ArticleNature methods2023
TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 14 citations in OpenAlex.
- Morphometric analysis reveals that the chick cranial neural tube expands as an active shell.bioRxiv : the preprint server for biology · 2026Article
- MultiCell: geometric learning in multicellular development.Nature methods · 2026Article
- DynamicAtlas: a morphodynamic atlas for Drosophila development.Nature methods · 2026Article
- Capturing nematic order on tissue surfaces of arbitrary geometry.Nature communications · 2025Article
- Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data.bioRxiv : the preprint server for biology · 2025Article
- Article
- Novel imaging and biophysical approaches to study tissue hydraulics in mammalian folliculogenesis.Biophysical reviews · 2024Review
- Movies tell us how tissues develop a 3D shape.Nature methods · 2023Article
- Method of the Year 2023: methods for modeling development.Nature methods · 2023Article
- Septins regulate border cell surface geometry, shape, and motility downstream of Rho in Drosophila.Developmental cell · 2023Article
- Article
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2 authors at 1 institution in 1 country.
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Abstract
A common motif in biology is the arrangement of cells into tubes, which further transform into complex shapes. Traditionally, analysis of dynamic tissues has relied on inspecting static snapshots, live imaging of cross-sections or tracking isolated cells in three dimensions. However, capturing the interplay between in-plane and out-of-plane behaviors requires following the full surface as it deforms and integrating cell-scale motions into collective, tissue-scale deformations. Here, we present an analysis framework that builds in toto maps of tissue deformations by following tissue parcels in a static material frame of reference. Our approach then relates in-plane and out-of-plane behaviors and decomposes complex deformation maps into elementary contributions. The tube-like surface Lagrangian analysis resource (TubULAR) provides an open-source implementation accessible either as a standalone toolkit or as an extension of the ImSAnE package used in the developmental biology community. We demonstrate our approach by analyzing shape change in the embryonic Drosophila midgut and beating zebrafish heart. The method naturally generalizes to in vitro and synthetic systems and provides ready access to the mechanical mechanisms relating genetic patterning to organ shape change.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.