Index

A

active() (Program.GUI.dialogues static method) activity_components (Program.GUIHandling attribute) activity_format_stack() (Program.GUIHandling static method) activity_update_x_ticks() (Program.GUIHandling static method) add_channel() (Program.Handlers.channels static method) add_deterministic_ids() (Neurons.Image method) add_meta_data() (Neurons.Image method) add_neuron() (Neurons.Image method) add_probabilistic_ids() (Neurons.Image method) add_probabilistic_probs() (Neurons.Image method) add_ranks() (Neurons.Image method) add_reference() (Program.Handlers.channels static method) add_task() (Program.GUI.dialogues static method) add_to_image() (Methods.AutoId method) addToBrain() (Neurons.Neuron method) age (Program.subject attribute), [1] aligned_xyzRGB (Neurons.Neuron attribute) annotate() (Neurons.Neuron method) annotation (Neurons.Neuron attribute) annotation_confidence (Neurons.Neuron attribute) annotation_weight (Methods.AutoId attribute)

app() (Program.GUIHandling static method) (Program.ProgramInfo static method), [1] apply_255_lut() (in module zephir.zephod.channels) apply_colormap() (Methods.ChunkyMethods static method), [1] apply_mask() (Program.rotation_gui static method) apply_slice() (Methods.ChunkyMethods static method) apply_video() (Methods.ChunkyMethods static method), [1] apply_vol() (Methods.ChunkyMethods static method), [1] area_filter() (Methods.Preprocess static method) arr_idx (Program.channel attribute), [1] assign_gui() (Program.channel method), [1] asym_deterministic_LR_neurons (Neurons.Hermaphrodite attribute) (Neurons.Male attribute) asym_stochastic_LR_neurons (Neurons.Hermaphrodite attribute) (Neurons.Male attribute) atlas_version (Neurons.Image attribute) auto_annotate() (in module zephir.methods.auto_annotate) AutoDetect (class in Methods) AutoId (class in Methods) autosort() (DataHandling.Helpers.nd2 static method), [1], [2] axes (Program.GUI.Panels.image_editing_canvas attribute)

B

baseline (Neurons.Neuron attribute) BatchDetect() (Methods.AutoDetect static method) (Methods.NNDetect static method) BatchId() (Methods.AutoId static method) body (Program.subject attribute), [1]

bodypart (Neurons.Image attribute) bug_URL (Program.ProgramInfo attribute) build_annotations() (in module zephir.methods.build_annotations) build_models() (in module zephir.methods.build_models) build_springs() (in module zephir.methods.build_springs) buttons (Program.GUI.Panels.image_editing_gui attribute)

C

c (Program.volume attribute), [1] cache (Program.GUI.Panels.image_editing_gui attribute) cache() (Program.GUI.dialogues static method) (Program.GUIHandling static method) calc_pp_size() (Methods.ChunkyMethods static method) canvas (Program.GUI.preprocessing_gui attribute) channel (class in Program), [1] channel() (Program.channel method), [1] channel_handler() (Program.GUIHandling static method) channel_keys (DataHandling.Helpers.nd2 attribute), [1], [2] channel_map (Program.GUIHandling attribute) channel_names (Program.GUIHandling attribute) channels (class in Program.Handlers) (Program.volume attribute), [1] channels_from_file() (DataHandling.Helpers.nd2 static method), [1], [2] check_channels() (Program.GUIHandling static method) check_data_size() (Program.GUI.preprocessing_gui static method) check_for_preprocessing_threshold() (Program.GUI.preprocessing_gui static method) checkUpdates() (Program.ProgramInfo static method) choice() (Program.GUI.dialogues static method) ChunkyMethods (class in Methods) close() (Program.rotation_gui static method) cm_exclusive_gui (Program.GUIHandling attribute) color (Neurons.Neuron attribute) (Program.channel attribute), [1]

