16. Reference API

16.1. Fusion

astec.algorithms.fusion.fusion_control(experiment, parameters)
Parameters:
  • experiment

  • parameters

Returns:

16.2. Mars

astec.algorithms.mars.build_seeds(input_image, difference_image, output_seed_image, experiment, parameters, operation_type='min', check_background_label=False)

Extract regional minima or maxima from an image and label them.

Parameters:
  • input_image – input grey image

  • difference_image – difference_image is the difference between the reconstructed image after addition of height h and the original image. This way, valley are transformed into hills. Note that the resulting image has its values in [0, h]. Such an image can be used as an input for further regional minima computation with smaller h. Note that minima of the input image become maxima of the difference image.

  • output_seed_image – labeled seeds

  • experiment

  • parameters

  • operation_type – ‘min’ for regional h-minima, ‘max’ for regional h-maxima

  • check_background_label – check whether the largest seed (assumed to be the background one) is labeled 1. If not, the largest seed/connected component is relabeled 1 (while the seed with label 1 is also relabeled).

Returns:

astec.algorithms.mars.mars_control(experiment, parameters)
Parameters:
  • experiment – class describing the experiment

  • parameters – class describing the mars parameters

Returns:

astec.algorithms.mars.mars_process(current_time, experiment, parameters)

MARS segmentation of one timepoint image. :param current_time: :param experiment: :param parameters: :return:

astec.algorithms.mars.watershed(seed_image, membrane_image, result_image, parameters)
Parameters:
  • seed_image

  • membrane_image

  • result_image

  • parameters

Returns:

16.3. Manual correction

astec.algorithms.manualcorrection.correction_control(experiment, parameters)
Parameters:
  • experiment

  • parameters

Returns:

16.4. Astec

astec.algorithms.astec.astec_control(experiment, parameters)
Parameters:
  • experiment

  • parameters

Returns:

astec.algorithms.astec.astec_process(previous_time, current_time, lineage_tree_information, experiment, parameters)
Parameters:
  • previous_time

  • current_time

  • lineage_tree_information

  • experiment

  • parameters

Returns:

astec.algorithms.astec.build_seeds_from_previous_segmentation(label_image, output_image, parameters, nprocessors=26)

Erodes all the labels in the segmented image seg :param label_image: image whose cells are to be eroded :param output_image: :param parameters: :param nprocessors: number maximum of processors allowed to be used :return:

16.5. Post correction

astec.algorithms.postcorrection.contact_surface_computation(experiment, parameters)
Parameters:
  • experiment

  • parameters

Returns:

16.6. Motion compensation aka intra-registration

astec.algorithms.intraregistration.intraregistration_control(experiment, parameters)
Parameters:
  • experiment

  • parameters

Returns:

16.7. Atlas building

16.8. Name propagation from atlases

16.9. Name initialization from atlases