mouse-standard-brain-mapping

PyQt5-based brain imaging analysis tool for NIfTI files with patch clamp recording point management.

Features

• Load and display NIfTI files (.nii, .nii.gz) in 3-plane view
• Manage patch clamp recording points with Bregma coordinate conversion
• Import/export recording data (CSV)
• Spatial distribution analysis and visualization

Installation

pip install PyQt5 nibabel numpy matplotlib pandas

Usage

python main.py

1. File > Open Main File - Load NIfTI file
2. Right-click image > Add Recording Point - Add recording points
3. Records > Export Recording Points - Export data

Recommended Dataset

Allen Brain Atlas v3: Download P56_Atlas.nii from Scalable Brain Atlas

Data Format

Recording points are saved in CSV format with voxel and Bregma coordinates:

ID,View,I,J,K,AP,ML,DV,Valid,Notes
A1,axial,228,317,21,0.0,0.0,0.0,True,Good cell

Visualization Tool

Independent analysis tool for electrophysiological data:

python visualize.py

License

MIT

Acknowledgments

Developed with support from Claude (Anthropic AI Assistant).