color_readout (Neurons.Neuron attribute) compute_assignments() (Methods.AutoId method) config (Program.Handlers.channels attribute) constrain_eigenvalues() (Methods.AutoDetect static method) Container (class in zephir.models.container) conv() (in module zephir.zephod.model) convert() (Program.volume method), [1] corr_loss() (in module zephir.models.losses) covariance (Neurons.Neuron attribute) create() (Program.GUI.dialogues static method) create_channels() (DataHandling.writeNWB static method), [1], [2] create_device() (DataHandling.writeNWB static method), [1], [2] create_file() (DataHandling.writeNWB static method), [1], [2] create_module() (DataHandling.writeNWB static method), [1], [2] create_neurons() (DataHandling.Helpers.npal static method), [1], [2] create_patches() (Methods.NNDetect static method) create_segmentation() (DataHandling.writeNWB static method), [1], [2] create_traces() (DataHandling.writeNWB static method), [1], [2] create_volume() (DataHandling.writeNWB static method), [1], [2] crop() (in module Program.Routines.Processing) crop_routine() (Program.GUIHandling static method) crop_size (Methods.NNDetect attribute) current_frame() (Program.GUIHandling static method)

D

DataHandling (module), [1], [2] DataHandling.Helpers (module), [1] debleed() (Methods.ChunkyMethods static method) decimate_frame() (Methods.Preprocess static method) del_neuron() (Neurons.Image method) delete() (Program.GUI.preprocessing_gui static method) (Program.Handlers.channels static method) delete_annotation() (Neurons.Neuron method) delete_annotations() (Neurons.Image method) delete_channel() (Program.channel method), [1] delete_model_ID() (Neurons.Neuron method) delete_model_IDs() (Neurons.Image method) detect() (Methods.AutoDetect method) (Methods.NNDetect static method)

deterministic_id (Neurons.Neuron attribute) device (Program.volume attribute), [1] device_handler() (Program.GUIHandling static method) device_lists (Program.GUIHandling attribute) dialogues (class in Program.GUI) dims (Program.volume attribute), [1] disable_activity_menu() (Program.GUI.neuron_gui method) downsample() (in module zephir.annotator.main) drag_manager() (Program.GUIHandling static method) draw() (Program.Handlers.histograms static method) (Program.rotation_gui static method) dropper() (Program.GUIHandling static method) dtype (Program.volume attribute), [1] dtype_max (Program.volume attribute), [1] dtype_str (Program.volume attribute), [1]

E

edit_channels() (Program.Handlers.channels static method) emission (Program.channel attribute), [1] enable_gui() (Program.GUI.identification_gui static method) (Program.GUI.tracking_gui static method)

evaluation() (Methods.AutoDetect static method) event2struct() (Program.GUIHandling static method) excitation (Program.channel attribute), [1]

F

fade_log() (Program.GUIHandling static method) filter_frame() (Methods.Preprocess static method) filter_gut() (Methods.Preprocess static method) filter_gut_lysosomes() (Methods.Preprocess static method) filter_small_artifacts() (Methods.Preprocess static method) find_outlier() (in module Methods) find_rank() (Neurons.Image method) find_user_id_neuron() (Neurons.Image method) find_user_id_neurons() (Neurons.Image method) fit_gaussian() (Methods.AutoDetect method) flat_rotate() (Program.GUIHandling static method)

flipLR() (Neurons.Hermaphrodite static method) (Neurons.Male static method) flipLR_annotations() (Neurons.Image method) fluorophore (Program.channel attribute), [1] fluorophore_map (Program.Handlers.channels attribute) (Program.ProgramInfo attribute) fmt (Program.volume attribute), [1] forward() (zephir.models.zephir.ZephIR method) (zephir.zephod.model.ZephOD method) freeze() (Program.channel method), [1] fsize (Methods.AutoDetect attribute)

