytest-randomly", "pytest-xdist"]
 test-integration = ["ipykernel", "jupyter-server (!=2.11)", "nbconvert", "pytest", "pytest-randomly", "pytest-xdist"]
 test-ui = ["calysto-bash"]
 
 [[package]]
 name = "keyring"
-version = "25.2.1"
+version = "25.3.0"
 description = "Store and access your passwords safely."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "keyring-25.2.1-py3-none-any.whl", hash = "sha256:2458681cdefc0dbc0b7eb6cf75d0b98e59f9ad9b2d4edd319d18f68bdca95e50"},
-    {file = "keyring-25.2.1.tar.gz", hash = "sha256:daaffd42dbda25ddafb1ad5fec4024e5bbcfe424597ca1ca452b299861e49f1b"},
+    {file = "keyring-25.3.0-py3-none-any.whl", hash = "sha256:8d963da00ccdf06e356acd9bf3b743208878751032d8599c6cc89eb51310ffae"},
+    {file = "keyring-25.3.0.tar.gz", hash = "sha256:8d85a1ea5d6db8515b59e1c5d1d1678b03cf7fc8b8dcfb1651e8c4a524eb42ef"},
 ]
 
 [package.dependencies]
@@ -1747,8 +1769,8 @@ SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
 completion = ["shtab (>=1.1.0)"]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "kiwisolver"
@@ -1952,13 +1974,13 @@ test = ["codecov (==2.1.12)", "coverage (==6.5.0)", "pre-commit (==2.20.0)", "py
 
 [[package]]
 name = "lightning-utilities"
-version = "0.11.3.post0"
+version = "0.11.6"
 description = "Lightning toolbox for across the our ecosystem."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "lightning_utilities-0.11.3.post0-py3-none-any.whl", hash = "sha256:2aec1d067e5ab61a8978f879998850a97f9a3764ee54aade329552706b0d189b"},
-    {file = "lightning_utilities-0.11.3.post0.tar.gz", hash = "sha256:7485fad0e3c5607a6bde4507935689c553a2c91325de2127b4bb8171a601e236"},
+    {file = "lightning_utilities-0.11.6-py3-none-any.whl", hash = "sha256:ecd9953c316cbaf56ad820fbe7bd062187b9973c4a23d47b076cd59dc080a310"},
+    {file = "lightning_utilities-0.11.6.tar.gz", hash = "sha256:79fc27ef8ec8b8d55a537920f2c7610270c0c9e037fa6efc78f1aa34ec8cdf04"},
 ]
 
 [package.dependencies]
@@ -2114,40 +2136,40 @@ files = [
 
 [[package]]
 name = "matplotlib"
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 [package.dependencies]
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 tzdata = ">=2022.7"
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 [[package]]
@@ -3121,13 +3147,13 @@ files = [
 
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 python-versions = "*"
 files = [
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@@ -3239,34 +3265,33 @@ six = ">=1.5"
 
 [[package]]
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 python-versions = ">=3.8"
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 [[package]]
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 [package.dependencies]
@@ -3576,110 +3624,114 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.18.1"
+version = "0.20.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [[package]]
@@ -3873,18 +3925,19 @@ stdlib_list = "*"
 
 [[package]]
 name = "setuptools"
-version = "70.2.0"
+version = "72.1.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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 [[package]]
 name = "six"
@@ -3921,27 +3974,27 @@ files = [
 
