README.md

ctc-tools

Python tools to help import Cell Tracking Challenge datasets.

Usage

import ctctools

# note: `scale` allows representation of anisotropy in the image data
dataset = ctctools.load("/path/to/data", experiment="01", scale=(1., 1., 1.))

and to visualize in napari:

viewer = napari.Viewer()
viewer.add_image(
    dataset.images, 
    name=dataset.name
)
viewer.add_tracks(
    dataset.nodes.to_numpy(), 
    graph=dataset.graph, 
    name="GT tracks"
)

Usage in Google Colab

An example colab notebook is provided below.