Morphodynamic atlas for Drosophila development
Creators: name: Mitchell, Noah
name: Lefebvre, Matthew
name: Jain-Sharma, Vishank
name: Claussen, Nikolas
name: Raich, Marion
name: Gustafson, Hannah
name: Bausch, Andreas
name: Streichan, Sebastian
Publisher: name: Zenodo
Year: 2024
Subjects: Developmental biology
Lightsheet microscopy
Drosophila

description: This data repository contains the Drosophila morphodynamic atlas, a collection of 478 in-toto lightsheet-microscopy recordings of the Drosophila embryo at the blastoderm stage (stages 6-9). The repository comprises 18 different genotypes. For details on the data and its formating, please see "README.md". A table of all recordings can be found in "MorphodynamicAtlas.csv". A tutorial for querying and loading data from the atlas using Python can be found in "Morphodynamic_Atlas_Tutorial.ipynb". For details of how the atlas was created and how it can be used, please see the publication.

Publication abstract: During morphogenesis, diverse cell-scale and tissue-scale processes couple to dynamically sculpt organs. In this coupling, genetic expression patterns and biochemical signals regulate and respond to mechanical deformations to ensure reproducible and robust changes in tissue geometry. A long-standing approach to characterize these interactions has been the construction of expression atlases, and these atlases have necessarily relied on fixed snapshots of embryogenesis. Addressing how expression profiles relate to tissue dynamics, however, requires a scheme for spatiotemporal registration across different classes of data that incorporates both live samples and fixed datasets. Here, we construct a morphodynamic atlas that unifies fixed and live datasets – from gene expression profiles to cytoskeletal components – into a single, morphological consensus timeline. This resource and our computational approach to global alignment facilitate hypothesis testing using quantitative comparison of data both within and across ensembles, with resolution in both space and time to relate genes to tissue rearrangement, cell behaviors, and out-of-plane motion. Examination of embryo kinematics reveals stages in which tissue flow patterns are quasi-stationary, arranged as a sequence of 'morphodynamic modules'. Temperature perturbations tune the duration of one such module – during body axis elongation – according to a simple, parameter-free scaling in which the total integrated tissue deformation is achieved at a temperature-dependent rate. By extending our approach to visceral organ formation during later stages of embryogenesis, we highlight how morphodynamic atlases can incorporate complex shapes deforming in 3D. In this context, morphodynamic modules are reflected in some, but not all, measures of tissue motion. Our approach and the resulting atlas open up the ability to quantitatively test hypotheses with resolution in both space and time, relating genes to tissue rearrangement, cell behaviors, and organ motion.
description: Program to view multi-page .tif files, e.g. Fiji. Spreadsheet program to view list of datasets. For the Python tutorial, a working python+jupyter installation (e.g. via anaconda).
Funding provided by: National Institute of General Medical SciencesROR ID: https://ror.org/04q48ey07Award Number: R35 GM138203
Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: PHY- 1748958
Funding provided by: National Science Foundation of Sri LankaROR ID: https://ror.org/010xaa060Award Number: PHY-1707973
description: Dynamic atlas of early Drosophila development, collected using in-toto lightsheet microscopy and tissue cartography.