Index

_

__getitem__() (byotrack.video.video.Video method)

A

active_positions (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborLinker attribute) active_states (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker attribute) active_tracks (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) add_true_frames (byotrack.api.detector.detector.BatchDetector attribute) aggregate (byotrack.video.video.VideoTransformConfig attribute) all_positions (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) all_states (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker attribute) allow_gap_closing (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) allow_track_merging (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) allow_track_splitting (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) alternative_linking_cost_factor (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) always_measure_velocity (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) anisotropy (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute)

associate() (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) association_method (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) association_threshold (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) AssociationMethod (class in byotrack.implementation.linker.frame_by_frame.base) ax_slice (byotrack.video.reader.TiffVideoReader attribute) axes (byotrack.video.reader.FrameTiffLoader attribute)

B

B3SplineUWT (class in byotrack.implementation.detector.wavelet) B3SplineUWTApprox1 (class in byotrack.implementation.detector.wavelet) B3SplineUWTApprox2 (class in byotrack.implementation.detector.wavelet) b3swt (byotrack.implementation.detector.wavelet.WaveletDetector attribute) batch_size (byotrack.api.detector.detector.BatchDetector attribute) BatchDetector (class in byotrack.api.detector.detector) BatchMultiStepTracker (class in byotrack.api.tracker) bbox (byotrack.api.detector.detections.Detections attribute) BioMetrics (class in byotrack.metrics.ctc) blocking_value (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) blur (byotrack.api.optical_flow.optical_flow.OpticalFlow attribute) byotrack.api.detector.detections module byotrack.api.detector.detector module byotrack.api.linker module byotrack.api.optical_flow.optical_flow module byotrack.api.parameters module byotrack.api.refiner module byotrack.api.tracker module byotrack.api.tracks module byotrack.dataset.ctc module byotrack.dataset.sinetra module byotrack.fiji.io module byotrack.fiji.run module byotrack.icy.io module byotrack.icy.run module

byotrack.implementation.detector.wavelet module byotrack.implementation.linker.frame_by_frame.base module byotrack.implementation.linker.frame_by_frame.greedy_lap module byotrack.implementation.linker.frame_by_frame.kalman_linker module byotrack.implementation.linker.frame_by_frame.koft module byotrack.implementation.linker.frame_by_frame.nearest_neighbor module byotrack.implementation.linker.icy_emht.icy_emht module byotrack.implementation.linker.trackmate.trackmate module byotrack.implementation.optical_flow.opencv module byotrack.implementation.optical_flow.skimage module byotrack.implementation.refiner.cleaner module byotrack.implementation.refiner.interpolater module byotrack.implementation.refiner.propagation module byotrack.implementation.refiner.stitching.dist_stitcher module byotrack.implementation.refiner.stitching.emc2 module byotrack.metrics.ctc module byotrack.video.reader module byotrack.video.transforms module byotrack.video.video module byotrack.visualize module

C

capture_outputs (byotrack.fiji.run.FijiRunner attribute) channel (byotrack.video.transforms.ChannelSelect attribute) ChannelAvg (class in byotrack.video.transforms) channels (byotrack.video.reader.VideoReader attribute) (byotrack.video.video.Video attribute) ChannelSelect (class in byotrack.video.transforms) check_tracks() (byotrack.api.tracks.Track static method) clean_tracks() (byotrack.implementation.refiner.cleaner.Cleaner static method) Cleaner (class in byotrack.implementation.refiner.cleaner) collect() (byotrack.api.linker.OnlineLinker method) (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker method) compose_slice() (in module byotrack.video.video) compute() (byotrack.api.optical_flow.optical_flow.DummyOpticalFlow method) (byotrack.api.optical_flow.optical_flow.OpticalFlow method) (byotrack.implementation.optical_flow.opencv.OpenCVOpticalFlow method) (byotrack.implementation.optical_flow.skimage.SkimageOpticalFlow method) (byotrack.metrics.ctc.BioMetrics method) compute_detection_metric() (byotrack.metrics.ctc.CTCMetrics method)

