Tracking cells and lineage with deep learning.
deepcell-tracking uses deep learning models from deepcell-tf within an assignment problem framework to track cells through time-lapse sequences and build cell lineages. The assignment problem is solved using the Hungarian algorithm.
deepcell-tracking is a Python package that can be installed with
pip install deepcell-tracking
Or it can be installed from source:
git clone https://github.com/vanvalenlab/deepcell-tracking.git cd deepcell-tracking # install the dependencies pip install .
How to Use
from deepcell_tracking import CellTracker # X and y are the time-sequence data and their corresponding segmentations (labels), respectively. # model is a deepcell-tf tracking model. tracker = CellTracker(X, y, model) tracker.track_cells() # runs in place, builds tracks # Save all tracked data and lineage files to a .trk file tracker.dump('./results.trk') # Open the track file from deepcell_tracking.utils import load_trks data = load_trks('./results.trk') lineage = data['lineages'] # linage information X = data['X'] # raw X data y = data['y'] # tracked y data
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