diff --git a/.github/copilot-setup-steps.yml b/.github/copilot-setup-steps.yml
deleted file mode 100644
index 0bfd93cf..00000000
--- a/.github/copilot-setup-steps.yml
+++ /dev/null
@@ -1,141 +0,0 @@
-# GitHub Copilot Coding Agent Environment Setup
-#
-# This file configures the development environment for the Copilot coding agent
-# to enable running ALL make targets from the Makefile, including tests, linting,
-# documentation generation, Docker builds, napari tests, and notebook examples.
-#
-# Configuration Overview:
-# -----------------------
-# - System dependencies for building scientific Python packages (HDF5, ATLAS, etc.)
-# - Python version management via pyenv (supports Python 3.10-3.13)
-# - Network access to PyPI and related package repositories
-# - Automatic installation of development dependencies
-# - Docker support (pre-installed in environment)
-#
-# Supported Make Targets (ALL):
-# -----------------------------
-# Unit Testing & Quality:
-#   - make all / make fast    : Run lint, mypy, fast-test, and docs-html
-#   - make test               : Run full test suite (including napari tests)
-#   - make fast-test          : Run fast test suite (exclude slow and napari tests)
-#   - make slow-test          : Run slow tests only
-#   - make napari-test        : Run napari-specific tests (requires GUI libraries)
-#   - make lint               : Run flake8 linting on all modules
-#   - make mypy               : Run mypy type checking
-#
-# Documentation:
-#   - make docs-html          : Generate HTML documentation with Sphinx
-#   - make docs-clean         : Clean documentation build artifacts
-#   - make docs-*             : Any docs target (passes to docs/Makefile)
-#
-# Requirements Management:
-#   - make pin-requirements   : Pin requirements with minimal changes
-#   - make pin-all-requirements : Regenerate all pinned requirements
-#   - make check-requirements : Verify requirements files are unchanged
-#
-# Integration & Examples:
-#   - make run-notebooks      : Run all Jupyter notebook examples
-#   - make test-examples      : Run example pipelines
-#   - make slow               : Run fast + notebooks + examples + docker
-#
-# Docker:
-#   - make docker             : Build Docker image and run smoke test
-#
-# Installation:
-#   - make install-dev        : Install development dependencies
-#   - make install-src        : Install from source
-#   - make install-released-notebooks-support : Install for released version
-#
-# Deployment (for maintainers):
-#   - make release-*          : Various release preparation and upload targets
-#   - make clean              : Clean build artifacts
-#
-# Python Version Management:
-# --------------------------
-# This setup installs Python versions based on pyproject.toml (3.10-3.13 supported).
-# The agent can switch versions using: pyenv global X.Y
-#
-# Additional Requirements:
-# ------------------------
-# Development dependencies include:
-# - requirements/REQUIREMENTS-CI.txt (main CI dependencies, includes Sphinx)
-# - requirements/REQUIREMENTS-NAPARI-CI.txt (napari-related dependencies)
-# - requirements/REQUIREMENTS-JUPYTER.txt (Jupyter notebook support)
-
-steps:
-  # Install system dependencies required for scientific Python packages
-  - run: |
-      sudo apt-get update
-      sudo apt-get install -y \
-        build-essential \
-        libhdf5-dev \
-        libatlas-base-dev \
-        gfortran \
-        pkg-config \
-        curl \
-        git \
-        make \
-        libbz2-dev \
-        libreadline-dev \
-        libsqlite3-dev \
-        libssl-dev \
-        libffi-dev \
-        liblzma-dev \
-        zlib1g-dev
-
-  # Set up pyenv for Python version management
-  # This allows switching between Python 3.9, 3.10, 3.11, 3.12, and 3.13
-  - run: |
-      curl https://pyenv.run | bash
-      echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc
-      echo 'command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
-      echo 'eval "$(pyenv init -)"' >> ~/.bashrc
-      source ~/.bashrc
-
-  # Install multiple Python versions (using latest from each major.minor version)
-  # Based on pyproject.toml requires-python: ">= 3.10, <3.14"
-  - run: |
-      export PYENV_ROOT="$HOME/.pyenv"
-      export PATH="$PYENV_ROOT/bin:$PATH"
-      eval "$(pyenv init -)"
-      pyenv install 3.10
-      pyenv install 3.11
-      pyenv install 3.12
-      pyenv install 3.13
-      pyenv global 3.10
-
-  # Upgrade pip and install build tools
-  - run: |
-      export PYENV_ROOT="$HOME/.pyenv"
-      export PATH="$PYENV_ROOT/bin:$PATH"
-      eval "$(pyenv init -)"
-      python -m pip install --upgrade pip==25.1 setuptools wheel
-
-  # Install starfish development dependencies
-  # Includes CI, napari, and Jupyter requirements
-  - run: |
-      export PYENV_ROOT="$HOME/.pyenv"
-      export PATH="$PYENV_ROOT/bin:$PATH"
-      eval "$(pyenv init -)"
-      make install-dev
-      pip install -r requirements/REQUIREMENTS-NAPARI-CI.txt || true
-      pip install -r requirements/REQUIREMENTS-JUPYTER.txt || true
-
-# Network access configuration
-# Allow access to PyPI, GitHub, and documentation sites
-network:
-  allowed-domains:
-    - pypi.org
-    - files.pythonhosted.org
-    - pythonhosted.org
-    - github.com
-    - raw.githubusercontent.com
-    - objects.githubusercontent.com
-    - codeload.github.com
-    - pyenv.run
-    - python.org
-    - www.python.org
-    - npmjs.org
-    - registry.npmjs.org
-    - spacetx-starfish.readthedocs.io
-    - readthedocs.org
diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml
new file mode 100644
index 00000000..75d416b3
--- /dev/null
+++ b/.github/workflows/copilot-setup-steps.yml
@@ -0,0 +1,50 @@
+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.13"]
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    permissions:
+      # If you want to clone the repository as part of your setup steps,
+      # for example to install dependencies, you'll need the `contents: read` permission.
+      contents: read
+
+    # Any steps you define will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v5
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
+
+      - name: Install Dependencies
+        run: |
+          make install-dev
+
+      - name: flake8 linting and mypy static type checker
+        run: |
+          make lint mypy