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
      • 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
        • Submodules
        • Module contents
      • organoid_tracker.text_popup package
      • organoid_tracker.util package
      • organoid_tracker.visualizer package
    • Module contents
OrganoidTracker
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  • organoid_tracker package »
  • organoid_tracker.position_detection_cnn package
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organoid_tracker.position_detection_cnn package

Submodules

  • organoid_tracker.position_detection_cnn.convolutional_neural_network module
  • organoid_tracker.position_detection_cnn.custom_filters module
  • organoid_tracker.position_detection_cnn.image_with_positions_to_tensor_loader module
  • organoid_tracker.position_detection_cnn.loss_functions module
  • organoid_tracker.position_detection_cnn.peak_calling module
  • organoid_tracker.position_detection_cnn.prediction_dataset module
  • organoid_tracker.position_detection_cnn.split_images module
  • organoid_tracker.position_detection_cnn.training_data_creator module
  • organoid_tracker.position_detection_cnn.training_dataset module

Module contents

Predicts where the nucleus centers are in an image using a convolutional neural network.

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