compute_dist() (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher method) compute_stats_on (byotrack.video.transforms.ScaleAndNormalize attribute) (byotrack.video.video.VideoTransformConfig attribute) compute_threshold() (byotrack.implementation.detector.wavelet.WaveletDetector method) compute_tracking_metric() (byotrack.metrics.ctc.CTCMetrics method) confidence (byotrack.api.detector.detections.Detections attribute) constant_directed_propagate() (in module byotrack.implementation.refiner.propagation) copy_ground_truth() (byotrack.metrics.ctc.CTCMetrics static method) Cost (class in byotrack.implementation.linker.frame_by_frame.kalman_linker) cost() (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker method) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker method) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborLinker method) cost_method (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) ctc_software (byotrack.metrics.ctc.CTCSoftwareRunner attribute) CTCMetrics (class in byotrack.metrics.ctc) CTCSoftwareRunner (class in byotrack.metrics.ctc) cutoff_percentile (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute)

D

data (byotrack.api.detector.detections.Detections attribute) detect() (byotrack.api.detector.detector.BatchDetector method) (byotrack.dataset.ctc.GroundTruthDetector method) (byotrack.implementation.detector.wavelet.WaveletDetector method) detection_ids (byotrack.api.tracks.Track attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) detection_std (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) Detections (class in byotrack.api.detector.detections) detections_fnr (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) detections_fpr (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) detections_sequence (byotrack.visualize.InteractiveVisualizer attribute)

detector (byotrack.api.tracker.BatchMultiStepTracker attribute) (byotrack.api.tracker.MultiStepTracker attribute) Detector (class in byotrack.api.detector.detector) device (byotrack.implementation.detector.wavelet.WaveletDetector attribute) dim (byotrack.api.detector.detections.Detections attribute) DirectedPropagate (class in byotrack.implementation.refiner.propagation) display_lifetime() (in module byotrack.visualize) dist (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher attribute) DistStitcher (class in byotrack.implementation.refiner.stitching.dist_stitcher) downscale (byotrack.api.optical_flow.optical_flow.OpticalFlow attribute) draw_disk() (in module byotrack.dataset.ctc) DummyOpticalFlow (class in byotrack.api.optical_flow.optical_flow)

E

ema (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) EMC2Stitcher (class in byotrack.implementation.refiner.stitching.emc2) EMHTParameters (class in byotrack.implementation.linker.icy_emht.icy_emht) eta (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher attribute) (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher attribute)

existence_prob (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) expected_initial_particles (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) expected_new_particles (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) expected_track_length (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) extract_flows_on_detections (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute)

F

features_extractor (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) fiji_path (byotrack.fiji.run.FijiRunner attribute) FijiRunner (class in byotrack.fiji.run) fill_gap (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) filter_small_objects() (in module byotrack.implementation.detector.wavelet) flow_at() (byotrack.api.optical_flow.optical_flow.OpticalFlow method) flow_std (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) flow_to_rgb() (in module byotrack.visualize) forward() (byotrack.implementation.detector.wavelet.B3SplineUWT method) (byotrack.implementation.detector.wavelet.B3SplineUWTApprox1 method) (byotrack.implementation.detector.wavelet.B3SplineUWTApprox2 method) forward_backward_propagation() (in module byotrack.implementation.refiner.propagation)

ForwardBackwardInterpolater (class in byotrack.implementation.refiner.interpolater) fps (byotrack.video.reader.VideoReader attribute) frame_id (byotrack.api.detector.detections.Detections attribute) (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) (byotrack.video.reader.VideoReader attribute) frame_loader (byotrack.video.reader.MultiFrameReader attribute) frame_shape (byotrack.visualize.InteractiveVisualizer attribute) FrameByFrameLinker (class in byotrack.implementation.linker.frame_by_frame.base) FrameByFrameLinkerParameters (class in byotrack.implementation.linker.frame_by_frame.base) FrameTiffLoader (class in byotrack.video.reader) full (byotrack.implementation.refiner.interpolater.ForwardBackwardInterpolater attribute) full_specs (byotrack.implementation.linker.icy_emht.icy_emht.IcyEMHTLinker attribute)

