Surface Morphometrics GUI

A graphical interface for analyzing and quantifying membrane ultrastructure in cryo-electron tomography data. Built on the surface morphometrics pipeline by Barad et al.

What it does

Surface Morphometrics GUI lets you run the full surface morphometrics pipeline without touching the command line. Load your cryo-ET segmentations, generate surface meshes, measure curvature and distances, and visualize results — all from one interface.

Component	What it does
Mesh Generation	Converts voxel segmentations into surface meshes using screened Poisson reconstruction
PyCurv	Computes curvature measurements using a vector voting framework
Distance & Orientation	Measures distances and relative orientations between surfaces
3D Visualization	Interactive rendering of surfaces with property colormaps, ambient occlusion, and protein loading

Installation

Prerequisites

• Python 3.8+
• Conda (Miniconda or Anaconda)
• Git

The GUI drives the packaged surface morphometrics pipeline through its morphometrics command-line interface, so it must be installed into the same conda environment as the pipeline.

Already have the pipeline installed?

If you already have the morphometrics conda environment (the surface morphometrics pipeline), installing the GUI is one command:

conda activate morphometrics
pip install git+https://github.com/baradlab/surface-morphometrics-gui.git
morphometrics gui

The pipeline environment already provides the heavy scientific stack (vtk, numpy, libigl, …), so pip only adds the GUI's own layer (napari, magicgui, …).

From scratch

# Install the surface morphometrics pipeline with the GUI extra ([gui] pulls in
# the GUI alongside the `morphometrics` CLI in one step)
git clone https://github.com/GrotjahnLab/surface_morphometrics.git
cd surface_morphometrics
conda env create -f environment.yml
conda activate morphometrics
pip install -e .[gui]       # installs the `morphometrics` CLI and the gui
morphometrics --help        # verify the CLI is on PATH

For development, clone the GUI and install it editable instead: git clone … && cd surface-morphometrics-gui && pip install -e .

Launch

conda activate morphometrics
morphometrics gui

surface-morphometrics-gui is also available as a secondary, development-only launcher.

Quick start

1. Create an experiment — Set your work directory, data directory, and select a config template
2. Generate meshes — Run mesh generation from segmentations in the Mesh Generation tab
3. Curvature analysis — Compute curvature measurements in the PyCurv tab
4. Distance & orientation — Measure inter/intra-membrane distances in the Distance tab
5. Visualize — View meshes colored by properties with the built-in 3D viewer

Requires the morphometrics CLI: The GUI runs each pipeline step by invoking the installed morphometrics command (see Installation). If you see a "morphometrics CLI not found" error, activate the conda environment where you ran pip install -e . for the pipeline, then launch the GUI from that same environment.

Documentation

Full documentation: baradlab.github.io/surface-morphometrics-gui

• Installation guide
• Quick start walkthrough
• User guide

License

This project is licensed under the MIT License — see the LICENSE file for details.

Acknowledgments

• Surface morphometrics pipeline by the Grotjahn Lab
• Barad et al. (2023) — Quantitative analysis of membrane ultrastructure using cryo-ET surface morphometrics