diff --git a/software/setup_windows.ps1 b/software/setup_windows.ps1
new file mode 100644
index 000000000..0c15d2f8f
--- /dev/null
+++ b/software/setup_windows.ps1
@@ -0,0 +1,524 @@
+#Requires -Version 5.1
+<#
+.SYNOPSIS
+    Setup script for Squid on Windows.
+.DESCRIPTION
+    Installs Python 3.12 and Git if they are missing, clones the repository if
+    needed, installs Python dependencies, and creates a desktop shortcut.
+
+    Both prerequisites are fetched from their official download hosts, checked
+    against a pinned SHA256 before being run, and installed silently per-user
+    so no admin rights or UAC prompts are involved. -SkipPythonInstall and
+    -SkipGitInstall opt out of either.
+
+    This script targets Python 3.12 and napari 0.7:
+
+      1. Python 3.12 is required exactly. napari 0.7 supports 3.10-3.14, but
+         3.12 is the newest version with wheels for every dependency here
+         (notably PyQt5 and hidapi), and pinning one interpreter keeps every
+         Windows install reproducible.
+
+         If no 3.12 is present the script downloads the official installer
+         from python.org and runs it silently, per-user, so no admin rights
+         or UAC prompt are needed. It installs 3.12.10 specifically: that is
+         the final 3.12 release with a Windows binary installer (3.12.11 and
+         later are source-only security releases). Pass -SkipPythonInstall to
+         require a pre-existing interpreter instead.
+
+      2. napari is installed as napari[pyqt5]==0.7.1, NOT napari[all]. As of
+         napari 0.7 the "all"/"qt" extras resolve to PyQt6, but Squid's GUI is
+         PyQt5 (control/widgets.py, control/gui_hcs.py via qtpy). Installing
+         both bindings makes qtpy's choice non-deterministic and crashes the
+         GUI, so the PyQt5 extra is requested explicitly.
+
+      3. numpy is not capped at <2. The <2 cap on setup_22.04.sh exists for
+         aicsimageio, which is not installed here (see 4).
+
+      4. aicsimageio and basicpy are NOT installed. Their only importer is
+         control/stitcher.py, which nothing in the codebase imports (the
+         active stitcher is tools/stitcher.py, an ImageJ/Fiji-based path).
+         Both are hard to build on Windows, so dropping the dead dependency
+         de-risks the install. If control/stitcher.py is ever revived, add
+         them back here.
+
+      5. Packages the Ubuntu scripts get from apt (pyqtgraph, PyQt5) are
+         installed from PyPI here, since Windows has no system package
+         manager providing them.
+.PARAMETER RepoPath
+    Path where Squid repository should be cloned. Defaults to Desktop\Squid.
+.PARAMETER SkipPythonInstall
+    Fail instead of installing Python 3.12 when no suitable interpreter is
+    found. Useful on machines where Python is managed centrally.
+.PARAMETER SkipGitInstall
+    Fail instead of installing Git when it is not found.
+#>
+
+param(
+    [string]$RepoPath = "$env:USERPROFILE\Desktop\Squid",
+    [switch]$SkipPythonInstall,
+    [switch]$SkipGitInstall
+)
+
+$ErrorActionPreference = "Stop"
+
+# Required Python version. napari 0.7 also runs on 3.10/3.11/3.13/3.14, but we
+# pin one version so every Windows machine ends up with the same environment.
+$REQUIRED_PYTHON_MAJOR = 3
+$REQUIRED_PYTHON_MINOR = 12
+$REQUIRED_PYTHON = "$REQUIRED_PYTHON_MAJOR.$REQUIRED_PYTHON_MINOR"
+
+# 3.12.10 is the last 3.12 with a Windows binary installer; 3.12.11+ are
+# source-only security releases, so this version does not float.
+#
+# The hash is of https://www.python.org/ftp/python/3.12.10/python-3.12.10-amd64.exe.
