From d126d65f546ffb544e882445f23622d57dd0f135 Mon Sep 17 00:00:00 2001
From: Hongquan Li <hqlisu@gmail.com>
Date: Thu, 1 Jan 2026 13:24:44 -0800
Subject: [PATCH] feat: Add Windows setup script
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
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Adds PowerShell setup script for Windows that:
- Checks for Python and Git prerequisites
- Clones the Squid repository
- Installs Python dependencies via pip
- Creates desktop shortcut with icon

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 software/setup_windows.ps1 | 101 +++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 software/setup_windows.ps1

diff --git a/software/setup_windows.ps1 b/software/setup_windows.ps1
new file mode 100644
index 000000000..b790f9776
--- /dev/null
+++ b/software/setup_windows.ps1
@@ -0,0 +1,101 @@
+#Requires -Version 5.1
+<#
+.SYNOPSIS
+    Setup script for Squid on Windows.
+.DESCRIPTION
+    Installs Python dependencies, clones the repository if needed, and creates a desktop shortcut.
+.PARAMETER RepoPath
+    Path where Squid repository should be cloned. Defaults to Desktop\Squid.
+#>
+
+param(
+    [string]$RepoPath = "$env:USERPROFILE\Desktop\Squid"
+)
+
+$ErrorActionPreference = "Stop"
+
+Write-Host "Using SQUID_REPO_PATH='$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
+
+# Check if Python is installed
+try {
+    $pythonVersion = python --version 2>&1
+    Write-Host "Found $pythonVersion"
+} catch {
+    Write-Error "Python is not installed or not in PATH. Please install Python 3.10+ from https://python.org"
+    exit 1
+}
+
+# Check if git is installed
+try {
+    $gitVersion = git --version 2>&1
+    Write-Host "Found $gitVersion"
+} catch {
+    Write-Error "Git is not installed or not in PATH. Please install Git from https://git-scm.com"
+    exit 1
+}
+
+# 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..."
+    git clone $SQUID_REPO_HTTP $RepoPath
+} else {
+    $currentHead = git -C $RepoPath rev-parse HEAD
+    Write-Host "Using existing repo at '$RepoPath' at HEAD=$currentHead"
+}
+
+# Create cache directory
+$cacheDir = Join-Path $SQUID_SOFTWARE_ROOT "cache"
+if (-not (Test-Path $cacheDir)) {
+    New-Item -ItemType Directory -Path $cacheDir -Force | Out-Null
+}
+
+# Install Python libraries
+Write-Host "Installing Python dependencies..."
+python -m pip install --upgrade pip
+
+python -m pip install qtpy pyserial pandas imageio "crc==1.3.0" lxml numpy tifffile scipy napari pyreadline3
+python -m pip install opencv-python-headless opencv-contrib-python-headless
+python -m pip install "napari[all]" scikit-image dask_image ome_zarr aicsimageio basicpy pytest pytest-qt gitpython matplotlib pydantic_xml pyvisa hidapi psutil
+
+# Camera driver notes
+Write-Host ""
+Write-Host "========================================" -ForegroundColor Yellow
+Write-Host "CAMERA DRIVER INSTALLATION" -ForegroundColor Yellow
+Write-Host "========================================" -ForegroundColor Yellow
+Write-Host "Please install camera drivers manually:"
+Write-Host "  - Daheng Camera: Download Galaxy SDK from https://www.dahengimaging.com/"
+Write-Host "  - ToupCam: DLL is included in the repository"
+Write-Host ""
+
+# Create desktop shortcut
+Write-Host "Creating desktop shortcut..."
+$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)
+$shortcut.TargetPath = "python"
+$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."