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: