Index

A

add_coordinates() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) add_daughter() (morphonet.plot.Dataset method) add_dropdown() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) add_filepicker() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) add_filesaver() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) add_inputfield() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) add_link() (morphonet.plot.Dataset method) add_mother() (morphonet.plot.Dataset method)

add_property() (morphonet.data.dataset.DatasetStep method) add_seed() (morphonet.plot.Dataset method) add_segmentation() (morphonet.data.dataset.DatasetStep method) add_toggle() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) Addlink (class in morphonet.plugins.EditTemporalLinks.Addlink) AdvancedParameters (class in morphonet.data.dataset) Annotation (class in morphonet.plot) ask_regionprop() (morphonet.plot.Dataset method) augmenter() (in module morphonet.plugins.DeNovoSegmentation.StardistTrain)

B

Binarize (class in morphonet.plugins.DeNovoSegmentation.Binarize)

BinBox (class in morphonet.plugins.DeNovoSegmentation.BinBox) BinCha (class in morphonet.plugins.DeNovoSegmentation.BinCha)

C

cancel() (morphonet.plot.Dataset method) CellposePredict (class in morphonet.plugins.DeNovoSegmentation.CellposePredict) CellposeTrain (class in morphonet.plugins.DeNovoSegmentation.CellPoseTrain) change_dataset_owner() (morphonet.net.Net method) change_property_owner() (morphonet.net.Net method) clean_at() (morphonet.data.dataproperty.DataProperty method) clean_property_at() (morphonet.data.dataset.DatasetStep method) clear_dataset() (morphonet.net.Net method) clear_mesh_at() (morphonet.net.Net method) Close (class in morphonet.plugins.ShapeTransform.Close)

compute_lineage_distance() (morphonet.plot.Dataset method) compute_property() (morphonet.data.dataset.DatasetAnalysis method) compute_property_all_steps() (morphonet.data.dataset.DatasetAnalysis method) compute_property_at() (morphonet.data.dataset.DatasetAnalysis method) compute_property_at_time_step() (morphonet.data.dataset.DatasetAnalysis method) contains_property_at() (morphonet.data.dataset.DatasetStep method) contains_segmentation_image_at() (morphonet.data.dataset.DatasetStep method) Convex (class in morphonet.plugins.ShapeTransform.Convex) copy_previous_vtk() (morphonet.plot.Dataset method) CopyPaste (class in morphonet.plugins.SegmentationCorrection.CopyPaste) create_dataset() (morphonet.net.Net method)

D

DataProperty (class in morphonet.data.dataproperty) Dataset (class in morphonet.plot) DatasetAnalysis (class in morphonet.data.dataset) DatasetStep (class in morphonet.data.dataset) Deform (class in morphonet.plugins.ShapeTransform.Deform) del_cell_from_properties() (morphonet.plot.Dataset method) del_daughter() (morphonet.plot.Dataset method) del_link() (morphonet.plot.Dataset method) del_mother() (morphonet.plot.Dataset method) Delete (class in morphonet.plugins.SegmentationCorrection.Delete) delete_dataset() (morphonet.net.Net method) delete_dataset_by_id() (morphonet.net.Net method) delete_image_at() (morphonet.net.Net method)

delete_images() (morphonet.net.Net method) delete_primitive() (morphonet.net.Net method) delete_primitives() (morphonet.net.Net method) delete_property() (morphonet.data.dataset.DatasetAnalysis method) delete_property_all_steps() (morphonet.data.dataset.DatasetAnalysis method) delete_property_at() (morphonet.data.dataset.DatasetAnalysis method) delete_property_at_time_step() (morphonet.data.dataset.DatasetAnalysis method) delete_property_by_id() (morphonet.net.Net method) delete_property_by_name() (morphonet.net.Net method) Deli (class in morphonet.plugins.SegmentationCorrection.Deli) Delink (class in morphonet.plugins.EditTemporalLinks.Delink) Dilate (class in morphonet.plugins.ShapeTransform.Dilate) Disco (class in morphonet.plugins.SegmentationCorrection.Disco)

