Morphodynamic domains enable integration of live tissue imaging and spatial transcriptomics - Data + code

Data and code for Leroy, Van Leen et al. : spatial transcriptomics of the Drosophila pupal notum This archive contains the data and analysis code to allow reviewers to reproduce every panel of the manuscript. The Data contains : Live-imaging tissue-mechanics tensors (velocity, deformation rate, cell anisotropy, apoptosis/division rates on a spatial grid, as a single-animal zarr and cross-animal averages in both Eulerian (lab-fixed) and Lagrangian (tissue-tracking) frames, for vRNAi (control) and TolloRNAi. Single-cell transcriptomes of the notum at 15 h APF (h5ad + raw counts). A spatial transcriptome of 4,312 genes reconstructed by vGEP from the scRNA-seq, benchmarked against novoSpaRc and PERLER on a 24-gene smFISH/GFP reference atlas. Auxiliary layers: PIV fields, morphology annotations (macrochaete positions, domain cluster labels), caspase fluorescence, pathway components. The code/ tree bundles four Python packages : morphodomains (figure framework + four walkthrough notebooks), vgep (reconstruction + GRN inference), pyanimalprocessing (tissue mechanics + napari plotting), and pyap_legacy(supplementary delamination pipeline). Installation and usage are in code/morphodomains/README.md; running python scripts/figures/generate.py reproduces every manuscript panel from the shipped data. An interactive browser for the spatial transcriptome is also available at : https://ybellaichelab.shinyapps.io/NotumvGEP/.