 [[package]]
 name = "sphinx"
-version = "7.3.7"
+version = "7.4.7"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.9"
 files = [
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-babel = ">=2.9"
-colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.18.1,<0.22"
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+colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
+docutils = ">=0.20,<0.22"
 imagesize = ">=1.3"
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-packaging = ">=21.0"
-Pygments = ">=2.14"
-requests = ">=2.25.0"
-snowballstemmer = ">=2.0"
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+Jinja2 = ">=3.1"
+packaging = ">=23.0"
+Pygments = ">=2.17"
+requests = ">=2.30.0"
+snowballstemmer = ">=2.2"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = ">=2.0.0"
@@ -3952,18 +4005,18 @@ tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
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-test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=6.0)", "setuptools (>=67.0)"]
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+test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
-version = "2.2.2"
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 description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
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 python-versions = ">=3.9"
 files = [
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 [package.dependencies]
@@ -3995,49 +4048,49 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
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+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
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 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
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+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.6"
+version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
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 python-versions = ">=3.9"
 files = [
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 [package.extras]
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+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.5"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
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 python-versions = ">=3.9"
 files = [
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 [package.extras]
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+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
@@ -4071,92 +4124,92 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
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+version = "2.0.0"
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 [package.extras]
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+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
-test = ["pytest"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
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 python-versions = ">=3.9"
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 [package.extras]
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+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
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 [package.dependencies]
@@ -4272,13 +4325,13 @@ test = ["coverage[toml]", "pytest", "pytest-cov"]
 
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+    {file = "sympy-1.13.2.tar.gz", hash = "sha256:401449d84d07be9d0c7a46a64bd54fe097667d5e7181bfe67ec777be9e01cb13"},
 ]
 
 [package.dependencies]
@@ -4422,13 +4475,12 @@ optree = ["optree (>=0.11.0)"]
 
 [[package]]
 name = "torchmetrics"
-version = "1.4.0.post0"
+version = "1.4.1"
 description = "PyTorch native Metrics"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "torchmetrics-1.4.0.post0-py3-none-any.whl", hash = "sha256:ab234216598e3fbd8d62ee4541a0e74e7e8fc935d099683af5b8da50f745b3c8"},
-    {file = "torchmetrics-1.4.0.post0.tar.gz", hash = "sha256:ab9bcfe80e65dbabbddb6cecd9be21f1f1d5207bb74051ef95260740f2762358"},
+    {file = "torchmetrics-1.4.1-py3-none-any.whl", hash = "sha256:c2e7cd56dd8bdc60ae63d712f3bdce649f23bd174d9180bdd0b746e0230b865a"},
 ]
 
 [package.dependencies]
@@ -4438,15 +4490,14 @@ packaging = ">17.1"
 torch = ">=1.10.0"
 
