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]


Creation of  reproducible neural tube organoids from human stem cells

More to come!