G

gamma (Program.channel attribute), [1] gaussian_cost() (Methods.AutoDetect static method) generate_synthetic_data() (in module zephir.zephod.augment) get() (Program.volume method), [1] (zephir.models.container.Container method) get_3d_reconstruction() (Neurons.Neuron method) get_3d_segments() (Neurons.Image method) get_3d_shape() (Neurons.Image method) get_active_volume() (Program.GUIHandling static method) get_aligned_xyzRGBs() (Neurons.Image method) get_annotation_confidences() (Neurons.Image method) get_annotations() (in module zephir.annotator.main) (Neurons.Image method) get_app_metadata() (in module zephir.annotator.main) get_baselines() (Neurons.Image method) get_binary_image() (in module zephir.annotator.main) get_bools() (Program.Handlers.channels static method) get_channel_names() (DataHandling.Helpers.nd2 static method), [1], [2] (DataHandling.Helpers.nwb static method), [1], [2] get_channel_struct() (Program.Handlers.channels static method) get_channels() (DataHandling.Helpers.mat static method), [1] (DataHandling.Helpers.nd2 static method), [1], [2] get_child_properties() (Program.GUIHandling static method) get_colors() (Neurons.Image method) get_colors_readout() (Neurons.Image method) get_corners() (Program.rotation_gui static method) get_covariances() (Neurons.Image method) get_deterministic_ids() (Neurons.Image method) get_dimensions() (DataHandling.Helpers.mat static method), [1] (DataHandling.Helpers.nd2 static method), [1], [2] get_edges() (Program.rotation_gui static method) get_filter() (Methods.AutoDetect static method) get_gaussian() (Methods.AutoDetect static method) get_gvol() (in module zephir.annotator.main) get_is_annotations_on() (Neurons.Image method) get_is_emphasized() (Neurons.Image method) get_line_sizes() (Neurons.Image method) get_marker_color() (Neurons.Neuron method) get_marker_colors() (Neurons.Image method) get_marker_size() (Neurons.Neuron method) get_marker_sizes() (Neurons.Image method) get_max_idx() (Program.Handlers.channels static method) get_maximum_array_size() (Program.system static method) get_meta_data() (Neurons.Image method) get_mip_x() (in module zephir.annotator.main) get_mip_y() (in module zephir.annotator.main) get_mip_z() (in module zephir.annotator.main) get_optimization_trajectory() (in module zephir.methods.get_optimization_trajectory) get_parent_app() (Program.GUIHandling static method) get_plane() (DataHandling.Helpers.mat static method), [1] (DataHandling.Helpers.nd2 static method), [1], [2] (DataHandling.Helpers.nwb static method), [1], [2] get_positions() (Neurons.Image method) get_probabilistic_ids() (Neurons.Image method) get_probabilistic_probs() (Neurons.Image method) get_ranks() (Neurons.Image method) get_rgb() (Program.GUIHandling static method) get_rgba_volume() (in module zephir.annotator.main) get_time_string() (Program.GUIHandling static method) get_truncations() (Neurons.Image method) get_ttl() (DataHandling.Helpers.nd2 static method), [1], [2] get_ttl_data() (DataHandling.Helpers.nd2 static method), [1], [2] get_ttl_keys() (DataHandling.Helpers.nd2 static method), [1], [2] get_vol() (in module zephir.annotator.main) get_volume() (in module zephir.annotator.main) get_x() (in module zephir.annotator.main) get_y() (in module zephir.annotator.main) get_z() (in module zephir.annotator.main) getAboutMsg() (Program.ProgramInfo static method) getAnteriorMidbody() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getAnteriorPharynx() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getCentralMidbody() (Neurons.Hermaphrodite static method) (Neurons.Male static method)

getClasses() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getColors() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getDorsalGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getDorsoRectalGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getGanglia() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getGanglionNames() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getHermaphroditeBirthText() (Neurons.NeuronBirth static method) getHermaphroditeBirthTimes() (Neurons.NeuronBirth static method) getHermaphroditeStages() (Neurons.NeuronBirth static method) getKeyboardShortcutsMsg() (Program.ProgramInfo static method) getLeftAnteriorGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getLeftCloacalGanglion() (Neurons.Male static method) getLeftLateralGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getLeftLumbarGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getLeftPreAnalGanglion() (Neurons.Male static method) getLeftRays() (Neurons.Male static method) getMaleBirthText() (Neurons.NeuronBirth static method) getMaleBirthTimes() (Neurons.NeuronBirth static method) getNeuronClass() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getNeuronColor() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getNeuronsOrderedByGanglia() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getNeuronsOrderedByGangliaLR() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getNeuroPALColorClass() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getNeuroPALName() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getOutliers() (Neurons.Image method) getPosteriorMidbody() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getPosteriorPharynx() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getPreAnalGanglion() (Neurons.Hermaphrodite static method) getRetroVesicularGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getRightAnteriorGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getRightCloacalGanglion() (Neurons.Male static method) getRightLateralGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getRightLumbarGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getRightPreAnalGanglion() (Neurons.Male static method) getRightRays() (Neurons.Male static method) getVariableNeurons() (Neurons.Male static method) getVentralGanglion() (Neurons.Hermaphrodite static method) (Neurons.Male static method) getVentralNerveCord() (Neurons.Hermaphrodite static method) (Neurons.Male static method) GFP_color (Program.GUIPreferences attribute) global_alignment() (Methods.AutoId method) global_grab() (Program.GUIHandling static method) grab_land() (Program.GUIHandling static method) grid (Program.GUI.Panels.image_editing_canvas attribute) (Program.GUI.Panels.image_editing_gui attribute) (Program.GUI.Panels.preprocessing_sidebar attribute) gui (Program.channel attribute), [1] gui_idx (Program.channel attribute), [1] gui_init() (Program.GUIHandling static method) gui_lock() (Program.GUIHandling static method) GUIHandling (class in Program) GUIPreferences (class in Program)