 [package.extras]
-all = ["SciencePlots (>=2.0.0)", "ipadic (>=1.0.0)", "matplotlib (>=3.3.0)", "mecab-python3 (>=1.0.6)", "mypy (==1.9.0)", "nltk (>=3.6)", "piq (<=0.8.0)", "pretty-errors (>=1.2.0)", "pycocotools (>2.0.0)", "pystoi (>=0.3.0)", "regex (>=2021.9.24)", "scipy (>1.0.0)", "sentencepiece (>=0.2.0)", "torch (==2.3.0)", "torch-fidelity (<=0.4.0)", "torchaudio (>=0.10.0)", "torchvision (>=0.8)", "tqdm (>=4.41.0)", "transformers (>4.4.0)", "transformers (>=4.10.0)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
-audio = ["pystoi (>=0.3.0)", "torchaudio (>=0.10.0)"]
-debug = ["pretty-errors (>=1.2.0)"]
+all = ["SciencePlots (>=2.0.0)", "gammatone (>1.0.0)", "ipadic (>=1.0.0)", "matplotlib (>=3.3.0)", "mecab-python3 (>=1.0.6)", "mypy (==1.11.0)", "nltk (>=3.6)", "pesq (>=0.0.4)", "piq (<=0.8.0)", "pycocotools (>2.0.0)", "pystoi (>=0.3.0)", "regex (>=2021.9.24)", "scipy (>1.0.0)", "sentencepiece (>=0.2.0)", "torch (==2.3.1)", "torch-fidelity (<=0.4.0)", "torchaudio (>=0.10.0)", "torchvision (>=0.8)", "tqdm (>=4.41.0)", "transformers (>4.4.0)", "transformers (>=4.42.3)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
+audio = ["gammatone (>1.0.0)", "pesq (>=0.0.4)", "pystoi (>=0.3.0)", "torchaudio (>=0.10.0)"]
 detection = ["pycocotools (>2.0.0)", "torchvision (>=0.8)"]
-dev = ["SciencePlots (>=2.0.0)", "bert-score (==0.3.13)", "dython (<=0.7.5)", "fairlearn", "fast-bss-eval (>=0.1.0)", "faster-coco-eval (>=1.3.3)", "huggingface-hub (<0.23)", "ipadic (>=1.0.0)", "jiwer (>=2.3.0)", "kornia (>=0.6.7)", "lpips (<=0.1.4)", "matplotlib (>=3.3.0)", "mecab-ko (>=1.0.0)", "mecab-ko-dic (>=1.0.0)", "mecab-python3 (>=1.0.6)", "mir-eval (>=0.6)", "monai (==1.3.0)", "mypy (==1.9.0)", "netcal (>1.0.0)", "nltk (>=3.6)", "numpy (<1.27.0)", "pandas (>1.0.0)", "pandas (>=1.4.0)", "piq (<=0.8.0)", "pretty-errors (>=1.2.0)", "pycocotools (>2.0.0)", "pystoi (>=0.3.0)", "pytorch-msssim (==1.0.0)", "regex (>=2021.9.24)", "rouge-score (>0.1.0)", "sacrebleu (>=2.3.0)", "scikit-image (>=0.19.0)", "scipy (>1.0.0)", "sentencepiece (>=0.2.0)", "sewar (>=0.4.4)", "statsmodels (>0.13.5)", "torch (==2.3.0)", "torch-complex (<=0.4.3)", "torch-fidelity (<=0.4.0)", "torchaudio (>=0.10.0)", "torchvision (>=0.8)", "tqdm (>=4.41.0)", "transformers (>4.4.0)", "transformers (>=4.10.0)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
+dev = ["SciencePlots (>=2.0.0)", "bert-score (==0.3.13)", "dython (<=0.7.6)", "fairlearn", "fast-bss-eval (>=0.1.0)", "faster-coco-eval (>=1.3.3)", "gammatone (>1.0.0)", "huggingface-hub (<0.25)", "ipadic (>=1.0.0)", "jiwer (>=2.3.0)", "kornia (>=0.6.7)", "lpips (<=0.1.4)", "matplotlib (>=3.3.0)", "mecab-ko (>=1.0.0)", "mecab-ko-dic (>=1.0.0)", "mecab-python3 (>=1.0.6)", "mir-eval (>=0.6)", "monai (==1.3.2)", "mypy (==1.11.0)", "netcal (>1.0.0)", "nltk (>=3.6)", "numpy (<2.1.0)", "pandas (>1.0.0)", "pandas (>=1.4.0)", "pesq (>=0.0.4)", "piq (<=0.8.0)", "pycocotools (>2.0.0)", "pystoi (>=0.3.0)", "pytorch-msssim (==1.0.0)", "regex (>=2021.9.24)", "rouge-score (>0.1.0)", "sacrebleu (>=2.3.0)", "scikit-image (>=0.19.0)", "scipy (>1.0.0)", "sentencepiece (>=0.2.0)", "sewar (>=0.4.4)", "statsmodels (>0.13.5)", "torch (==2.3.1)", "torch-complex (<0.5.0)", "torch-fidelity (<=0.4.0)", "torchaudio (>=0.10.0)", "torchvision (>=0.8)", "tqdm (>=4.41.0)", "transformers (>4.4.0)", "transformers (>=4.42.3)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
 image = ["scipy (>1.0.0)", "torch-fidelity (<=0.4.0)", "torchvision (>=0.8)"]
-multimodal = ["piq (<=0.8.0)", "transformers (>=4.10.0)"]
+multimodal = ["piq (<=0.8.0)", "transformers (>=4.42.3)"]
 text = ["ipadic (>=1.0.0)", "mecab-python3 (>=1.0.6)", "nltk (>=3.6)", "regex (>=2021.9.24)", "sentencepiece (>=0.2.0)", "tqdm (>=4.41.0)", "transformers (>4.4.0)"]
-typing = ["mypy (==1.9.0)", "torch (==2.3.0)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
+typing = ["mypy (==1.11.0)", "torch (==2.3.1)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
 visual = ["SciencePlots (>=2.0.0)", "matplotlib (>=3.3.0)"]
 
