Utility to visualize tracks in napari

SchmollerLab / Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

BSD 3-Clause "New" or "Revised" License

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Utility to visualize tracks in napari #151

Open ElpadoCan opened 2 years ago

ElpadoCan commented 2 years ago

Allow visualization of the tracks into napari via utiliy and via menu or button in the gui. Pseudo code:

video_path = 'path/to/video'

video_data = np.load(video_path)['arr_0']

acdc_df_path =  'path/to/acdc_output.csv'

acdc_df = pd.read_csv(acdc_df_path)

tracks_data = acdc_df[['Cell_ID', 'frame_i', 'y_centroid', 'x_centroid']].to_numpy()

viewer = napari.Viewer()
viewer.add_image(video_data, name='phase contrast')
viewer.add_tracks(tracks_data, name='phase contrast')

napari.run()

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