badprograms/lineagetree-1

Module to read and "work" with lineage trees

LineageTree

This library allows to import and work with cell (but not limited to cells) lineage trees. With LineageTree you can read from:

• TGMM algorithm outputs described in Fernando et al. 2014
• TrackMate files described in Tinevez et al. 2017
• MaMuT files described in Wolff et al. 2018
• SVF algorithm outputs described in McDole, Guignard et al. 2018
• ASTEC algorithm outputs described in Guignard, Fiuza et al. 2020
• and few others

Basic usage

Once installed the library can be called the following way (as an example):

from LineageTree import lineageTree

and one can then load lineage trees the following way:

For .lT files:

lT = lineageTree('path/to/file.lT')

For ASTEC data:

lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')

or

lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')

For SVF:

lT = lineageTree('path/to/SVF.bin')

For MaMuT:

lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')

For TrackMate:

lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')

For TGMM:

lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')

For Mastodon:

lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')

or, for Mastodon csv file:

lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')

Dependencies

Some dependecies are requiered:

• general python dependecies:
  • numpy, scipy
• specific dependency:
  • svgwrite if svg output is needed

Quick install

To quickly install the library together with its dependencies one can run:

pip install LineageTree

or, for the latest version if you have cloned the directory:

pip install .

or for the latest version wihtout cloning the directory

pip install git+https://github.com/leoguignard/LineageTree