E

end_step() (morphonet.plot.Dataset method) Erode (class in morphonet.plugins.ShapeTransform.Erode) export() (morphonet.plot.Dataset method)

export_dataset_at_step() (morphonet.data.dataset.DatasetAnalysis method) export_image() (morphonet.data.dataset.DatasetAnalysis method) export_properties_as_txt() (morphonet.data.dataset.DatasetAnalysis method) export_properties_as_xml() (morphonet.data.dataset.DatasetAnalysis method)

F

filter_objects() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) find_properties_path_at_step() (morphonet.data.dataset.DatasetAnalysis method) find_properties_path_at_step_no_name() (morphonet.data.dataset.DatasetAnalysis method)

find_property_path_at_step() (morphonet.data.dataset.DatasetAnalysis method) find_segmentation_path_at_step() (morphonet.data.dataset.DatasetAnalysis method) Fuse (class in morphonet.plugins.SegmentationCorrection.Fuse)

G

Gaumi (class in morphonet.plugins.SegmentationCorrection.Gaumi) gaussian_rawdata() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) generate_init_naming_parameters() (in module morphonet.data.utils) generate_prop_naming_parameters() (in module morphonet.data.utils) generate_txt() (morphonet.data.dataproperty.DataProperty method) generate_xml() (morphonet.data.dataproperty.DataProperty method) get_action() (morphonet.data.dataset.DatasetStep method) get_action_at() (morphonet.data.dataset.DatasetAnalysis method) get_actions() (morphonet.plot.Dataset method) get_all_properties() (morphonet.data.dataset.DatasetAnalysis method) get_all_regionprop_names() (in module morphonet.data.utils) get_annotation_by_id() (morphonet.net.Net method) get_cells_by_gene() (morphonet.net.Net method) get_cells_by_gene_by_stage() (morphonet.net.Net method) get_cells_updated_at() (morphonet.data.dataset.DatasetAnalysis method) get_cells_updated_by_selection_at() (morphonet.data.dataset.DatasetAnalysis method) get_center() (morphonet.plot.Dataset method) get_channels() (morphonet.plot.Dataset method) get_coordinates() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_developmental_table() (morphonet.net.Net method) get_dropdown() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_filepicker() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_filesaver() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_float_values_at() (morphonet.data.dataproperty.DataProperty method) get_genes() (morphonet.net.Net method) get_genes_by_cell() (morphonet.net.Net method) get_genes_by_cell_by_stage() (morphonet.net.Net method) get_genes_by_stage() (morphonet.net.Net method) get_group_by_name() (morphonet.net.Net method) get_guy_by_id() (morphonet.net.Net method) get_guy_by_name() (morphonet.net.Net method) get_image_at() (morphonet.net.Net method) get_image_size() (morphonet.net.Net method) get_inputfield() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_intensity_image() (morphonet.data.dataset.DatasetAnalysis method) get_iou_bbox() (in module morphonet.plugins.EditTemporalLinks.Tracko) get_keys() (morphonet.data.dataproperty.DataProperty method) get_last_step() (morphonet.plot.Dataset method) get_last_version() (morphonet.plot.Dataset method) get_last_version_glob_channels() (morphonet.plot.Dataset method) get_local_dataset() (in module morphonet.data.data) get_log() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_mask_cell() (morphonet.plot.Dataset method) get_max_time() (morphonet.data.dataset.DatasetAnalysis method) get_mesh() (morphonet.plot.Dataset method) get_mesh_at() (morphonet.net.Net method)

