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

2. Install required packages:

pip install -r requirements.txt

Running the Program

1. Navigate to the program directory:

cd regioner

2. 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