+# To re-derive it after a version bump:
+#   (Get-FileHash .\python-3.12.10-amd64.exe -Algorithm SHA256).Hash
+$PYTHON_INSTALLER_VERSION = "3.12.10"
+$PYTHON_INSTALLER_SHA256 = "67B5635E80EA51072B87941312D00EC8927C4DB9BA18938F7AD2D27B328B95FB"
+$PYTHON_INSTALLER_URL =
+    "https://www.python.org/ftp/python/$PYTHON_INSTALLER_VERSION/python-$PYTHON_INSTALLER_VERSION-amd64.exe"
+
+# Git is pinned too, for reproducibility rather than compatibility - Squid
+# works with any modern Git. To bump: pick a release from
+# https://github.com/git-for-windows/git/releases and take the SHA256 that
+# the release notes publish next to the .exe.
+$GIT_INSTALLER_VERSION = "2.55.0.3"
+$GIT_INSTALLER_TAG = "v2.55.0.windows.3"
+$GIT_INSTALLER_SHA256 = "AF12577D0FDFF74243A5988197AA49B957D5044EDC17004F6DDF0768996F1DCA"
+$GIT_INSTALLER_URL =
+    "https://github.com/git-for-windows/git/releases/download/$GIT_INSTALLER_TAG/Git-$GIT_INSTALLER_VERSION-64-bit.exe"
+
+Write-Host "Using SQUID_REPO_PATH='$RepoPath'"
+
+$SQUID_REPO_HTTP = "https://github.com/Cephla-Lab/Squid.git"
+$SQUID_SOFTWARE_ROOT = Join-Path $RepoPath "software"
+$SQUID_REPO_PATH_PARENT = Split-Path $RepoPath -Parent
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+# PowerShell's $ErrorActionPreference does not apply to native executables:
+# a failing python/pip/git call only sets $LASTEXITCODE, and the script would
+# otherwise sail past a broken install and still create a desktop shortcut.
+function Assert-LastExitCode {
+    param([string]$What)
+
+    if ($LASTEXITCODE -ne 0) {
+        throw "$What failed with exit code $LASTEXITCODE"
+    }
+}
+
+# Probe a candidate interpreter. Returns a hashtable with its version, bitness
+# and real executable path, or $null if the candidate cannot be run at all.
+function Get-PythonInfo {
+    param(
+        [string]$Exe,
+        [string[]]$Prefix = @()
+    )
+
+    $probe = "import sys; print(sys.version_info[0]); print(sys.version_info[1]); " +
+             "print(64 if sys.maxsize > 2**32 else 32); print(sys.executable)"
+
+    # A wrong-version py launcher, or the Microsoft Store python.exe stub,
+    # writes to stderr and exits non-zero. Under $ErrorActionPreference =
+    # "Stop" Windows PowerShell can turn that into a terminating
+    # NativeCommandError, so probing runs with the preference relaxed and we
+    # judge the candidate on its exit code instead.
+    $previousPreference = $ErrorActionPreference
+    $ErrorActionPreference = "Continue"
+    try {
+        $output = & $Exe @Prefix -c $probe 2>$null
+    } catch {
+        return $null
+    } finally {
+        $ErrorActionPreference = $previousPreference
+    }
+    if ($LASTEXITCODE -ne 0 -or $null -eq $output -or $output.Count -lt 4) {
+        return $null
+    }
+
+    return @{
+        Major      = [int]$output[0]
+        Minor      = [int]$output[1]
+        Bits       = [int]$output[2]
+        Executable = $output[3]
+    }
+}
+
+# Locate a 64-bit Python 3.12, or return $null. Interpreters that were found
+# but rejected are recorded in $script:FoundPythonVersions for the error path.
+function Find-Python312 {
+    # The py launcher is tried first because it can select an exact version
+    # even when a different Python owns the PATH.
