lineagetree 2.0.3

Structure for 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 Amat 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
• Data from the Digital development Database described in Du et al. 2014 and Du et al. 2015
• 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.load('path/to/file.lT')

For ASTEC data:

from LineageTree import read_from_ASTEC
lT = read_from_ASTEC('path/to/ASTEC.pkl')

For MaMuT or TrackMate:

from LineageTree import read_from_mamut_xml
lT = read_from_mamut_xml('path/to/MaMuT.xml')

For TGMM:

from LineageTree import read_from_tgmm_xml
lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)

For Mastodon:

from LineageTree import read_from_mastodon
lT = read_from_mastodon('path/to/Mastodon.mastodon')

or, for Mastodon csv file:

from LineageTree import read_from_mastodon_csv
lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])

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