G

gap_closing_max_distance (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) gate_factor (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) get_flow_wheel() (in module byotrack.visualize) grab() (byotrack.video.reader.MultiFrameReader method) (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.PILVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader method)

greedy_assignment_solver() (in module byotrack.implementation.linker.frame_by_frame.greedy_lap) grid_step (byotrack.visualize.InteractiveFlowVisualizer attribute) GroundTruthDetector (class in byotrack.dataset.ctc)

H

handle_actions() (byotrack.visualize.InteractiveFlowVisualizer method) (byotrack.visualize.InteractiveVisualizer method)

I

icy_path (byotrack.icy.run.IcyRunner attribute) IcyEMHTLinker (class in byotrack.implementation.linker.icy_emht.icy_emht) IcyRunner (class in byotrack.icy.run) identifier (byotrack.api.tracks.Track attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) in_axes (byotrack.video.reader.TiffVideoReader attribute) inactive_tracks (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute)

inertia (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) InteractiveFlowVisualizer (class in byotrack.visualize) InteractiveVisualizer (class in byotrack.visualize) is_split (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) is_valid() (byotrack.api.parameters.ParameterBound method) (byotrack.api.parameters.ParameterEnum method) (byotrack.api.parameters.ParameterRange method)

K

k (byotrack.implementation.detector.wavelet.WaveletDetector attribute) kalman_filter (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker attribute) kalman_order (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) kalman_search_radius (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute)

KalmanLinker (class in byotrack.implementation.linker.frame_by_frame.kalman_linker) KalmanLinkerParameters (class in byotrack.implementation.linker.frame_by_frame.kalman_linker) KOFTLinker (class in byotrack.implementation.linker.frame_by_frame.koft) KOFTLinkerParameters (class in byotrack.implementation.linker.frame_by_frame.koft) kwargs (byotrack.implementation.refiner.interpolater.ForwardBackwardInterpolater attribute) (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher attribute)

L

lap_solver (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher attribute) last_association (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) last_detections (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker attribute) last_log (byotrack.metrics.ctc.CTCSoftwareRunner attribute) last_metrics (byotrack.metrics.ctc.BioMetrics attribute) last_outputs (byotrack.fiji.run.FijiRunner attribute) length (byotrack.api.detector.detections.Detections attribute) (byotrack.video.reader.VideoReader attribute) level (byotrack.video.reader.FrameTiffLoader attribute) (byotrack.video.reader.TiffVideoReader attribute) linker (byotrack.api.tracker.BatchMultiStepTracker attribute) (byotrack.api.tracker.MultiStepTracker attribute)

Linker (class in byotrack.api.linker) linking_max_distance (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) load() (byotrack.api.detector.detections.Detections static method) (byotrack.api.tracks.Track static method) load_metadata() (in module byotrack.dataset.sinetra) load_multi_frames_detections() (byotrack.api.detector.detections.Detections static method) load_tracks() (in module byotrack.dataset.ctc) (in module byotrack.dataset.sinetra) (in module byotrack.fiji.io) (in module byotrack.icy.io)