+    $candidates = @()
+    if (Get-Command py -ErrorAction SilentlyContinue) {
+        $candidates += @{ Exe = "py"; Prefix = @("-$REQUIRED_PYTHON") }
+    }
+    foreach ($name in @("python$REQUIRED_PYTHON", "python3", "python")) {
+        if (Get-Command $name -ErrorAction SilentlyContinue) {
+            $candidates += @{ Exe = $name; Prefix = @() }
+        }
+    }
+    # Default per-user install location, checked explicitly because a Python
+    # this script just installed is not on this process's PATH.
+    $defaultInstall = Join-Path $env:LOCALAPPDATA "Programs\Python\Python312\python.exe"
+    if (Test-Path $defaultInstall) {
+        $candidates += @{ Exe = $defaultInstall; Prefix = @() }
+    }
+
+    $script:FoundPythonVersions = @()
+    foreach ($candidate in $candidates) {
+        $info = Get-PythonInfo -Exe $candidate.Exe -Prefix $candidate.Prefix
+        if ($null -eq $info) {
+            continue
+        }
+
+        $version = "$($info.Major).$($info.Minor)"
+        $script:FoundPythonVersions += "$version ($($info.Executable))"
+
+        if ($info.Major -ne $REQUIRED_PYTHON_MAJOR -or $info.Minor -ne $REQUIRED_PYTHON_MINOR) {
+            continue
+        }
+        if ($info.Bits -ne 64) {
+            Write-Warning "Ignoring 32-bit Python at $($info.Executable); Squid needs 64-bit Python."
+            continue
+        }
+
+        # Return sys.executable rather than the launcher so every later call
+        # (pip, the desktop shortcut) is pinned to this exact interpreter.
+        return $info.Executable
+    }
+
+    return $null
+}
+
+# Locate git.exe, or return $null.
+function Find-Git {
+    $command = Get-Command git -ErrorAction SilentlyContinue
+    if ($command) {
+        return $command.Source
+    }
+
+    # Not on PATH. A Git this script just installed will not be either, since
+    # the installer only edits PATH for new processes - but it does record
+    # where it landed: HKLM for an elevated install, HKCU for a per-user one.
+    foreach ($key in @("HKCU:\Software\GitForWindows", "HKLM:\Software\GitForWindows")) {
+        $installPath = (Get-ItemProperty -Path $key -Name InstallPath -ErrorAction SilentlyContinue).InstallPath
+        if ($installPath) {
+            $exe = Join-Path $installPath "cmd\git.exe"
+            if (Test-Path $exe) {
+                return $exe
+            }
+        }
+    }
+
+    foreach ($dir in @("$env:LOCALAPPDATA\Programs\Git", "$env:ProgramFiles\Git")) {
+        $exe = Join-Path $dir "cmd\git.exe"
+        if (Test-Path $exe) {
+            return $exe
+        }
+    }
+
+    return $null
+}
+
+# Download an installer, verify it against a known SHA256, and run it silently.
+function Invoke-SilentInstaller {
+    param(
+        [string]$DisplayName,
+        [string]$Url,
+        [string]$Sha256,
+        [string]$FileName,
+        [string[]]$InstallerArgs,
+        # Inno Setup and the Python installer both use 3010 for "succeeded,
+        # reboot pending" - the payload is usable immediately either way.
+        [int[]]$SuccessExitCodes = @(0, 3010),
+        [string]$ManualUrl
+    )
+
+    $installer = Join-Path $env:TEMP $FileName
+
+    Write-Host "Downloading $DisplayName from $Url"
+    # Invoke-WebRequest renders a progress bar per chunk in Windows PowerShell,
+    # which turns a 30-70 MB download into a multi-minute one. Older Windows
+    # also defaults to TLS 1.0, which both download hosts refuse.
