Index

_

__init__() (zedprofiler.IO.loading_classes.ObjectLoader method) (zedprofiler.IO.loading_classes.TwoObjectLoader method)

A

anisotropy_factor (zedprofiler.IO.loading_classes.ImageSetLoader attribute)

anisotropy_spacing (zedprofiler.featurization.volumesizeshape.SupportsImageSetLoader attribute) (zedprofiler.IO.loading_classes.ImageSetLoader attribute)

B

bisection_costes_threshold_calculation() (in module zedprofiler.featurization.colocalization)

C

calculate_centroid() (in module zedprofiler.featurization.neighbors) calculate_colocalization() (in module zedprofiler.featurization.colocalization) calculate_surface_area() (in module zedprofiler.featurization.volumesizeshape) channel (zedprofiler.IO.feature_writing_utils.FeatureMetadata attribute) check_for_xy_squareness() (in module zedprofiler.image_utils.image_utils) classify_cells_into_shells() (in module zedprofiler.featurization.neighbors) compartment (zedprofiler.featurization.colocalization.SupportsTwoObjectLoader attribute) (zedprofiler.IO.feature_writing_utils.FeatureMetadata attribute) (zedprofiler.IO.loading_classes.TwoObjectLoader attribute) compartments (zedprofiler.IO.loading_classes.ImageSetLoader attribute)

compute_colocalization() (in module zedprofiler.featurization.colocalization) compute_granularity() (in module zedprofiler.featurization.granularity) compute_intensity() (in module zedprofiler.featurization.intensity) compute_neighbors() (in module zedprofiler.featurization.neighbors) compute_texture() (in module zedprofiler.featurization.texture) compute_volume_size_shape() (in module zedprofiler.featurization.volumesizeshape) config (zedprofiler.IO.loading_classes.ObjectLoader attribute) cpu_or_gpu (zedprofiler.IO.feature_writing_utils.FeatureMetadata attribute) create_results_dataframe() (in module zedprofiler.featurization.neighbors) crop_3D_image() (in module zedprofiler.featurization.neighbors) (in module zedprofiler.image_utils.image_utils)

E

euclidean_distance_from_centroid() (in module zedprofiler.featurization.neighbors)

expand_box() (in module zedprofiler.image_utils.image_utils)

F

feature_type (zedprofiler.IO.feature_writing_utils.FeatureMetadata attribute)

FeatureMetadata (class in zedprofiler.IO.feature_writing_utils) format_morphology_feature_name() (in module zedprofiler.IO.feature_writing_utils)

G

get_anisotropy() (zedprofiler.IO.loading_classes.ImageSetLoader method) get_compartments() (zedprofiler.IO.loading_classes.ImageSetLoader method) get_coordinates() (in module zedprofiler.featurization.neighbors)

get_image() (zedprofiler.IO.loading_classes.ImageSetLoader method) get_image_names() (zedprofiler.IO.loading_classes.ImageSetLoader method) get_outline() (in module zedprofiler.featurization.intensity) get_unique_objects_in_compartments() (zedprofiler.IO.loading_classes.ImageSetLoader method)

I

image1 (zedprofiler.featurization.colocalization.SupportsTwoObjectLoader attribute) (zedprofiler.IO.loading_classes.TwoObjectLoader attribute) image2 (zedprofiler.featurization.colocalization.SupportsTwoObjectLoader attribute) (zedprofiler.IO.loading_classes.TwoObjectLoader attribute) image_names (zedprofiler.IO.loading_classes.ImageSetLoader attribute) image_set_dict (zedprofiler.IO.loading_classes.ImageSetLoader attribute)

image_set_loader (zedprofiler.featurization.colocalization.SupportsTwoObjectLoader attribute) (zedprofiler.IO.loading_classes.ObjectLoader attribute) (zedprofiler.IO.loading_classes.TwoObjectLoader attribute) image_set_name (zedprofiler.IO.loading_classes.ImageSetConfig attribute) (zedprofiler.IO.loading_classes.ImageSetLoader attribute) ImageSetConfig (class in zedprofiler.IO.loading_classes) ImageSetLoader (class in zedprofiler.IO.loading_classes)

L

label_image (zedprofiler.featurization.colocalization.SupportsTwoObjectLoader attribute) (zedprofiler.featurization.volumesizeshape.SupportsObjectLoader attribute) (zedprofiler.IO.loading_classes.TwoObjectLoader attribute)

label_key_name (zedprofiler.IO.loading_classes.ImageSetConfig attribute) linear_costes_threshold_calculation() (in module zedprofiler.featurization.colocalization)

M

mahalanobis_distance_from_centroid() (in module zedprofiler.featurization.neighbors) measure_3D_volume_size_shape() (in module zedprofiler.featurization.volumesizeshape) module zedprofiler.featurization.colocalization zedprofiler.featurization.granularity zedprofiler.featurization.intensity zedprofiler.featurization.neighbors zedprofiler.featurization.texture zedprofiler.featurization.volumesizeshape zedprofiler.image_utils.image_utils zedprofiler.IO.feature_writing_utils zedprofiler.IO.loading_classes

N

neighbors_expand_box() (in module zedprofiler.featurization.neighbors)

new_crop_border() (in module zedprofiler.image_utils.image_utils)

O

object_ids (zedprofiler.featurization.colocalization.SupportsTwoObjectLoader attribute) (zedprofiler.featurization.volumesizeshape.SupportsObjectLoader attribute) (zedprofiler.IO.loading_classes.TwoObjectLoader attribute)

ObjectLoader (class in zedprofiler.IO.loading_classes)

P

plot_distance_distributions() (in module zedprofiler.featurization.neighbors)

prepare_two_images_for_colocalization() (in module zedprofiler.featurization.colocalization)

R

raw_image_key_name (zedprofiler.IO.loading_classes.ImageSetConfig attribute)

remove_underscores_from_string() (in module zedprofiler.IO.feature_writing_utils)

S

save_features_as_parquet() (in module zedprofiler.IO.feature_writing_utils) scale_image() (in module zedprofiler.featurization.texture) select_objects_from_label() (in module zedprofiler.image_utils.image_utils) single_3D_image_expand_bbox() (in module zedprofiler.image_utils.image_utils)

square_off_xy_crop_bbox() (in module zedprofiler.image_utils.image_utils) SupportsImageSetLoader (class in zedprofiler.featurization.volumesizeshape) SupportsObjectLoader (class in zedprofiler.featurization.volumesizeshape) SupportsTwoObjectLoader (class in zedprofiler.featurization.colocalization)

T

TwoObjectLoader (class in zedprofiler.IO.loading_classes)

U

unique_compartment_objects (zedprofiler.IO.loading_classes.ImageSetLoader attribute)

unique_label_objects (zedprofiler.IO.loading_classes.ImageSetLoader attribute)

V

visualize_organoid_shells() (in module zedprofiler.featurization.neighbors)

Z

zedprofiler.featurization.colocalization module zedprofiler.featurization.granularity module zedprofiler.featurization.intensity module zedprofiler.featurization.neighbors module zedprofiler.featurization.texture module

zedprofiler.featurization.volumesizeshape module zedprofiler.image_utils.image_utils module zedprofiler.IO.feature_writing_utils module zedprofiler.IO.loading_classes module