A production-ready Python tool for automated nuclei counting and proliferation analysis from fluorescence microscopy images. Processes DAPI (total nuclei) and proliferation marker channels (e.g., EdU/BrdU/Ki-67 in CY5, FITC, TRITC, etc.) to calculate proliferation percentages.
Note: The tool identifies proliferation marker images by the _CY5 suffix in filenames, but this is configurable. If your proliferation marker is imaged in a different channel (e.g., FITC, TRITC, Alexa Fluor 488), you can easily adapt the code or rename your files to match.
- Multi-channel Analysis: Processes DAPI (total nuclei) and any proliferation marker channel
- Channel Flexibility: Configured for CY5 by default, adaptable to FITC, TRITC, Alexa Fluor channels
- Advanced Segmentation: Uses watershed with peak_local_max for accurate nucleus separation
- Batch Processing: Automatically processes folders of image pairs
- 16-bit Support: Preserves microscopy image quality and dynamic range
- GUI Interface: User-friendly Tkinter interface for easy operation
- Comprehensive Outputs: CSV measurements, diagnostic plots, proliferation percentages
# Clone the repository
git clone https://github.com/siddhesh-0409/Dapi-nuclei-counter.git
cd Dapi-nuclei-counter
# Install dependencies
pip install -r requirements.txt