get_mesh_object() (morphonet.plot.Dataset method) get_min_time() (morphonet.data.dataset.DatasetAnalysis method) get_next_cells_in_lineage() (in module morphonet.data.utils) get_number_of_curations() (morphonet.data.dataset.DatasetAnalysis method) get_number_of_mesh_at() (morphonet.net.Net method) get_object() (morphonet.plot.Dataset method) get_object_id() (in module morphonet.data.utils) get_object_ids_at() (morphonet.data.dataproperty.DataProperty method) get_object_t_id_ch() (in module morphonet.data.utils) get_object_value() (morphonet.data.dataproperty.DataProperty method) get_objects() (morphonet.plot.Dataset method) get_objects_at() (morphonet.plot.Dataset method) get_objects_from_property_by_id() (morphonet.net.Net method) get_objects_from_property_by_name() (morphonet.net.Net method) get_path() (morphonet.data.dataproperty.DataProperty method) get_plugin_name() (morphonet.data.dataset.DatasetStep method) get_plugin_name_at() (morphonet.data.dataset.DatasetAnalysis method) get_plugin_parameters() (morphonet.data.dataset.DatasetStep method) get_plugin_parameters_at() (morphonet.data.dataset.DatasetAnalysis method) get_previous_cell_in_lineage() (in module morphonet.data.utils) get_properties() (morphonet.net.Net method) get_property() (morphonet.data.dataset.DatasetAnalysis method) (morphonet.data.dataset.DatasetStep method) (morphonet.plot.Dataset method) get_property_annotated_by_id() (morphonet.net.Net method) get_property_at() (morphonet.data.dataset.DatasetAnalysis method) get_property_at_time_step() (morphonet.data.dataset.DatasetAnalysis method) get_property_by_id() (morphonet.net.Net method) get_property_by_name() (morphonet.net.Net method) get_property_last_step() (morphonet.data.dataset.DatasetAnalysis method) get_raw() (morphonet.plot.Dataset method) get_regionprop_at() (morphonet.plot.Dataset method) get_regionprops_at() (morphonet.plot.Dataset method) get_scikit_property_last_step() (morphonet.data.dataset.DatasetAnalysis method) get_seeds() (morphonet.plot.Dataset method) get_seg() (morphonet.plot.Dataset method) get_segmentation() (morphonet.data.dataset.DatasetAnalysis method) get_segmentation_at() (morphonet.data.dataset.DatasetStep method) get_segmentation_at_step() (morphonet.data.dataset.DatasetAnalysis method) get_segmentation_last_step() (morphonet.data.dataset.DatasetAnalysis method) get_stages() (morphonet.net.Net method) get_step() (morphonet.data.dataproperty.DataProperty method) get_times() (morphonet.plot.Dataset method) get_toggle() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) get_updated_properties() (morphonet.data.dataset.DatasetAnalysis method) get_values() (morphonet.data.dataproperty.DataProperty method) get_values_at() (morphonet.data.dataproperty.DataProperty method)

H

has_intensities_images_at() (morphonet.data.dataset.DatasetAnalysis method)

I

Image (class in morphonet.data.dataset) indent_xml() (in module morphonet.data.utils) init_regionprop() (morphonet.plot.Dataset method)

init_regionprops() (morphonet.plot.Dataset method) initialize_external_step() (morphonet.data.dataset.DatasetAnalysis method) is_image_at() (morphonet.net.Net method) is_property_a_regionprop() (in module morphonet.data.utils)

L

list_all_properties() (morphonet.data.dataset.DatasetAnalysis method) list_cells_in_action() (morphonet.data.dataset.DatasetStep method) list_cells_in_action_by_label() (morphonet.data.dataset.DatasetStep method) list_dataset() (morphonet.net.Net method) list_local_datasets() (in module morphonet.data.data)

list_my_dataset() (morphonet.net.Net method) list_properties_in_pickle() (in module morphonet.data.utils) load_cell_list() (in module morphonet.data.utils) load_from_scikit() (morphonet.data.dataproperty.DataProperty method) load_from_txt() (morphonet.data.dataproperty.DataProperty method) load_properties_from_xml() (in module morphonet.data.utils)

