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/src/main/

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-dshmig05: 5 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.

Images

Contains raw microscopy data that was used to generate the meshes. resolution.csv contains a list of Z, Y and X resolutions (micron / pixel).

Changelog

0.1.0

• Initial upload

0.2.0

• Added microscopy images.
• Removed cells 6 and 7 from dsh-2 / mig-5 dataset, which were not supposed to be included there.
• Removed Python cache files.