/TLS-morpho

A script to measure Trunk like structure morphology

Primary LanguagePythonMIT LicenseMIT

Computing some morphological metrics

This code is related to the article Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites.

Globally, it allows to compute some morphological metrics from binary images in 2D and 3D.

Provided a isotropic masked image, its distance transform (see this scipy module for example), a voxel size and potentially an anterior and posterior position (only for 2D images), it allows to compute:

  • length

  • width

  • aspect ratio: $\frac{length}{width}$

  • volume ($V$) or area ($A$) in 2D

  • surface ($S$) or perimeter ($p$) in 2D

  • solidity: $\frac{V}{V_{conv-hull}}$

  • the sphericity (circularity in 2D): $\frac{\pi^\frac{1}{3}(6V)^{\frac{2}{3}}}{S}$ (or $\frac{4\pi A}{p^2}$ in 2D)

In this repository

You can find:

  • Computing_metrics.py which contains the main script

  • example.py which shows an example on how to use the script

  • LICENSE, the license

  • data/* are example images on which you can test the script

Dependencies