H

h5 (class in DataHandling.Helpers), [1], [2] handle_annotation() (in module zephir.annotator.main) handle_annotations() (in module zephir.annotator.main) handle_load() (in module zephir.annotator.main) handle_rpc() (in module zephir.annotator.main) handle_save() (in module zephir.annotator.main) handle_worldline() (in module zephir.annotator.main)

handle_worldlines() (in module zephir.annotator.main) handles (Program.Handlers.channels attribute) (Program.Handlers.histograms attribute) Hermaphrodite (class in Neurons) histmatch_frame() (Methods.Preprocess static method) histogram_handler() (Program.GUIHandling static method) histograms (class in Program.Handlers) (Program.GUI.preprocessing_gui attribute)

I

id() (Methods.AutoId method) id_components (Program.GUIHandling attribute) identification_gui (class in Program.GUI) identification_gui() (Program.GUI.identification_gui method) identifiers (Program.GUI.dialogues attribute) identify() (in module zephir.zephod.augment) (Program.channel method), [1] Image (class in Neurons) Image() (Neurons.Image method) image_dir (Program.GUIPreferences attribute) image_editing_canvas (class in Program.GUI.Panels) image_editing_canvas() (Program.GUI.Panels.image_editing_canvas method) image_editing_gui (class in Program.GUI.Panels) image_editing_gui() (Program.GUI.Panels.image_editing_gui method) image_only_components (Program.GUI.Panels.image_editing_canvas attribute) imreadAny() (in module DataHandling), [1], [2] imreadCZI() (in module DataHandling), [1], [2] imreadLif() (in module DataHandling), [1], [2] imreadND2() (in module DataHandling), [1], [2] imreadVlab() (in module DataHandling), [1], [2] info() (Program.volume method), [1] init_click_states() (Program.GUIHandling static method) init_neuron_marker() (Program.GUIHandling static method) inputGFPColor() (Program.GUIPreferences static method) inputNeuronDot() (Program.GUIPreferences static method) instance() (Methods.AutoDetect static method) (Methods.AutoId static method) (Methods.NNDetect static method) (Methods.Preprocess static method) (Program.GUIPreferences static method)

is_all_annotated() (Neurons.Image method) is_annotation_on (Neurons.Neuron attribute) is_any_annotated() (Neurons.Image method) is_any_auto_ID() (Neurons.Image method) is_auto_name (Program.GUIPreferences attribute) is_autoID_updates (Program.GUIPreferences attribute) is_emphasized (Neurons.Neuron attribute) is_known (Program.channel attribute), [1] is_MP_detect (Program.GUIPreferences attribute) is_opening_file (Program.GUI.identification_gui attribute) is_pseudocolor() (Program.channel method), [1] is_rendered (Program.channel attribute), [1] is_rgb (Program.channel attribute), [1] is_selected (Neurons.Neuron attribute) is_show_birth_times (Program.GUIPreferences attribute) is_valid_dtype (Program.volume attribute), [1] is_video (Program.volume attribute), [1] is_working_with_video() (Program.GUI.Panels.image_editing_canvas static method) isAWC() (Neurons.Hermaphrodite static method) (Neurons.Male static method) isBodyID() (Methods.AutoId static method) isCell() (Neurons.Hermaphrodite static method) (Neurons.Male static method) isNeuron() (Neurons.Hermaphrodite static method) (Neurons.Male static method) iter_rwc (Methods.AutoId attribute) iter_sinkhorn (Methods.AutoId attribute)

J

java (class in DataHandling.Helpers), [1], [2]

K

key_map (DataHandling.Helpers.nd2 attribute), [1], [2]

