Installation

Prerequisites

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

If you already have morphometrics installed, but not the gui:

If you already have the morphometrics conda environment (the surface morphometrics pipeline), installing the GUI is a single command into that environment:

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 dependencies (napari, magicgui, …).

From scratch

Install the surface morphometrics pipeline with the [gui] extra, which 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

For development, clone the GUI and install it editable: pip install -e . from the GUI repo root.

Launch the GUI

With the morphometrics conda environment active:

conda activate morphometrics
morphometrics gui

surface-morphometrics-gui is also available as a secondary, development-only launcher (the GUI's own console script).

Tip

Always activate the conda environment before launching the GUI:

conda activate morphometrics

Verify the installation

When the GUI opens, you should see the experiment manager panel on the right side. If you see any import errors, make sure you installed all dependencies from both the pipeline and GUI repositories.