Microscope Scan Tool

This project provides an interactive, GUI-based microscope scanning tool that works with Micro-Manager to capture tiled images using a motorized XY stage and live camera feed. It supports objective selection, white balance calibration, and automated metadata generation compatible with FIJI.

Features

• Objective turret control and scan setup via GUI
• Snake-pattern tiling with user-defined scan bounds
• Live camera preview with flipped display
• White patch selection for white balance correction
• Adjustable scan step sizes per objective
• Automated folder creation and scan logging
• FIJI-compatible TileConfiguration.txt export

Requirements

• Python 3.8+
• Micro-Manager (with pycromanager server running)
• Windows OS (default save directory is Windows-specific)
• Python packages:
  • pycromanager
  • opencv-python
  • numpy
  • tkinter (usually preinstalled)

Install dependencies:

pip install pycromanager opencv-python numpy

File Structure

├── main.py                          # Entry point: launches live preview, GUI, and scanning logic
├── microscope_scan_tool/            # Core package with all supporting functions
│   ├── camera_preview.py             # Handles live camera feed display and white patch overlay
│   ├── user_input_gui.py             # GUI for entering coordinates and selecting objectives
│   ├── scan_logic.py                 # Controls snake-pattern scanning and image capture sequence
│   ├── white_balance_utils.py        # Performs frame white-balance correction and median 
│   ├── shared_state.py               # Stores global camera settings, patch info, and scan state
│   ├── stage_controller.py           # Controls XY stage movement and enforces position 
│   ├── logger.py                     # Handles scan folder creation and error logging
│   └── metadata_writer.py            # Writes FIJI-compatible tile metadata (positions, overlap, 
├── archive/                          # Deprecated/older versions of modules
│   ├── camera_preview_depreciated.py
│   ├── scan_logic_depreciated.py
│   ├── user_input_gui_depreciated.py
│   └── user_input_gui_depreciated2.py
├── environment.yml                   # Conda environment for minimal project dependencies
├── environment_full.yml              # Conda environment with full optional dependencies
└── README.md                         # Project description, setup instructions, and usage guide

Usage

1. Run main.py
2. A live preview window will open and a GUI will prompt you to enter:
   • Top/Bottom Y coordinates
   • Left/Right X coordinates
   • Objective selection (4x or 20x)
3. Optionally click "White Balance Patch Select" to draw a white patch on the preview.
4. Submit to begin scanning. Captured tiles will be stored under:

C:\Users\admin\Desktop\TestCamera\Scan_YYYY-MM-DD_HH-MM-SS_Objective

Includes:

• All tile images
• A TileConfiguration_*.txt metadata file for FIJI
• A timestamped scan log

Dry Run Mode

To test scan logic without hardware movement, set dry_run=True in the snake_like_scan() function in main.py.

Notes

• Default scan bounds and step sizes are hardcoded; adjust STEP_SIZES_BY_OBJECTIVE and bounds in scan_logic.py as needed.
• This tool assumes the camera is at index 0 and that the microscope's stage is controllable via Micro-Manager.
• Supports only 4x and 20x objective labels by default.

Author

Developed by Amal Guptan with the help of LLM for the Shoykhet Lab. Contributions and suggestions welcome.