M

mass (byotrack.api.detector.detections.Detections attribute) max (byotrack.video.transforms.ScaleAndNormalize attribute) max_dist (byotrack.implementation.refiner.cleaner.Cleaner attribute) (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher attribute) max_frame_gap (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) max_gap (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher attribute) max_overlap (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher attribute) maxi (byotrack.video.transforms.ScaleAndNormalize attribute) merge() (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher static method) (in module byotrack.implementation.refiner.propagation) merge_factor (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) merge_id (byotrack.api.tracks.Track attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) merge_links (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) merging_max_distance (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) MetaVideoReader (class in byotrack.video.reader) method (byotrack.implementation.optical_flow.skimage.SkimageOpticalFlow attribute) (byotrack.implementation.refiner.interpolater.ForwardBackwardInterpolater attribute) (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher attribute) min_area (byotrack.implementation.detector.wavelet.WaveletDetector attribute) min_length (byotrack.implementation.refiner.cleaner.Cleaner attribute) mini (byotrack.video.transforms.ScaleAndNormalize attribute) module byotrack.api.detector.detections byotrack.api.detector.detector byotrack.api.linker byotrack.api.optical_flow.optical_flow byotrack.api.parameters byotrack.api.refiner byotrack.api.tracker byotrack.api.tracks byotrack.dataset.ctc byotrack.dataset.sinetra byotrack.fiji.io byotrack.fiji.run byotrack.icy.io byotrack.icy.run byotrack.implementation.detector.wavelet byotrack.implementation.linker.frame_by_frame.base byotrack.implementation.linker.frame_by_frame.greedy_lap byotrack.implementation.linker.frame_by_frame.kalman_linker byotrack.implementation.linker.frame_by_frame.koft byotrack.implementation.linker.frame_by_frame.nearest_neighbor byotrack.implementation.linker.icy_emht.icy_emht byotrack.implementation.linker.trackmate.trackmate byotrack.implementation.optical_flow.opencv byotrack.implementation.optical_flow.skimage byotrack.implementation.refiner.cleaner byotrack.implementation.refiner.interpolater byotrack.implementation.refiner.propagation byotrack.implementation.refiner.stitching.dist_stitcher byotrack.implementation.refiner.stitching.emc2 byotrack.metrics.ctc byotrack.video.reader byotrack.video.transforms byotrack.video.video byotrack.visualize

motion (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) (byotrack.implementation.linker.icy_emht.icy_emht.IcyEMHTLinker attribute) Motion (class in byotrack.implementation.linker.icy_emht.icy_emht) motion_model() (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker method) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker method) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborLinker method) MultiFrameReader (class in byotrack.video.reader) MultiStepTracker (class in byotrack.api.tracker)

N

n_frames (byotrack.visualize.InteractiveVisualizer attribute) n_gap (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) n_initial (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker attribute) n_valid (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute)

ndim (byotrack.video.video.Video attribute) NearestNeighborLinker (class in byotrack.implementation.linker.frame_by_frame.nearest_neighbor) NearestNeighborParameters (class in byotrack.implementation.linker.frame_by_frame.nearest_neighbor) normalize (byotrack.video.video.VideoTransformConfig attribute) normalize() (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher static method)

O

online_process_std (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) OnlineFlowExtractor (class in byotrack.implementation.linker.frame_by_frame.base) OnlineLinker (class in byotrack.api.linker) open() (byotrack.video.reader.VideoReader static method) OpenCVOpticalFlow (class in byotrack.implementation.optical_flow.opencv) OpenCVVideoReader (class in byotrack.video.reader) optflow (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) (byotrack.visualize.InteractiveFlowVisualizer attribute)

optical_flow (byotrack.implementation.optical_flow.opencv.OpenCVOpticalFlow attribute) optical_flow_directed_propagate() (in module byotrack.implementation.refiner.propagation) OpticalFlow (class in byotrack.api.optical_flow.optical_flow) optimize() (byotrack.implementation.detector.wavelet.WaveletDetector method) out_axes (byotrack.video.reader.FrameTiffLoader attribute) (byotrack.video.reader.TiffVideoReader attribute) overlaps_with() (byotrack.api.tracks.Track method)

P

ParameterBound (class in byotrack.api.parameters) ParameterEnum (class in byotrack.api.parameters) ParameterRange (class in byotrack.api.parameters) parameters (byotrack.api.parameters.ParametrizedObjectMixin attribute) (byotrack.implementation.optical_flow.skimage.SkimageOpticalFlow attribute) parametrized (byotrack.api.parameters.ParametrizedObjectMixin attribute) ParametrizedObjectMixin (class in byotrack.api.parameters) parent_id (byotrack.api.tracks.Track attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) path (byotrack.video.reader.VideoReader attribute) paths (byotrack.video.reader.MultiFrameReader attribute) PauseableTQDM (class in byotrack.api.tracker) pil_loader() (in module byotrack.video.reader)

