Data and code for "Cell shape characterization, alignment and comparison using FlowShape"

Code

This folder contains a snapshot of the FlowShape Python package at the time of paper submission. The latest version is available at: https://bitbucket.org/pgmsembryogenesis/flowshape/

Data

Contain 3D meshes of C. elegans early embryo cells, in Wavefront .obj format. Each filename has three parts sepparated by underscores

• Embryo identifier
• Cell name
• Timestep For example: wt13_ABar_18 Embryo = wt13 Cell = ABar Timestep = 18

The timesteps are frames from the original timelapse, where one frame corresponds to 90 seconds. The starting point is arbitrary, so time is aligned by EMS division.

Embryo labels:

• 7cell01-7cell07: 7 wild-type embryos imaged only around the seven-cell stage.
• wt01-wt19: 19 wild-type embryos imaged for a longer time.
• dshmig01-dshmig07: 7 dsh-2 / mig-5 RNAi knockdown embryos, imaged around seven-cell stage.

cell_filters.csv is a CSV file containing identifiers of embryos left out of the analysis because of automatically detected errors. Further, wt06 was also left out because of problems with labeling the cells.