A graphical user interface for analyzing and quantifying membrane ultrastructure in cryo-electron tomography data. This tool provides and accessible interface to the surface morphometrics pipeline developed by Barad et al. (2023).
The Surface Morphometrics GUI enables researchers to:
- Load and visualize 3D membrane segmentations from cryo-ET data
- Generate high-quality surface mesh reconstructions using screened Poisson reconstruction
- Analyze membrane features including:
- Inter and Intra membrane spacing
- Membrane curvature
- Relative orientation between membrane surfaces
- Statistical analysis of membrane features across multiple samples
- Install the surface morphometrics pipeline here
- Python 3.8 or higher
- Clone the repositories
git clone https://github.com/baradlab/surface_morphometrics.git
git clone https://github.com/baradlab/surface-morphometrics-gui.git- Go to the surface morphometrics directory
cd surface_morphometrics
- Install conda environment
conda env create -f environment.yml
- Activate the conda environment
conda activate morphometrics
- Install additional dependencies
pip install -r pip_requirements.txt
- exit the surface morphometrics directory and open the gui directory
cd surface-morphometrics-gui/src
- Run the GUI
python main.py
- Interactive visualization of membrane segmentations
- Configuration file editor
- Tabs for running each step of the surface morphometrics pipeline
- Interactive Color coding for segmentation classes
This project is licensed under the MIT licence - see the LICESNSE file for details
- OG surface morphometrics pipeline by Barad et al