 [[package]]
@@ -4471,13 +4522,13 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.66.4"
+version = "4.66.5"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
-    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
+    {file = "tqdm-4.66.5-py3-none-any.whl", hash = "sha256:90279a3770753eafc9194a0364852159802111925aa30eb3f9d85b0e805ac7cd"},
+    {file = "tqdm-4.66.5.tar.gz", hash = "sha256:e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad"},
 ]
 
 [package.dependencies]
@@ -4799,13 +4850,13 @@ multidict = ">=4.0"
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
+    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
 ]
 
 [package.extras]
@@ -4814,5 +4865,5 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">= 3.9, < 3.11"
-content-hash = "78380f8f6b3d0f82d6ee40c00804542f88b7fc45f0a2ea15091a9b7557d8f23a"
+python-versions = ">= 3.9, < 3.13"
+content-hash = "e1a6ffd72d2d7124a20d852de1bab0149fb7334baba3ae705ac0c49119679f53"
diff --git a/pyproject.toml b/pyproject.toml
index 2a48f79..f37372a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "biostarling"
 packages = [{ include = "starling" }]
-version = "0.1.3"
+version = "0.1.4"
 description = "Segmentation error aware clustering single-cell spatial expression data"
 repository = "https://github.com/camlab-bioml/starling"
 authors = ["Jett (Yuju) Lee <yulee@lunenfeld.ca>"]
@@ -10,17 +10,21 @@ keywords = ["imaging cytometry classifier single-cell"]
 classifiers = [
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 license = "See License.txt"
 
 [tool.poetry.dependencies]
-python = ">= 3.9, < 3.11"
+python = ">= 3.9, < 3.13"
 phenograph = "^1.5.7"
 flowsom = "^0.1.1"
 numpy = "^1.26"
-torch = "^2.4.0"
+pandas = ">= 0.23.0"
 pytorch-lightning = "^2.3.3"
 scanpy = "^1.10.2"
+torch = "^2.4.0"
 
