Triangular meshes of the 3D apical surface of the Drosophila wing disc tissue over development

Overview: This dataset contains all triangular meshes of the 3D apical surface of the Drosophila wing imaginal disc over its development from early larval stages to early pupal stages. These meshes were used to quantify fold shape progression during larval growth and unfolding during early pupal stages in Fuhrmann, Schimmenti et al 2025. This dataset was generated at the Max Planck Institute for Molecular Cell Biology and Genetics (Dresden, Germany), Cluster of Excellence Physics of Life (TU-Dresden, Germany), and the Max Planck Institute for Physics of Complex Systems. The work was supported by funding from the Max Planck Society and Deutsche Forschungsgemeinschaft. Method: The methods for imaging, segmentation, and mesh generation are described in Fuhrmann, Krishna et al 2024 and Fuhrmann, Schimmenti et al 2025. Briefly, live wing discs were explanted at different stages of development, embedded in agarose, and imaged from multiple angles using multi-angle light sheet microscopy. All lines expressed the knock-in fluorescent reporter Ecadherin::GFP; some were also labeled on the membrane with the fluorescent dye FM4-64. Images from multiple angles were fused and then the apical surface was segmented using APOC in Napari, with manual correction. A triangular mesh was generated and processed from the basal-facing edge of this segmentation, in order to be able to visualize and quantify tissue shape within deeply folded regions that have apical surfaces very closely apposed. Note that the meshes describe the 3D shape of the apical surface, but it is not a full 3D cellular segmentation, as the basal side of the epithelium is not considered. See Fuhrmann, Schimmenti et al 2025 for full methods. Contents: The "aecm_final_meshes.zip" contains the extracted meshes (ply filetype) for various genotypes. Wildtype is w';EcadGFP/nub-Gal4,EcadGFP. Folder contains 3-4 different discs for each of the following timepoints: 74hAEL (3dAEL), 96hAEL (4dAEL), 120hAEL (5dAEL), 0hAPF(whitepupa), 2hAPF, 4hAPF. These were used for quantification of folds in Fuhrmann, Schimmenti et al 2025. Most of the images used to generate these meshes were also described in Fuhrmann, Krishna et al 2024, although the meshes were only generated later. Protease_overexpression: refers to the overexpression of Notopleural (Np) using Gal4/UAS (aka NpOX). Included are different drivers, some with constant 25C and some with a temperature shift to control the timing of Np overexpression. nub-Gal4, NpOX: genotype is w-;;UAS-Np;/w-;nub-Gal4,ecadGFP;;. Constitutive (grown at constant 25C) are those without the G80ts in the filename. Included are 3-4 different discs of 4dAEL, 5dAEL, and wL3 stages. nub-Gal4, NpOXts: genotype is w-;;UAS-Np;/w-;nub-Gal4,tub-Gal80ts,ecadGFP;;. Included are 5 discs grown for 24h up to wL3 and 3 discs grown for 26h to 2hAPF. Outside of that 24-26h, they were grown at 18C (before and after). c765-Gal4, NpOX: genotype is w-;;UAS-Np;/w-;ecadGFP;c765-Gal4;. Only wL3 stage (6 discs). Only constitutive (all grown at constant 25C). Control (for NpOX): refers to a temperature-shifted control for the NpOXts experiments (called "controlts" in Fuhrmann, Schimmenti et al 2025). Genotype: w-;ecadGFP;UAS-mCherry/w-;nub-Gal4,tub-Gal80ts,ecadGFP. Included are meshes for 2 at wL3 and 3 at 2hAPF. Temperature shift as in the NpOXts (24h to wL3 or rougly 2hr more to 2hAPF). Protease_knockdown: refers to the double knockdown of the aECM proteases Np and Stubble (Sb), included here with different drivers, timepoints up to 4hAPF. nub-Gal4i: Included are 1-4 lines at 2hAPF, 4hAPF, and 5hAPF. c765-Gal4: Included are 6 at 2hAPF and 4 at 4hAPF. zfh2-Gal4: Included are 3 each at 2hAPF and 4hAPF. 6hAPF folder contains all the meshes for this timepoint. Genotypes are either w-;ecadGFP;;/w-;nub-Gal4,ecadGFP (wild type, 4 meshes) or w-;nub-Gal4,ecadGFP;/w-;UAS-SbRNAi;UAS-NpRNAi (protease knockdown using nub-Gal4, 5 meshes). The metadata files corresponding to the folders contains information needed for scaling the meshes to microns. We also include some "flip" flags used to flip the first and second axis of the mesh, in order to have the pouch pointing upward (flip0, first axis of the vertices) and on the right (flip1, second axis) Each mesh is a different biological sample. The "aecm_cut_meshes_pouch.zip" contains meshes of the pouch that were cut from the original ones in order to quantify tissue shape changes in the pouch during eversion. They are already scaled in microns. Genotypes are either wild type (w-;ecadGFP;;/w-;nub-Gal4,ecadGFP;;) or protease knockdown (w-;nub-Gal4,ecadGFP;;/UAS-SbRNAi;UAS-NpRNAi;). For wild type, there are 3-4 meshs for each timepoints from wL3/upcrawling, 2hAPF, 4hAPF, and 6hAPF. For protease knockdown there are 3-5 meshs for each timepoint from 4hAPF to 6hAPF. We used wild type wL3 as a reference. Abbreviations that may be found in data/filenames: ecadGFP=E-cadherin::GFP, knockin GFP fusion to the adherens junction protein E-cadherin AEL=after egg laying (this is used for timing larval stages of development) wL3=wandering third larval instar (last stage of larval development); also sometimes referred to as "upcrawling" whitepupa=white pupae, corresponding to the onset of pupariation (first timepoint of pupariation; all other pupal stages are relative to this timepoint; also referred to as "0hAPF") APF=after puparium formation (used for pupal developmental stages) JF20=w-;UAS-sb-RNAi/cyoGFP;UAS-np-RNAi/tm6b; FM464=membrane dye added to some of the wing discs before imaging. Paired analysis code: Code used to analyze these meshes are included here: 10.5281/zenodo.22871940