L

late_herm_neuron_stages (Neurons.NeuronBirth attribute) late_herm_neuron_times (Neurons.NeuronBirth attribute) late_herm_neurons (Neurons.NeuronBirth attribute) lh_in (Program.channel attribute), [1] lh_out (Program.channel attribute), [1] load() (Program.GUIPreferences static method) (Program.volume method), [1]

load_file() (in module Program.Routines.Processing) load_metadata() (DataHandling.Helpers.mat static method), [1] load_proc_image() (Methods.ChunkyMethods static method) load_tracks() (DataHandling.Helpers.h5 method), [1], [2] (DataHandling.Helpers.nwb static method), [1], [2] loaded_file_check() (Program.GUIHandling static method) local_alignment() (Methods.AutoId static method) logsumexp() (in module Methods)

M

main() (in module zephir.annotator.main) (in module zephir.main) (in module zephir.methods.auto_annotate) (in module zephir.methods.overwrite_checkpoint) (in module zephir.zephod.main) (in module zephir.zephod.train) major_axis_align() (Methods.AutoId static method) Male (class in Neurons) manual_artifact_removal() (Methods.Preprocess static method) mat (class in DataHandling.Helpers), [1] MatchHist() (in module Methods) max_characters (DataHandling.Helpers.java attribute), [1], [2] max_fp (Methods.AutoId attribute) max_log_likelihood (Methods.AutoId attribute) maximum_bytes (Program.GUI.preprocessing_gui attribute) MCR_solver() (Methods.AutoId static method) meta_data (Neurons.Image attribute) min_log_likelihood (Methods.AutoId attribute) mirror_image_Z() (Neurons.Image method) mirror_neurons_Z() (Neurons.Image method) model (Methods.NNDetect attribute) model_version (Methods.NNDetect attribute) module zephir.annotator.main zephir.main zephir.methods.auto_annotate zephir.methods.build_annotations zephir.methods.build_models zephir.methods.build_springs zephir.methods.get_optimization_trajectory zephir.methods.overwrite_checkpoint zephir.methods.plot_loss_maps zephir.methods.save_annotations zephir.methods.track_frame zephir.models.container zephir.models.losses zephir.models.zephir zephir.zephod.augment zephir.zephod.channels zephir.zephod.main zephir.zephod.model zephir.zephod.train

mouse_poll() (Program.GUIHandling static method) munkres() (in module Methods) munkres_extended() (in module Methods) mutually_exclusive() (Program.GUIHandling static method)

N

name (Program.ProgramInfo attribute) (Program.volume attribute), [1] name_substr (DataHandling.Helpers.nd2 attribute), [1], [2] names (Program.Handlers.channels attribute) native_dims (Program.volume attribute), [1] nc (Program.volume attribute), [1] ncandidates (Methods.AutoId attribute) nd2 (class in DataHandling.Helpers), [1], [2] nearest_unannotated() (Neurons.Image method) nearest_unannotated_z() (Neurons.Image method) Neuron (class in Neurons) neuron_components (Program.GUIHandling attribute) neuron_dot (Program.GUIPreferences attribute) neuron_gui (class in Program.GUI) (Program.GUI.identification_gui attribute) neuron_gui() (Program.GUI.neuron_gui method) NeuronBirth (class in Neurons) neurons (Neurons.Image attribute) (Program.GUI.neuron_gui attribute) neuronStartsWith() (Neurons.Hermaphrodite static method) (Neurons.Male static method) NeuroPALImage (class in DataHandling), [1], [2], [3] NN_model (Methods.NNDetect attribute) NNDetect (class in Methods) NNDetect() (Methods.NNDetect method) non_LR_neurons (Neurons.Hermaphrodite attribute) (Neurons.Male attribute)

non_neuronal_cells (Neurons.Hermaphrodite attribute) (Neurons.Male attribute) notes (Program.subject attribute), [1] npal (class in DataHandling.Helpers), [1], [2] nt (Program.volume attribute), [1] num_auto_id_neurons() (Neurons.Image method) num_neurons() (Neurons.Image method) num_user_id_neurons() (Neurons.Image method) num_user_unid_neurons() (Neurons.Image method) numAnteriorMidbodyNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) numCentralMidbodyNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) numHeadNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) numMidbodyNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) numNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) numPosteriorMidbodyNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) numTailNeurons() (Neurons.Hermaphrodite static method) (Neurons.Male static method) nwb (class in DataHandling.Helpers), [1], [2] nwb_init() (Program.GUIHandling static method) nx (Program.volume attribute), [1] ny (Program.volume attribute), [1] nz (Program.volume attribute), [1]