+    $previousProgress = $ProgressPreference
+    $ProgressPreference = "SilentlyContinue"
+    try {
+        [Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12
+        Invoke-WebRequest -Uri $Url -OutFile $installer -UseBasicParsing
+    } finally {
+        $ProgressPreference = $previousProgress
+    }
+
+    $actualHash = (Get-FileHash -Path $installer -Algorithm SHA256).Hash
+    if ($actualHash -ne $Sha256) {
+        Remove-Item $installer -Force -ErrorAction SilentlyContinue
+        throw ("Downloaded $DisplayName installer failed its integrity check; not running it.`n" +
+               "  expected SHA256: $Sha256`n" +
+               "  actual   SHA256: $actualHash")
+    }
+
+    Write-Host "Installing $DisplayName (per-user, no admin rights needed)..."
+    $process = Start-Process -FilePath $installer -ArgumentList $InstallerArgs -Wait -PassThru
+    Remove-Item $installer -Force -ErrorAction SilentlyContinue
+
+    if ($SuccessExitCodes -notcontains $process.ExitCode) {
+        throw ("$DisplayName installer failed with exit code $($process.ExitCode). " +
+               "Install it manually from $ManualUrl and re-run this script.")
+    }
+
+    # The installers edit PATH for *new* processes; refresh this one so the
+    # re-probe by the caller can see what was just installed.
+    $machinePath = [Environment]::GetEnvironmentVariable("Path", "Machine")
+    $userPath = [Environment]::GetEnvironmentVariable("Path", "User")
+    $env:Path = (@($machinePath, $userPath) | Where-Object { $_ }) -join ";"
+}
+
+function Install-Python312 {
+    # InstallAllUsers=0 and InstallLauncherAllUsers=0 keep this out of Program
+    # Files, so the install runs without a UAC prompt. Both PrependPath and the
+    # py launcher are wanted: PrependPath for interactive use, the launcher so
+    # `py -3.12` finds this interpreter regardless of PATH order.
+    Invoke-SilentInstaller `
+        -DisplayName "Python $PYTHON_INSTALLER_VERSION" `
+        -Url $PYTHON_INSTALLER_URL `
+        -Sha256 $PYTHON_INSTALLER_SHA256 `
+        -FileName "python-$PYTHON_INSTALLER_VERSION-amd64.exe" `
+        -ManualUrl "https://www.python.org/downloads/" `
+        -InstallerArgs @(
+            "/quiet",
+            "InstallAllUsers=0",
+            "PrependPath=1",
+            "Include_launcher=1",
+            "InstallLauncherAllUsers=0",
+            "Include_test=0",
+            "AssociateFiles=0",
+            "Shortcuts=0"
+        )
+}
+
+function Install-Git {
+    # Git for Windows is an Inno Setup installer built with
+    # PrivilegesRequired=none, so an unelevated run installs per-user into
+    # %LOCALAPPDATA%\Programs\Git with no UAC prompt, and records itself under
+    # HKCU instead of HKLM. Run elevated it installs machine-wide instead;
+    # both are fine, and Find-Git handles either.
+    #
+    # The default PathOption already puts git on PATH, which is what the clone
+    # below and everyday use both need.
+    Invoke-SilentInstaller `
+        -DisplayName "Git $GIT_INSTALLER_VERSION" `
+        -Url $GIT_INSTALLER_URL `
+        -Sha256 $GIT_INSTALLER_SHA256 `
+        -FileName "Git-$GIT_INSTALLER_VERSION-64-bit.exe" `
+        -ManualUrl "https://git-scm.com/download/win" `
+        -InstallerArgs @(
+            "/VERYSILENT",
+            "/NORESTART",
+            "/SP-",
+            "/SUPPRESSMSGBOXES",
+            "/NOCANCEL"
+        )
+}
+
+# ---------------------------------------------------------------------------
+# Prerequisites
+# ---------------------------------------------------------------------------
+
+$PythonExe = Find-Python312
+
+if ($null -eq $PythonExe) {
+    $detail = if ($script:FoundPythonVersions.Count -gt 0) {
+        "Found instead: " + ($script:FoundPythonVersions -join ", ") + "."
+    } else {
+        "No Python interpreter was found on PATH."
