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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.

Getting Started

deepcell-tracking is a Python package that can be installed with pip:

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

fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data

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Track cells and build cell lineages

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GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
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DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
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35 stars
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6 forks
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GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
Skip to content
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Repository files navigation
DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
35 stars
Watchers
5 watching
Forks
6 forks
Report repository
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GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
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DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
35 stars
Watchers
5 watching
Forks
6 forks
Report repository
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
Skip to content
BranchesTags
Repository files navigation
DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
35 stars
Watchers
5 watching
Forks
6 forks
Report repository
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, 'i');
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var __m = "*";
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GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
Skip to content
BranchesTags
Repository files navigation
DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
35 stars
Watchers
5 watching
Forks
6 forks
Report repository
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Used by
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
Skip to content
BranchesTags
Repository files navigation
DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
35 stars
Watchers
5 watching
Forks
6 forks
Report repository
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GitHub - vanvalenlab/deepcell-tracking: Track cells and build cell lineages · GitHub
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BranchesTags
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DeepCell Tracking Banner
PyPI versionBuild StatusCoverage Status
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.
Getting Started
deepcell-tracking is a Python package that can be installed with pip:
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
fromdeepcell_trackingimportCellTracker# 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 filetracker.dump('./results.trk')
# Open the track filefromdeepcell_tracking.utilsimportload_trksdata=load_trks('./results.trk')
lineage=data['lineages'] # linage informationX=data['X'] # raw X datay=data['y'] # tracked y data
About
Track cells and build cell lineages
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
35 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
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Used by
Contributors
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