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Regional IF Analyzer

A GUI tool for analyzing immunofluorescence images with atlas region mapping and automated cell counting.

Description

The Regional IF Analyzer is designed to help researchers analyze immunofluorescence images by:

  • Overlaying atlas sections onto TIFF images
  • Highlighting and naming specific regions of interest
  • Detecting and counting cells within defined regions
  • Exporting results to Excel files
  • Saving annotated images

Installation

Prerequisites

  • Python 3.8 or higher
  • pip (Python package installer)
  • tkinter (usually comes with Python, but may need separate installation on Linux)

On Ubuntu/Debian Linux, you might need to install tkinter separately:

sudo apt-get install python3-tk

Setting Up

  1. Clone the repository:
git clone https://github.com/LaingLab/RegionalCounter.git
cd RegionalCounter
  1. Install required packages:
pip install -r requirements.txt

Running the Program

  1. Navigate to the program directory:
cd regioner
  1. Run the program:
python3 regioner6.00.py

Basic Usage

  1. Import TIFF Image:

    • Click "File > Import TIFF"
    • Select your TIFF image file

  2. Determine Regions

    a. Draw Region of Interest:

    • Click "Paint > Start Paint"
    • Draw a circle around the ROI
    • Once done, click "Paint > Stop Paint"

    b. Import Atlas Section:

    • Click "File > Import Atlas Section"
    • Select your PDF atlas file

  3. Align Atlas:

    • Use "Move Atlas" button to position the atlas over your image
    • Use rotation and scaling controls if needed

  4. Define Regions:

    • Click on regions to highlight them
    • Name each region when prompted

  5. Verify Mask:

    • Click "Mask > Show Mask"
    • Adjust detection with "Mask > Show Mask Settings"
    • Manually add and remove cells under "Mask > Add/Remove Cells"

  6. Count Cells:

    • Click "Count Cells" to analyze
    • Save results to Excel when prompted

Common Issues

  • If tkinter is missing: Install python3-tk package via your system's package manager
  • If images don't load: Ensure your TIFF files are in a compatible format
  • For PDF loading issues: Ensure PyMuPDF is properly installed

Support

For issues and feature requests, please open an issue in the GitHub repository.

License