OrganoidTracker

Tutorials

  • Manual tracking and error correction
  • Automatic tracking
  • Plugin tutorial
  • Training the neural network
  • Jupyter notebook
  • Working with custom metadata
  • Segmentation masks editor

For reference

  • API reference
  • Batch operations
  • Custom tracking formats
  • The data axes editor
  • Supported image formats
  • Installation instructions
  • The scripts
  • Supported tracking formats

Browse the code

  • organoid_tracker package
    • Subpackages
      • organoid_tracker.comparison package
      • organoid_tracker.config package
      • organoid_tracker.connecting package
      • organoid_tracker.connection_analysis package
      • organoid_tracker.coordinate_system package
      • organoid_tracker.core package
      • organoid_tracker.division_detection_cnn package
      • organoid_tracker.gui package
      • organoid_tracker.guizela_tracker_compatibility package
      • organoid_tracker.image_loading package
      • organoid_tracker.imaging package
      • organoid_tracker.link_detection_cnn package
        • Submodules
        • Module contents
      • organoid_tracker.linking package
      • organoid_tracker.linking_analysis package
      • organoid_tracker.local_marginalization package
      • organoid_tracker.plugin package
      • organoid_tracker.position_analysis package
      • organoid_tracker.position_detection package
      • organoid_tracker.position_detection_cnn package
      • organoid_tracker.text_popup package
      • organoid_tracker.util package
      • organoid_tracker.visualizer package
    • Module contents
OrganoidTracker
  • »
  • organoid_tracker package »
  • organoid_tracker.link_detection_cnn package »
  • organoid_tracker.link_detection_cnn.training_data_creator module
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organoid_tracker.link_detection_cnn.training_data_creator module

organoid_tracker.link_detection_cnn.training_data_creator.create_image_with_links_list(experiments: Iterable[Experiment], division_multiplier=5, mid_distance_multiplier=5, loose_end_multiplier=0, multiple_options_multiplier=0, div_window=3, medium_distance=(3, 7), min_cases=0)
organoid_tracker.link_detection_cnn.training_data_creator.create_image_with_possible_links_list(experiment: Experiment)
organoid_tracker.link_detection_cnn.training_data_creator.inside_image(position: ~organoid_tracker.core.position.Position, offset: <property object at 0x7fa8cc0260c0>, image_shape: ~typing.Tuple[int])
organoid_tracker.link_detection_cnn.training_data_creator.remove_random_positions(experiment, rate=0.02)
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