 [tool.poetry.group.dev]
 optional = true
diff --git a/requirements.txt b/requirements.txt
index d874ef8..2ff666f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,68 +1,86 @@
-aiohttp==3.9.1 ; python_version >= "3.9" and python_version < "4.0"
-aiosignal==1.3.1 ; python_version >= "3.9" and python_version < "4.0"
-anndata==0.10.4 ; python_version >= "3.9" and python_version < "4.0"
-array-api-compat==1.4 ; python_version >= "3.9" and python_version < "4.0"
+aiohappyeyeballs==2.3.5 ; python_version >= "3.9" and python_version < "3.13"
+aiohttp==3.10.3 ; python_version >= "3.9" and python_version < "3.13"
+aiosignal==1.3.1 ; python_version >= "3.9" and python_version < "3.13"
+anndata==0.10.8 ; python_version >= "3.9" and python_version < "3.13"
+array-api-compat==1.8 ; python_version >= "3.9" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.9" and python_version < "3.11"
-attrs==23.2.0 ; python_version >= "3.9" and python_version < "4.0"
-certifi==2023.11.17 ; python_version >= "3.9" and python_version < "4.0"
-charset-normalizer==3.3.2 ; python_version >= "3.9" and python_version < "4.0"
-colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and platform_system == "Windows"
-contourpy==1.2.0 ; python_version >= "3.9" and python_version < "4.0"
-cycler==0.12.1 ; python_version >= "3.9" and python_version < "4.0"
-decorator==5.1.1 ; python_version >= "3.9" and python_version < "4.0"
-exceptiongroup==1.2.0 ; python_version >= "3.9" and python_version < "3.11"
-fcsparser==0.2.8 ; python_version >= "3.9" and python_version < "4.0"
-flowcytometrytools==0.5.1 ; python_version >= "3.9" and python_version < "4.0"
-flowsom==0.1.1 ; python_version >= "3.9" and python_version < "4.0"
-fonttools==4.47.2 ; python_version >= "3.9" and python_version < "4.0"
-frozenlist==1.4.1 ; python_version >= "3.9" and python_version < "4.0"
-fsspec[http]==2023.12.2 ; python_version >= "3.9" and python_version < "4.0"
-h5py==3.10.0 ; python_version >= "3.9" and python_version < "4.0"
-idna==3.6 ; python_version >= "3.9" and python_version < "4.0"
-igraph==0.10.8 ; python_version >= "3.9" and python_version < "4.0"
-importlib-resources==6.1.1 ; python_version >= "3.9" and python_version < "3.10"
-joblib==1.3.2 ; python_version >= "3.9" and python_version < "4.0"
-kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4.0"
-leidenalg==0.10.1 ; python_version >= "3.9" and python_version < "4.0"
-lightning-utilities==0.10.0 ; python_version >= "3.9" and python_version < "4.0"
-llvmlite==0.41.1 ; python_version >= "3.9" and python_version < "4.0"
-matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "4.0"
-minisom==2.3.1 ; python_version >= "3.9" and python_version < "4.0"
-multidict==6.0.4 ; python_version >= "3.9" and python_version < "4.0"
-natsort==8.4.0 ; python_version >= "3.9" and python_version < "4.0"
-networkx==3.2.1 ; python_version >= "3.9" and python_version < "4.0"
-numba==0.58.1 ; python_version >= "3.9" and python_version < "4.0"
-numpy==1.26.3 ; python_version >= "3.9" and python_version < "4.0"
-packaging==23.2 ; python_version >= "3.9" and python_version < "4.0"
-pandas==2.1.4 ; python_version >= "3.9" and python_version < "4.0"
-patsy==0.5.6 ; python_version >= "3.9" and python_version < "4.0"
-phenograph==1.5.7 ; python_version >= "3.9" and python_version < "4.0"
-pillow==10.2.0 ; python_version >= "3.9" and python_version < "4.0"
-psutil==5.9.7 ; python_version >= "3.9" and python_version < "4.0"
-pynndescent==0.5.11 ; python_version >= "3.9" and python_version < "4.0"
-pyparsing==3.1.1 ; python_version >= "3.9" and python_version < "4.0"
-python-dateutil==2.8.2 ; python_version >= "3.9" and python_version < "4.0"
-pytorch-lightning==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
-pytz==2023.3.post1 ; python_version >= "3.9" and python_version < "4.0"
-pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0"
-requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0"
-scanpy==1.9.5 ; python_version >= "3.9" and python_version < "4.0"
-scikit-learn==1.4.0 ; python_version >= "3.9" and python_version < "4.0"
-scipy==1.11.4 ; python_version >= "3.9" and python_version < "4.0"
-seaborn==0.13.1 ; python_version >= "3.9" and python_version < "4.0"
-session-info==1.0.0 ; python_version >= "3.9" and python_version < "4.0"
-setuptools==69.0.3 ; python_version >= "3.9" and python_version < "4.0"
-six==1.16.0 ; python_version >= "3.9" and python_version < "4.0"
-statsmodels==0.14.1 ; python_version >= "3.9" and python_version < "4.0"
-stdlib-list==0.10.0 ; python_version >= "3.9" and python_version < "4.0"
-texttable==1.7.0 ; python_version >= "3.9" and python_version < "4.0"
-threadpoolctl==3.2.0 ; python_version >= "3.9" and python_version < "4.0"
-torch==1.12.1 ; python_version >= "3.9" and python_version < "4.0"
-torchmetrics==1.3.0.post0 ; python_version >= "3.9" and python_version < "4.0"
-tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0"
-typing-extensions==4.9.0 ; python_version >= "3.9" and python_version < "4.0"
-tzdata==2023.4 ; python_version >= "3.9" and python_version < "4.0"
-umap-learn==0.5.5 ; python_version >= "3.9" and python_version < "4.0"
-urllib3==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
-yarl==1.9.4 ; python_version >= "3.9" and python_version < "4.0"
-zipp==3.17.0 ; python_version >= "3.9" and python_version < "3.10"
+attrs==24.2.0 ; python_version >= "3.9" and python_version < "3.13"
+colorama==0.4.6 ; python_version >= "3.9" and python_version < "3.13" and platform_system == "Windows"
+contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
+cycler==0.12.1 ; python_version >= "3.9" and python_version < "3.13"
+decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
+exceptiongroup==1.2.2 ; python_version >= "3.9" and python_version < "3.11"
+fcsparser==0.2.8 ; python_version >= "3.9" and python_version < "3.13"
+filelock==3.15.4 ; python_version >= "3.9" and python_version < "3.13"
+flowcytometrytools==0.5.1 ; python_version >= "3.9" and python_version < "3.13"
+flowsom==0.1.1 ; python_version >= "3.9" and python_version < "3.13"
+fonttools==4.53.1 ; python_version >= "3.9" and python_version < "3.13"
+frozenlist==1.4.1 ; python_version >= "3.9" and python_version < "3.13"
+fsspec==2024.6.1 ; python_version >= "3.9" and python_version < "3.13"
+fsspec[http]==2024.6.1 ; python_version >= "3.9" and python_version < "3.13"
+get-annotations==0.1.2 ; python_version >= "3.9" and python_version < "3.10"
+h5py==3.11.0 ; python_version >= "3.9" and python_version < "3.13"
+idna==3.7 ; python_version >= "3.9" and python_version < "3.13"
+igraph==0.11.6 ; python_version >= "3.9" and python_version < "3.13"
+importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "3.10"
+jinja2==3.1.4 ; python_version >= "3.9" and python_version < "3.13"
+joblib==1.4.2 ; python_version >= "3.9" and python_version < "3.13"
+kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "3.13"
+legacy-api-wrap==1.4 ; python_version >= "3.9" and python_version < "3.13"
+leidenalg==0.10.2 ; python_version >= "3.9" and python_version < "3.13"
+lightning-utilities==0.11.6 ; python_version >= "3.9" and python_version < "3.13"
+llvmlite==0.43.0 ; python_version >= "3.9" and python_version < "3.13"
+markupsafe==2.1.5 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.9.1.post1 ; python_version >= "3.9" and python_version < "3.13"
+minisom==2.3.2 ; python_version >= "3.9" and python_version < "3.13"
+mpmath==1.3.0 ; python_version >= "3.9" and python_version < "3.13"
+multidict==6.0.5 ; python_version >= "3.9" and python_version < "3.13"
+natsort==8.4.0 ; python_version >= "3.9" and python_version < "3.13"
+networkx==3.2.1 ; python_version >= "3.9" and python_version < "3.13"
+numba==0.60.0 ; python_version >= "3.9" and python_version < "3.13"
+numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+nvidia-cublas-cu12==12.1.3.1 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cuda-cupti-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cuda-nvrtc-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cuda-runtime-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cudnn-cu12==9.1.0.70 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cufft-cu12==11.0.2.54 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-curand-cu12==10.3.2.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cusolver-cu12==11.4.5.107 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cusparse-cu12==12.1.0.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-nccl-cu12==2.20.5 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-nvjitlink-cu12==12.6.20 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-nvtx-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+packaging==24.1 ; python_version >= "3.9" and python_version < "3.13"
+pandas==2.2.2 ; python_version >= "3.9" and python_version < "3.13"
+patsy==0.5.6 ; python_version >= "3.9" and python_version < "3.13"
+phenograph==1.5.7 ; python_version >= "3.9" and python_version < "3.13"
+pillow==10.4.0 ; python_version >= "3.9" and python_version < "3.13"
+psutil==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
+pynndescent==0.5.13 ; python_version >= "3.9" and python_version < "3.13"
+pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "3.13"
+python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_version < "3.13"
+pytorch-lightning==2.4.0 ; python_version >= "3.9" and python_version < "3.13"
+pytz==2024.1 ; python_version >= "3.9" and python_version < "3.13"
+pyyaml==6.0.2 ; python_version >= "3.9" and python_version < "3.13"
+scanpy==1.10.2 ; python_version >= "3.9" and python_version < "3.13"
+scikit-learn==1.5.1 ; python_version >= "3.9" and python_version < "3.13"
+scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.13"
+seaborn==0.13.2 ; python_version >= "3.9" and python_version < "3.13"
+session-info==1.0.0 ; python_version >= "3.9" and python_version < "3.13"
+setuptools==72.1.0 ; python_version >= "3.9" and python_version < "3.13"
+six==1.16.0 ; python_version >= "3.9" and python_version < "3.13"
+statsmodels==0.14.2 ; python_version >= "3.9" and python_version < "3.13"
+stdlib-list==0.10.0 ; python_version >= "3.9" and python_version < "3.13"
+sympy==1.13.2 ; python_version >= "3.9" and python_version < "3.13"
+texttable==1.7.0 ; python_version >= "3.9" and python_version < "3.13"
+threadpoolctl==3.5.0 ; python_version >= "3.9" and python_version < "3.13"
+torch==2.4.0 ; python_version >= "3.9" and python_version < "3.13"
+torchmetrics==1.4.1 ; python_version >= "3.9" and python_version < "3.13"
+tqdm==4.66.5 ; python_version >= "3.9" and python_version < "3.13"
+triton==3.0.0 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version < "3.13" and python_version >= "3.9"
+typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.13"
+tzdata==2024.1 ; python_version >= "3.9" and python_version < "3.13"
+umap-learn==0.5.6 ; python_version >= "3.9" and python_version < "3.13"
+yarl==1.9.4 ; python_version >= "3.9" and python_version < "3.13"
+zipp==3.20.0 ; python_version >= "3.9" and python_version < "3.10"
diff --git a/starling/utility.py b/starling/utility.py
index b86c988..6bb449d 100644
--- a/starling/utility.py
+++ b/starling/utility.py
@@ -9,6 +9,8 @@
 import scanpy.external as sce
 import torch
 