+    }
+
+    if ($SkipPythonInstall) {
+        Write-Error ("64-bit Python $REQUIRED_PYTHON is required but was not found. $detail`n" +
+                     "Install it from https://www.python.org/downloads/ (check 'Add python.exe " +
+                     "to PATH'), or re-run without -SkipPythonInstall to install it automatically.")
+        exit 1
+    }
+
+    Write-Host "64-bit Python $REQUIRED_PYTHON not found. $detail"
+    Install-Python312
+
+    $PythonExe = Find-Python312
+    if ($null -eq $PythonExe) {
+        throw ("Python $REQUIRED_PYTHON still could not be found after installing it. " +
+               "Try opening a new terminal and re-running this script.")
+    }
+}
+Write-Host "Using Python $REQUIRED_PYTHON at $PythonExe"
+
+$GitExe = Find-Git
+
+if ($null -eq $GitExe) {
+    if ($SkipGitInstall) {
+        Write-Error ("Git was not found. Install it from https://git-scm.com/download/win, " +
+                     "or re-run without -SkipGitInstall to install it automatically.")
+        exit 1
+    }
+
+    Write-Host "Git not found."
+    Install-Git
+
+    $GitExe = Find-Git
+    if ($null -eq $GitExe) {
+        throw ("Git still could not be found after installing it. " +
+               "Try opening a new terminal and re-running this script.")
+    }
+}
+Write-Host "Using Git at $GitExe"
+Write-Host "Found $(& $GitExe --version)"
+
+# ---------------------------------------------------------------------------
+# Repository
+# ---------------------------------------------------------------------------
+
+# Clone the repo if we don't already have it
+if (-not (Test-Path $SQUID_REPO_PATH_PARENT)) {
+    New-Item -ItemType Directory -Path $SQUID_REPO_PATH_PARENT -Force | Out-Null
+}
+
+if (-not (Test-Path $RepoPath)) {
+    Write-Host "Cloning Squid repository..."
+    # --recurse-submodules: control/ndviewer_light and fluidics_v2 are
+    # submodules, and the GUI fails to start without them.
+    & $GitExe clone --recurse-submodules $SQUID_REPO_HTTP $RepoPath
+    Assert-LastExitCode "git clone"
+} else {
+    $currentHead = & $GitExe -C $RepoPath rev-parse HEAD
+    Assert-LastExitCode "git rev-parse"
+    Write-Host "Using existing repo at '$RepoPath' at HEAD=$currentHead"
+    Write-Host "Updating submodules..."
+    & $GitExe -C $RepoPath submodule update --init --recursive
+    Assert-LastExitCode "git submodule update"
+}
+
+# Create cache directory
+$cacheDir = Join-Path $SQUID_SOFTWARE_ROOT "cache"
+if (-not (Test-Path $cacheDir)) {
+    New-Item -ItemType Directory -Path $cacheDir -Force | Out-Null
+}
+
+# ---------------------------------------------------------------------------
+# Python dependencies
+# ---------------------------------------------------------------------------
+
+# Grouped for readability, but installed in a single pip call so the resolver
+# sees every constraint at once. Splitting the install lets a later call pull a
+# conflicting version of something an earlier call already placed - which is
+# exactly how a stray PyQt6 ends up beside PyQt5.
+$packages = @(
+    # Core runtime
+    "qtpy",
+    "pyserial",
+    "pandas",
+    "imageio",
+    "crc==1.3.0",
+    "lxml",
+    "lxml_html_clean",
+    "numpy",
+    "tifffile",
+    "scipy",
+    "psutil",
+    "platformdirs",
+    "pyyaml",
+    "filelock",
+    "gitpython",
+    "matplotlib",
+    "pydantic_xml",
+    # Windows-only readline replacement (control/console.py)
+    "pyreadline3",
+    # GUI. The pyqt5 extra is required - see the note at the top of this file.