PILVideoReader (class in byotrack.video.reader) points (byotrack.api.tracks.Track attribute) (byotrack.visualize.InteractiveFlowVisualizer attribute) position (byotrack.api.detector.detections.Detections attribute) post_association() (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker method) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker method) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborLinker method) precompute (byotrack.visualize.InteractiveFlowVisualizer attribute) preprocess() (byotrack.api.optical_flow.optical_flow.OpticalFlow method) process_noises (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker attribute) process_std (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) projections (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker attribute)

Q

q_max (byotrack.video.transforms.ScaleAndNormalize attribute) (byotrack.video.video.VideoTransformConfig attribute)

q_min (byotrack.video.transforms.ScaleAndNormalize attribute) (byotrack.video.video.VideoTransformConfig attribute)

R

read() (byotrack.video.reader.VideoReader method) reader (byotrack.video.video.Video attribute) Refiner (class in byotrack.api.refiner) refiners (byotrack.api.tracker.BatchMultiStepTracker attribute) (byotrack.api.tracker.MultiStepTracker attribute) register_track_id() (byotrack.implementation.linker.frame_by_frame.base.TrackHandler method) relabel_consecutive() (in module byotrack.api.detector.detections) release() (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.PILVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader method) released (byotrack.video.reader.VideoReader attribute) reset() (byotrack.api.linker.OnlineLinker method) (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) (byotrack.implementation.linker.frame_by_frame.base.OnlineFlowExtractor method) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker method) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker method) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborLinker method) retrieve() (byotrack.video.reader.MultiFrameReader method) (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.PILVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader method)

reverse() (byotrack.api.tracks.Track static method) run() (byotrack.api.detector.detector.BatchDetector method) (byotrack.api.detector.detector.Detector method) (byotrack.api.linker.Linker method) (byotrack.api.linker.OnlineLinker method) (byotrack.api.refiner.Refiner method) (byotrack.api.tracker.BatchMultiStepTracker method) (byotrack.api.tracker.MultiStepTracker method) (byotrack.api.tracker.Tracker method) (byotrack.fiji.run.FijiRunner method) (byotrack.icy.run.IcyRunner method) (byotrack.implementation.linker.icy_emht.icy_emht.IcyEMHTLinker method) (byotrack.implementation.linker.trackmate.trackmate.TrackMateLinker method) (byotrack.implementation.refiner.cleaner.Cleaner method) (byotrack.implementation.refiner.interpolater.ForwardBackwardInterpolater method) (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher method) (byotrack.metrics.ctc.BioMetrics method) (byotrack.metrics.ctc.CTCSoftwareRunner method) (byotrack.visualize.InteractiveFlowVisualizer method) (byotrack.visualize.InteractiveVisualizer method) runner (byotrack.implementation.linker.icy_emht.icy_emht.IcyEMHTLinker attribute) (byotrack.implementation.linker.trackmate.trackmate.TrackMateLinker attribute) (byotrack.metrics.ctc.BioMetrics attribute)

S

save() (byotrack.api.detector.detections.Detections method) (byotrack.api.tracks.Track static method) (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters method) save_all (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) save_detections() (in module byotrack.dataset.ctc) (in module byotrack.fiji.io) (in module byotrack.icy.io) save_multi_frames_detections() (byotrack.api.detector.detections.Detections static method) save_tracks() (in module byotrack.dataset.ctc) (in module byotrack.icy.io) scale (byotrack.implementation.detector.wavelet.WaveletDetector attribute) (byotrack.visualize.InteractiveFlowVisualizer attribute) (byotrack.visualize.InteractiveVisualizer attribute) ScaleAndNormalize (class in byotrack.video.transforms) seek() (byotrack.video.reader.MultiFrameReader method) (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.PILVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader method) segmentation (byotrack.api.detector.detections.Detections attribute) selected_channel (byotrack.video.video.VideoTransformConfig attribute) set_transform() (byotrack.video.video.Video method) shape (byotrack.api.detector.detections.Detections attribute) (byotrack.video.reader.VideoReader attribute) (byotrack.video.video.Video attribute)

