Surface Morphometrics in 2 Hours

A condensed, single-page Surface Morphometrics tutorial designed to run end-to-end in about two hours. It starts from a pre-made IMM/OMM mitochondrial segmentation from EMPIAR-12534 and walks through meshing, curvature, a shortened 2-iteration mesh refinement, inter-membrane distances, and thickness.

Live site: https://baradlab.com/morphometrics_2hr

This is a slimmed-down offshoot of the full U Michigan CryoET tutorial.

Getting the data

curl -LO https://raw.githubusercontent.com/baradlab/morphometrics_2hr/main/download_data.sh
bash download_data.sh

This downloads the tomogram + segmentation from EMPIAR-12534 and the ribosome STAR file, organizing them under morpho_run/ (tomograms/, segmentations/, star/) for the pipeline.

Building the docs

This is a Material for MkDocs site.

python -m venv .venv-docs
.venv-docs/bin/pip install mkdocs-material
.venv-docs/bin/mkdocs serve    # live preview

Pushing to main triggers .github/workflows/build-and-deploy-docs.yml, which runs mkdocs gh-deploy --force to publish to the gh-pages branch.

License

Licensed under the BSD license. Please reuse liberally!