O

open() (DataHandling.Helpers.mat static method), [1] (DataHandling.Helpers.nd2 static method), [1], [2] (DataHandling.Helpers.nwb static method), [1], [2] (DataHandling.NeuroPALImage static method), [1], [2], [3]

open_file() (Program.GUI.identification_gui method) optical_fields (Program.GUIHandling attribute) options (Methods.AutoDetect attribute) outlier (Neurons.Neuron attribute) overwrite_checkpoint() (in module zephir.methods.overwrite_checkpoint)

P

p_fp (Methods.AutoId attribute) pad_to_shape() (Methods.NNDetect static method) panel_instances (Program.GUI.Panels.preprocessing_sidebar attribute) panels (Program.GUI.Panels.image_editing_gui attribute) (Program.GUI.Panels.preprocessing_sidebar attribute) parent (Program.channel attribute), [1] parent_gui (Program.GUI.neuron_gui attribute) parse_channel_gui() (Program.Handlers.channels static method) parse_gui() (in module Program.Routines.Processing) parse_hashtable() (DataHandling.Helpers.java static method), [1], [2] parse_info() (Program.Handlers.channels static method) pass_to_main() (in module Program.Routines.Processing) (Program.GUI.preprocessing_gui method) path (Program.volume attribute), [1] patterns (Program.GUI.dialogues attribute) pdist2_maha() (Methods.AutoId static method) placement() (Methods.Utils static method) plot_loss_maps() (in module zephir.methods.plot_loss_maps) PNGViewer (class in DataHandling), [1], [2] populate() (Program.Handlers.channels static method) pos_prefixes (Program.GUIHandling attribute) position (Neurons.Neuron attribute) post_process() (Methods.NNDetect static method)

predict_nn() (Methods.NNDetect method) prefixes (Program.Handlers.histograms attribute) prefs_dir (Program.GUIPreferences attribute) prefs_file (Program.GUIPreferences attribute) prefs_name (Program.GUIPreferences attribute) prepare_image() (Methods.NNDetect static method) Preprocess (class in Methods) preprocess() (zephir.zephod.model.ZephOD method) preprocessing_gui (class in Program.GUI) preprocessing_gui() (Program.GUI.preprocessing_gui method) preprocessing_sidebar (class in Program.GUI.Panels) preprocessing_sidebar() (Program.GUI.Panels.preprocessing_sidebar method) preview_output() (Program.rotation_gui static method) probabilistic_ids (Neurons.Neuron attribute) probabilistic_probs (Neurons.Neuron attribute) proc_components (Program.GUIHandling attribute) proc_save_prompt() (Program.GUIHandling static method) proc_target_slices() (Methods.ChunkyMethods static method) processing_steps (Program.volume attribute), [1] Program.Routines.Processing (module) ProgramInfo (class in Program) projection (Program.GUI.Panels.image_editing_canvas attribute) Property1 (DataHandling.Helpers.tif attribute), [1] pst_shape (Methods.NNDetect attribute)

Q

quick_render() (in module Program.Routines.Processing)

R

rank (Neurons.Neuron attribute) rank_neuron_max() (Neurons.Image method) read() (Program.GUIPreferences static method) (Program.volume method), [1] read_class (Program.volume attribute), [1] read_gui() (Program.GUIHandling static method) read_metadata() (Program.volume method), [1] read_mod (Program.volume attribute), [1] read_obj (Program.volume attribute), [1] readAnnoH5() (in module DataHandling), [1], [2] readStimFile() (in module DataHandling), [1], [2] readTrackmate() (in module DataHandling), [1], [2] rect_to_freehand() (Program.GUIHandling static method) reg_d() (in module zephir.models.losses) reg_n() (in module zephir.models.losses) reg_t() (in module zephir.models.losses) remove() (Neurons.Neuron method) remove_reference() (Program.Handlers.channels static method) removeNearbyNeurons() (Methods.Utils static method) render() (in module Program.Routines.Processing) (Program.volume method), [1] reset() (in module Program.Routines.Processing) (Program.Handlers.histograms static method) reset_gui() (Program.GUI.neuron_gui method)

