Datasets
Morphodynamic Atlas for Drosophila Development - Dynamic atlas of early Drosophila development, collected using in-toto lightsheet microscopy and tissue cartography, comprising over recordings of early Drosophila embryos covering many different proteins and genotypes. Dataset available for download on Dryad, accompanying paper on bioRxiv.
Software
ImSAnE - a pipeline for tissue cartography [publication describing the toolkit here]
DynamicAtlas - software stack for aligning multiple datasets (both fixed and live imaging) across genotypes and proteins stained/expressed. Aligns all data into a unified developmental timeline. [docs website in prep]
TubULAR - tracks tissue motion in dynamic tube-like surfaces, returning fully covariant measurements of tissue flow. This package can be used within ImSAnE or as a standalone tool. [docs website in prep]
Protocols
Creation of reproducible neural tube organoids from human stem cells
More to come!