SkimageOpticalFlow (class in byotrack.implementation.optical_flow.skimage) skip_computation() (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher static method) slice_length() (in module byotrack.video.reader) smooth_clip (byotrack.video.transforms.ScaleAndNormalize attribute) (byotrack.video.video.VideoTransformConfig attribute) solve() (byotrack.implementation.linker.frame_by_frame.base.AssociationMethod method) specs (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinker attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinker attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborLinker attribute) (byotrack.implementation.linker.trackmate.trackmate.TrackMateLinker attribute) split_factor (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.nearest_neighbor.NearestNeighborParameters attribute) split_links (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker attribute) splitting_max_distance (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) start (byotrack.api.tracks.Track attribute) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) supported_extensions (byotrack.video.reader.VideoReader attribute) system (byotrack.metrics.ctc.CTCSoftwareRunner attribute)

T

tell() (byotrack.video.reader.VideoReader method) temporal_projection() (in module byotrack.visualize) tensorize() (byotrack.api.tracks.Track static method) termination_prob (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute) tiemout (byotrack.icy.run.IcyRunner attribute) TiffVideoReader (class in byotrack.video.reader) to_str() (byotrack.api.parameters.ParameterBound method) (byotrack.api.parameters.ParameterEnum method) (byotrack.api.parameters.ParameterRange method) to_xml() (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters method) tps_directed_propagate() (in module byotrack.implementation.refiner.propagation) Track (class in byotrack.api.tracks) track_building (byotrack.implementation.linker.frame_by_frame.kalman_linker.KalmanLinkerParameters attribute) (byotrack.implementation.linker.frame_by_frame.koft.KOFTLinkerParameters attribute)

track_ids (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) track_state (byotrack.implementation.linker.frame_by_frame.base.TrackHandler attribute) TrackBuilding (class in byotrack.implementation.linker.frame_by_frame.kalman_linker) Tracker (class in byotrack.api.tracker) TrackHandler (class in byotrack.implementation.linker.frame_by_frame.base) TrackHandler.TrackState (class in byotrack.implementation.linker.frame_by_frame.base) TrackMateLinker (class in byotrack.implementation.linker.trackmate.trackmate) TrackMateParameters (class in byotrack.implementation.linker.trackmate.trackmate) tracks (byotrack.visualize.InteractiveVisualizer attribute) tracks_colors (byotrack.visualize.InteractiveFlowVisualizer attribute) (byotrack.visualize.InteractiveVisualizer attribute) transform() (byotrack.api.optical_flow.optical_flow.OpticalFlow method) (byotrack.video.video.Video method) tree_depth (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute)

U

unpause() (byotrack.api.tracker.PauseableTQDM method) update() (byotrack.api.linker.OnlineLinker method) (byotrack.api.tracker.PauseableTQDM method) (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) (byotrack.implementation.linker.frame_by_frame.base.OnlineFlowExtractor method) (byotrack.implementation.linker.frame_by_frame.base.TrackHandler method)

update_active_tracks() (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) update_detection_ids() (in module byotrack.api.tracks) update_detections() (byotrack.implementation.linker.frame_by_frame.base.FrameByFrameLinker method) update_stats() (byotrack.video.transforms.ScaleAndNormalize method) use_median_position (byotrack.api.detector.detections.Detections attribute) use_most_likely_model (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute)

V

video (byotrack.video.reader.OpenCVVideoReader attribute) (byotrack.video.reader.PILVideoReader attribute) (byotrack.visualize.InteractiveFlowVisualizer attribute) (byotrack.visualize.InteractiveVisualizer attribute)

Video (class in byotrack.video.video) VideoReader (class in byotrack.video.reader) VideoTransformConfig (class in byotrack.video.video)

W

warp() (byotrack.api.optical_flow.optical_flow.OpticalFlow method)

WaveletDetector (class in byotrack.implementation.detector.wavelet)