resize_neuron() (in module zephir.zephod.augment) resolve() (Program.GUI.dialogues static method) restore_pointer() (Program.GUIHandling static method) rgb (Program.volume attribute), [1] rl_deconvolution() (in module zephir.zephod.channels) rotate() (Neurons.Image method) (Neurons.Neuron method) rotate_image_X_180() (Neurons.Image method) rotate_image_Y_180() (Neurons.Image method) rotate_image_Z_270() (Neurons.Image method) rotate_image_Z_90() (Neurons.Image method) rotate_neuron() (in module zephir.zephod.augment) rotate_neurons_X_180() (Neurons.Image method) rotate_neurons_Y_180() (Neurons.Image method) rotate_neurons_Z_270() (Neurons.Image method) rotate_neurons_Z_90() (Neurons.Image method) rotate_X_180() (Neurons.Image method) rotate_Y_180() (Neurons.Image method) rotate_Z_270() (Neurons.Image method) rotate_Z_90() (Neurons.Image method) rotation_gui (class in Program) rotmat() (Methods.AutoId static method) run_histmatch() (in module Methods) run_zephir() (in module zephir.main) run_zephod() (in module zephir.zephod.main)

S

save() (in module Program.Routines.Processing) (Program.GUIPreferences static method) save_annotations() (in module zephir.methods.save_annotations) save_array_to_cache() (Program.GUI.Panels.image_editing_gui method) save_for_parfor() (Methods.Utils static method) save_neuron_identities() (Program.GUI.neuron_gui method) save_prompt() (in module Program.Routines.Processing) scale (Methods.AutoDetect attribute) (Neurons.Image attribute) scaled_rotation() (Methods.AutoId static method) search() (DataHandling.Helpers.nwb static method), [1], [2] search_key() (DataHandling.Helpers.java static method), [1], [2] seg_path (Program.GUIPreferences attribute) send_focus() (Program.GUIHandling static method) serve_colormaps() (in module zephir.annotator.main) serve_dir_directory_index() (in module zephir.annotator.main) serve_favicon() (in module zephir.annotator.main) serve_manifest() (in module zephir.annotator.main) serve_static_css() (in module zephir.annotator.main) serve_static_js() (in module zephir.annotator.main) set() (Program.channel method), [1] (Program.subject method), [1] set_display_configuration() (Program.GUI.Panels.image_editing_canvas method) (Program.GUI.Panels.image_editing_gui method) set_gamma() (Program.Handlers.channels static method) set_gui_configuration() (Program.GUI.Panels.image_editing_canvas method) (Program.GUI.Panels.preprocessing_sidebar method) (Program.GUI.preprocessing_gui method) set_gui_limits() (Program.GUI.preprocessing_gui method) (Program.GUIHandling static method) set_idx() (Program.Handlers.channels static method) set_projection() (Program.GUI.Panels.image_editing_canvas method) set_references() (Program.Handlers.channels static method) set_thresholds() (Program.GUIHandling static method) set_value() (Program.GUI.dialogues static method) set_video_configuration() (Program.GUI.Panels.image_editing_gui method) settings (Program.rotation_gui attribute) (Program.volume attribute), [1] sex (Program.subject attribute), [1] sharpen() (in module zephir.zephod.channels)

shorten_knob_labels() (Program.GUIHandling static method) show() (DataHandling.PNGViewer static method), [1], [2] sidebar (Program.GUI.preprocessing_gui attribute) simulate_gaussian() (Methods.Utils static method) simulate_mvt() (Methods.Utils static method) sinkhorn_logspace() (Methods.AutoId static method) sinkhorn_logspace_extended() (Methods.AutoId static method) sliders (Program.GUI.Panels.image_editing_canvas attribute) sp2video() (Methods.Utils static method) spectral_unmix() (Methods.ChunkyMethods static method) states (class in Program) step() (Program.GUI.dialogues static method) strain (Program.subject attribute), [1] stream_neurons() (Methods.ChunkyMethods static method) stride (Methods.NNDetect attribute) stripLR() (Neurons.Hermaphrodite static method) (Neurons.Male static method) stripOnOff() (Neurons.Hermaphrodite static method) (Neurons.Male static method) styling (Program.channel attribute), [1] sub_sp() (Methods.Utils static method) subcube() (Methods.Utils static method) subject (class in Program), [1] (Program.volume attribute), [1] subject() (Program.subject method), [1] superpose() (Methods.Utils static method) supervoxels (Methods.AutoDetect attribute) swap_volumes() (Program.GUIHandling static method) switch_to() (Program.GUI.dialogues static method) sym_2_fold_DV_neurons (Neurons.Hermaphrodite attribute) (Neurons.Male attribute) sym_4_fold_DV_neurons (Neurons.Hermaphrodite attribute) (Neurons.Male attribute) sym_6_fold_DV_neurons (Neurons.Hermaphrodite attribute) (Neurons.Male attribute) symbols (Program.rotation_gui attribute) sync_channels() (Program.GUIHandling static method) sysOpenPDF() (in module DataHandling), [1], [2] system (class in Program) szext (Methods.AutoDetect attribute)

