Simple-Track-Builder

A very simple cell tracker from labeled images

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Installation

You can install Simple-Track-Builder via pip:

pip install Simple-Track-Builder

To install latest development version :

pip install git+https://github.com/GuignardLab/Simple-Track-Builder.git

Usage

Once installed, Simple-Track-Builder can be used multiple ways.

Command line call

Simple-Track-Builder can be called in the terminal the following way:

simple-track-builder --pathes p1.tiff p2.tiff [...] --output out_test.lT

where p1.tiff, p2.tiff, ... are the pathes to all the images to use in temporal order, from start to finish.

Instead of informing all the pathes manually, one can inform the path format, the starting and ending times:

simple-track-builder --path-format p{t:d}.tiff --start-time 0 --end-time 10 --output out_test.lT

If necessary, the background can be informed using the --background parameter.

Finally, a help for simple-track-builder can be called the following way:

simple-track-builder --help

Python

Simple-Track-Builder can be called in Python 2 different ways:

Direct function

from simple_track_builder import build_tracks

pathes = ["p1.tiff", "p2.tiff", ...]
out = "test.lT"
build_track(label_image_list=pathes, background=0, out=out)

label_image_list can also take np.ndarrays:

from simple_track_builder import build_tracks
from tifffile import imread
pathes = [imread("p1.tiff"), imread("p2.tiff"), ...]
out = "test.lT"
build_track(label_image_list=pathes, background=0, out=out)

That can be usefull when you are running tests and do not want to reload the images each time.

Class

For the most modularity, one can use the class itself:

from simple_track_builder import SimpleTrackBuilder
pathes = ["p1.tiff", "p2.tiff", ...]

lT = SimpleTrackBuilder(pathes, background=0)
lT.build_lineages()

lT.write("out.lT")

lT is a LineageTree instance that has all their properties (see there)

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the MIT license, "Simple-Track-Builder" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

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