M

Mars (class in morphonet.plugins.DeNovoSegmentation.Mars) Match (class in morphonet.plugins.SegmentationCorrection.Match) module morphonet.data.data morphonet.data.dataproperty morphonet.data.dataset morphonet.data.utils morphonet.net morphonet.plot morphonet.plugins.DeNovoSeed.Seedax morphonet.plugins.DeNovoSeed.Seedero morphonet.plugins.DeNovoSeed.Seedin morphonet.plugins.DeNovoSeed.Seedio morphonet.plugins.DeNovoSeed.Seedis morphonet.plugins.DeNovoSegmentation.Binarize morphonet.plugins.DeNovoSegmentation.BinBox morphonet.plugins.DeNovoSegmentation.BinCha morphonet.plugins.DeNovoSegmentation.CellposePredict morphonet.plugins.DeNovoSegmentation.CellPoseTrain morphonet.plugins.DeNovoSegmentation.Mars morphonet.plugins.DeNovoSegmentation.StardistPredict morphonet.plugins.DeNovoSegmentation.StardistTrain morphonet.plugins.EditTemporalLinks.Addlink morphonet.plugins.EditTemporalLinks.Delink morphonet.plugins.EditTemporalLinks.Tracko morphonet.plugins.MorphoPlugin morphonet.plugins.PropagateSegmentation.Propa morphonet.plugins.PropagateSegmentation.Prope morphonet.plugins.SegmentationCorrection.CopyPaste morphonet.plugins.SegmentationCorrection.Delete morphonet.plugins.SegmentationCorrection.Deli morphonet.plugins.SegmentationCorrection.Disco morphonet.plugins.SegmentationCorrection.Fuse morphonet.plugins.SegmentationCorrection.Gaumi morphonet.plugins.SegmentationCorrection.Match morphonet.plugins.SegmentationCorrection.Splax morphonet.plugins.SegmentationFromSeeds.Wata morphonet.plugins.SegmentationFromSeeds.Wati morphonet.plugins.SegmentationFromSeeds.Watio morphonet.plugins.SegmentationFromSeeds.Wato morphonet.plugins.ShapeTransform.Close morphonet.plugins.ShapeTransform.Convex morphonet.plugins.ShapeTransform.Deform morphonet.plugins.ShapeTransform.Dilate morphonet.plugins.ShapeTransform.Erode morphonet.plugins.ShapeTransform.Open morphonet.data.data module morphonet.data.dataproperty module morphonet.data.dataset module morphonet.data.utils module morphonet.net module morphonet.plot module morphonet.plugins.DeNovoSeed.Seedax module morphonet.plugins.DeNovoSeed.Seedero module morphonet.plugins.DeNovoSeed.Seedin module morphonet.plugins.DeNovoSeed.Seedio module

morphonet.plugins.DeNovoSeed.Seedis module morphonet.plugins.DeNovoSegmentation.Binarize module morphonet.plugins.DeNovoSegmentation.BinBox module morphonet.plugins.DeNovoSegmentation.BinCha module morphonet.plugins.DeNovoSegmentation.CellposePredict module morphonet.plugins.DeNovoSegmentation.CellPoseTrain module morphonet.plugins.DeNovoSegmentation.Mars module morphonet.plugins.DeNovoSegmentation.StardistPredict module morphonet.plugins.DeNovoSegmentation.StardistTrain module morphonet.plugins.EditTemporalLinks.Addlink module morphonet.plugins.EditTemporalLinks.Delink module morphonet.plugins.EditTemporalLinks.Tracko module morphonet.plugins.MorphoPlugin module morphonet.plugins.PropagateSegmentation.Propa module morphonet.plugins.PropagateSegmentation.Prope module morphonet.plugins.SegmentationCorrection.CopyPaste module morphonet.plugins.SegmentationCorrection.Delete module morphonet.plugins.SegmentationCorrection.Deli module morphonet.plugins.SegmentationCorrection.Disco module morphonet.plugins.SegmentationCorrection.Fuse module morphonet.plugins.SegmentationCorrection.Gaumi module morphonet.plugins.SegmentationCorrection.Match module morphonet.plugins.SegmentationCorrection.Splax module morphonet.plugins.SegmentationFromSeeds.Wata module morphonet.plugins.SegmentationFromSeeds.Wati module morphonet.plugins.SegmentationFromSeeds.Watio module morphonet.plugins.SegmentationFromSeeds.Wato module morphonet.plugins.ShapeTransform.Close module morphonet.plugins.ShapeTransform.Convex module morphonet.plugins.ShapeTransform.Deform module morphonet.plugins.ShapeTransform.Dilate module morphonet.plugins.ShapeTransform.Erode module morphonet.plugins.ShapeTransform.Open module MorphoPlugin (class in morphonet.plugins.MorphoPlugin)