+# patch outdated flowsom dependencies
+pd.DataFrame.as_matrix = pd.DataFrame.to_numpy
 collections.MutableMapping = abc.MutableMapping
 from flowsom import flowsom
 from scanpy import AnnData
@@ -107,7 +109,7 @@ def init_clustering(
     elif initial_clustering_method == "FS":
         ## needs to output to csv first
         # ofn = OPATH + "fs_" + ONAME + ".csv"
-        pd.DataFrame(X).to_csv("fs.csv")
+        pd.DataFrame(adata.X).to_csv("fs.csv")
         fsom = flowsom("fs.csv", if_fcs=False, if_drop=True, drop_col=["Unnamed: 0"])
 
         fsom.som_mapping(


Test patch:
diff --git a/tests/test_utility.py b/tests/test_utility.py
index f2c522d..2b8d180 100644
--- a/tests/test_utility.py
+++ b/tests/test_utility.py
@@ -35,6 +35,12 @@ def test_init_clustering_pg(simple_adata):
     assert_annotated(initialized, k)
 
 
+def test_init_clustering_fs(simple_adata):
+    k = 2
+    initialized = init_clustering("FS", simple_adata, k)
+    assert_annotated(initialized, k)
+
+
 def test_init_clustering_user(simple_adata):
     k = 3
     initialized = init_clustering(