Keyence Microscope Image Stitching Script

This repository contains a Python script that automates the stitching of images captured with a Keyence microscope using the BZ_X800 Analyzer Software. The script uses the pyautogui library to simulate user interactions, streamlining the stitching process.

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Features

• Automates the opening of image folders and .gci files.
• Simulates key presses and mouse clicks for the stitching workflow in the BZ_X800 Analyzer Software.
• Customizable delays to adapt to different system setups.
• Automatically stitches images and saves the channels and overlays in the specified folder.

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Prerequisites

• Keyence BZ_X800 Analyzer Software installed on your system.
• A Windows operating system (required for pyautogui operations).
• Python 3.7 or later.

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Installation

1. Clone this repository to your local machine:

   git clone https://github.com/MehdiAliomrani/keyence-image-stitching.git

2. Navigate to the project directory:

   cd keyence-image-stitching

3. Install the required Python dependencies:

   pip install -r requirements.txt

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Usage

1. Update the test_folder variable in stitch_images.py to point to the directory containing your images.
2. Open a terminal and navigate to the project directory.
3. Run the script:

   python stitch_images.py

Important Notes:

• Ensure all images to be stitched are organized in subfolders within the test_folder.
• The script uses pre-configured delays (time.sleep) and mouse/keyboard actions tailored for the Keyence BZ_X800 Analyzer Software. Adjust these as needed for your setup.

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Example

Here’s how the folder structure should look:

Captured slides/
├── XY01/
│   ├── Image_XY01.gci
├── XY02/
│   ├── Image_XY02.gci

The script will:

1. Open each folder.
2. Process the .gci files using the BZ_X800 software.
3. Automate the stitching process through key presses and mouse clicks.
4. Save all channels and overlays to the specified folder.

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Known Issues

• The script relies on hardcoded mouse coordinates. If your screen resolution or software layout differs, adjust the coordinates in the script.
• Ensure the Keyence BZ_X800 software is running and in focus when the script starts.

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Contributing

Contributions are welcome! If you have suggestions for improvements or new features, feel free to submit an issue or a pull request.

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License

This project is licensed under the MIT License.

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Acknowledgments

Thanks to the Ghashghaei Lab for supporting this work.