ArticlePLoS computational biology2020
Reliable estimation of membrane curvature for cryo-electron tomography.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography.Nature methods · 2026Article
- Structural plasticity of mouse intestinal microvilli revealed by tissue-level cryo-ET.Biophysics reports · 2026Article
- Spatial confinement shapes organelle architecture and remodeling in axons.bioRxiv : the preprint server for biology · 2026Article
- Electron tomography reveals mitochondrial network and cristae remodelling during cell differentiation in the human placenta.Nature communications · 2026Article
- ETSAM: Effectively Segmenting Cell Membranes in cryo-Electron Tomograms.Research square · 2026Article
- Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes.bioRxiv : the preprint server for biology · 2026Article
- Advances in Crystallography and Cryo-Electron Microscopy for the Study of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast.Molecular biology of the cell · 2025Article
- In situ cryo-electron microscopy and tomography of cellular and organismal samples.Current opinion in structural biology · 2025Review
- The bacterial type three secretion system induces mechanoporation of vacuolar membranes.PLoS biology · 2025Article
- Leveraging Virtual Reality for Immersive Segmentation and Analysis of Cryo-Electron Tomography Data.Journal of visualized experiments : JoVE · 2025Article
- Blik is an extensible 3D visualisation tool for the annotation and analysis of cryo-electron tomography data.PLoS biology · 2024Article
- Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline.The Journal of cell biology · 2023Article
- Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology.Nature methods · 2023Review
- In situ snapshots along a mammalian selective autophagy pathway.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 spike protein.Nature communications · 2023Article
- Objective analysis of facial bone fracture CT images using curvature measurement in a surface mesh model.Scientific reports · 2023Article
- Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 Spike protein.bioRxiv : the preprint server for biology · 2022Article
- In situ structural analysis reveals membrane shape transitions during autophagosome formation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry.Biophysical reports · 2022Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and molecular resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET, as these methods cannot cope with some of the artifacts introduced during image acquisition and membrane segmentation, such as quantization noise and open borders. Here, we developed and implemented a Python package for membrane curvature estimation from tomogram segmentations, which we named PyCurv. From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph, which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. PyCurv estimates curvature based on tensor voting. Beside curvatures, this algorithm also provides robust estimations of surface normals and principal directions. We tested PyCurv and three well-established methods on benchmark surfaces and biological data. This revealed the superior performance of PyCurv not only for cryo-ET, but also for data generated by other techniques such as light microscopy and magnetic resonance imaging. Altogether, PyCurv is a versatile open-source software to reliably estimate curvature of membranes and other surfaces in a wide variety of applications.
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