marcomusy / staging_system

Know the age of a mouse embryo by measuring its hind limb.

Embryonic Mouse Staging System

Given an experimental set of 2D lines + time, compute the average shapes for each of the time points and extrapolate the shapes at intermediate time points.

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Workflow

• Align each group using rigid procrustes alignment (PA). BUT: PA allows for improper rotations (subsample mirroring) so we keep the Left/Right samples separate this would also serve as control

• Apply Iterative Closest Point, using PA output as baseline

• Extract mean outlines:

• Refit the whole experimental sample

Scripts:

• python stages_builder.py creates the averages as described above

• python compareSizes.py plots the resulting growth of the limb for the 3 datasets as a function of time:

• python stages_fitter.py creates the animation at the header of this page.