T

t (Program.volume attribute), [1] theta (Methods.AutoId attribute) threshold() (in module zephir.zephod.channels) threshold_frame() (Methods.Preprocess static method) tif (class in DataHandling.Helpers), [1] to_npal() (DataHandling.Helpers.nd2 static method), [1], [2] (DataHandling.Helpers.nwb static method), [1], [2] (DataHandling.Helpers.tif static method), [1] to_superpixel() (Neurons.Image method)

to_valid() (DataHandling.Helpers.java static method), [1], [2] toggle_spectral_unmixing() (Program.GUI.Panels.preprocessing_sidebar static method) trace_path (Program.GUIPreferences attribute) track_frame() (in module zephir.methods.track_frame) tracking_gui (class in Program.GUI) tracking_gui() (Program.GUI.tracking_gui method) train_model() (in module zephir.zephod.train) trigger() (Program.rotation_gui static method) truncation (Neurons.Neuron attribute)

U

union_sp() (Methods.Utils static method) unmarshall() (Neurons.Neuron static method) unrank_neuron() (Neurons.Image method) unselect_neuron() (Program.GUI.neuron_gui method) update() (Program.channel method), [1] (Program.rotation_gui static method) (zephir.models.container.Container method) update_channels() (Program.volume method), [1]

update_colors() (Neurons.Image method) update_confidences() (Methods.AutoId method) update_id() (Methods.AutoId method) update_log_likelihood() (Methods.AutoId method) update_message() (Program.GUI.dialogues static method) update_permutation() (Methods.AutoId static method) user_id_neuron_names() (Neurons.Image method) user_id_neurons() (Neurons.Image method) Utils (class in Methods)

V

valid_image_formats (Program.GUI.identification_gui attribute) validate() (Program.channel method), [1] (Program.subject method), [1] validate_worm_properties() (Program.GUI.identification_gui static method) value_to_string() (DataHandling.Helpers.java static method), [1], [2] variable_neurons (Neurons.Male attribute) vec() (Methods.AutoId static method)

version (Program.ProgramInfo attribute) version_URL (Program.ProgramInfo attribute) video_only_components (Program.GUI.Panels.image_editing_canvas attribute) visualize() (Methods.AutoId method) (Methods.NNDetect static method) volume (class in Program), [1] volume() (Program.volume method), [1] volume_path() (DataHandling.Helpers.nwb static method), [1], [2]

W

website_URL (Program.ProgramInfo attribute) window() (Program.ProgramInfo static method), [1] window_fig() (Program.GUIHandling static method) write() (Program.volume method), [1]

write_data() (DataHandling.Helpers.nwb static method), [1], [2] write_order() (DataHandling.writeNWB static method), [1], [2] writeNWB (class in DataHandling), [1], [2] writeTrackMate() (in module DataHandling), [1], [2]

X

x (Program.volume attribute), [1]

Y

y (Program.volume attribute), [1]

Z

z (Program.volume attribute), [1] ZephIR (class in zephir.models.zephir) zephir.annotator.main module zephir.main module zephir.methods.auto_annotate module zephir.methods.build_annotations module zephir.methods.build_models module zephir.methods.build_springs module zephir.methods.get_optimization_trajectory module zephir.methods.overwrite_checkpoint module zephir.methods.plot_loss_maps module zephir.methods.save_annotations module

zephir.methods.track_frame module zephir.models.container module zephir.models.losses module zephir.models.zephir module zephir.zephod.augment module zephir.zephod.channels module zephir.zephod.main module zephir.zephod.model module zephir.zephod.train module ZephOD (class in zephir.zephod.model) zscore_frame() (Methods.Preprocess static method)