+    "napari[pyqt5]==0.7.1",
+    "pyqtgraph",
+    "ndv",
+    # Image processing
+    "opencv-python-headless",
+    "opencv-contrib-python-headless",
+    "scikit-image",
+    "dask_image",
+    "ome_zarr",
+    # Optional at import time (control/core/zarr_writer.py imports it lazily),
+    # but required for the ZARR_V3 file_saving_option to work at all.
+    "tensorstore",
+    # Hardware / instrument I/O
+    "pyvisa",
+    "hidapi",
+    # Claude Code control server (mcp_microscope_server.py)
+    "mcp",
+    # Test suite
+    "pytest",
+    "pytest-qt"
+)
+
+Write-Host "Installing Python dependencies..."
+& $PythonExe -m pip install --upgrade pip setuptools wheel
+Assert-LastExitCode "pip install --upgrade pip"
+
+& $PythonExe -m pip install @packages
+Assert-LastExitCode "pip install"
+
+# Catch a mixed-binding environment early: with both bindings present qtpy
+# picks PyQt5 or PyQt6 depending on import order, and the GUI fails in ways
+# that look nothing like an install problem.
+$pyqt6Probe = "import importlib.util, sys; sys.exit(0 if importlib.util.find_spec('PyQt6') is None else 1)"
+$previousPreference = $ErrorActionPreference
+$ErrorActionPreference = "Continue"
+try {
+    & $PythonExe -c $pyqt6Probe 2>$null
+} finally {
+    $ErrorActionPreference = $previousPreference
+}
+if ($LASTEXITCODE -ne 0) {
+    Write-Warning ("PyQt6 is installed alongside PyQt5. Squid requires PyQt5; run " +
+                   "'`"$PythonExe`" -m pip uninstall PyQt6 PyQt6-Qt6 PyQt6-sip' before launching.")
+}
+
+# ---------------------------------------------------------------------------
+# Camera drivers
+# ---------------------------------------------------------------------------
+
+Write-Host ""
+Write-Host "========================================" -ForegroundColor Yellow
+Write-Host "CAMERA DRIVER INSTALLATION" -ForegroundColor Yellow
+Write-Host "========================================" -ForegroundColor Yellow
+Write-Host "Please install camera drivers manually:"
+Write-Host "  - Daheng Camera: Download Galaxy SDK from https://www.dahengimaging.com/"
+Write-Host "  - ToupCam: DLL is included in the repository"
+Write-Host ""
+
+# ---------------------------------------------------------------------------
+# Desktop shortcut
+# ---------------------------------------------------------------------------
+
+Write-Host "Creating desktop shortcut..."
+$desktopPath = [Environment]::GetFolderPath("Desktop")
+$shortcutPath = Join-Path $desktopPath "Squid_hcs.lnk"
+$iconPath = Join-Path $SQUID_SOFTWARE_ROOT "icon\cephla_logo.ico"
+$mainScript = Join-Path $SQUID_SOFTWARE_ROOT "main_hcs.py"
+
+$WshShell = New-Object -ComObject WScript.Shell
+$shortcut = $WshShell.CreateShortcut($shortcutPath)
+# Full interpreter path, not "python": the shortcut must use the same 3.12 we
+# just installed into, even if PATH later resolves "python" to something else.
+$shortcut.TargetPath = $PythonExe
+$shortcut.Arguments = "`"$mainScript`""
+$shortcut.WorkingDirectory = $SQUID_SOFTWARE_ROOT
+if (Test-Path $iconPath) {
+    $shortcut.IconLocation = $iconPath
+}
+$shortcut.Save()
+
+Write-Host "Desktop shortcut created at: $shortcutPath" -ForegroundColor Green
+
+Write-Host ""
+Write-Host "========================================" -ForegroundColor Green
+Write-Host "Setup complete!" -ForegroundColor Green
+Write-Host "========================================" -ForegroundColor Green
+Write-Host "You can launch Squid by double-clicking the desktop shortcut."