N

Net (class in morphonet.net)

np_where() (morphonet.plot.Dataset method)

O

Object (class in morphonet.plot)

Open (class in morphonet.plugins.ShapeTransform.Open)

P

print_all_intensity_images() (morphonet.data.dataset.DatasetAnalysis method) print_all_segmentations() (morphonet.data.dataset.DatasetAnalysis method)

print_computable_properties() (morphonet.data.dataset.DatasetAnalysis method) Propa (class in morphonet.plugins.PropagateSegmentation.Propa) Prope (class in morphonet.plugins.PropagateSegmentation.Prope)

R

read_first_txt() (morphonet.plot.Dataset method) read_last_properties() (morphonet.plot.Dataset method) read_mesh() (morphonet.net.Net method) read_properties() (morphonet.plot.Dataset method)

remove_folder() (in module morphonet.data.utils) remove_from_property() (morphonet.data.dataproperty.DataProperty method) restart() (morphonet.plot.Dataset method) (morphonet.plugins.MorphoPlugin.MorphoPlugin method)

S

ScikitProperty (class in morphonet.plot) Seedax (class in morphonet.plugins.DeNovoSeed.Seedax) Seedero (class in morphonet.plugins.DeNovoSeed.Seedero) Seedin (class in morphonet.plugins.DeNovoSeed.Seedin) Seedio (class in morphonet.plugins.DeNovoSeed.Seedio) Seedis (class in morphonet.plugins.DeNovoSeed.Seedis) select_dataset_by_id() (morphonet.net.Net method) select_dataset_by_name() (morphonet.net.Net method) set_description() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) set_icon_name() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) set_image_name() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) set_name() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) set_object_value() (morphonet.data.dataproperty.DataProperty method)

set_parent() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) set_path() (morphonet.data.dataproperty.DataProperty method) set_seg() (morphonet.plot.Dataset method) set_step() (morphonet.data.dataproperty.DataProperty method) share_dataset_with_group() (morphonet.net.Net method) share_dataset_with_user() (morphonet.net.Net method) share_property_by_id() (morphonet.net.Net method) show_properties_type() (morphonet.net.Net method) Splax (class in morphonet.plugins.SegmentationCorrection.Splax) StardistPredict (class in morphonet.plugins.DeNovoSegmentation.StardistPredict) StardistTrain (class in morphonet.plugins.DeNovoSegmentation.StardistTrain) start() (morphonet.plugins.MorphoPlugin.MorphoPlugin method) start_step() (morphonet.plot.Dataset method)

T

Tracko (class in morphonet.plugins.EditTemporalLinks.Tracko)

U

unshare_dataset_with_group() (morphonet.net.Net method) unshare_dataset_with_user() (morphonet.net.Net method) unshare_property_by_id() (morphonet.net.Net method) update_cells_at() (morphonet.plot.Dataset method) update_dataset() (morphonet.net.Net method) update_properties() (morphonet.plot.Dataset method)

update_rawimage_link() (morphonet.net.Net method) upload_description() (morphonet.net.Net method) upload_image_at() (morphonet.net.Net method) upload_mesh_at() (morphonet.net.Net method) upload_mesh_with_primitive_at() (morphonet.net.Net method) upload_primitive() (morphonet.net.Net method) upload_property() (morphonet.net.Net method)

W

Wata (class in morphonet.plugins.SegmentationFromSeeds.Wata) Wati (class in morphonet.plugins.SegmentationFromSeeds.Wati) Watio (class in morphonet.plugins.SegmentationFromSeeds.Watio)

Wato (class in morphonet.plugins.SegmentationFromSeeds.Wato) write_lineage_to_step() (in module morphonet.data.utils) write_property_to_step() (morphonet.data.dataset.DatasetAnalysis method) write_segmentation_to_step() (morphonet.data.dataset.DatasetAnalysis method)