Index

_

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

A

add_true_frames (byotrack.api.detector.detector.BatchDetector attribute) aggregate (byotrack.video.video.VideoTransformConfig 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)

B

B3SplineUWT (class in byotrack.implementation.detector.wavelet) B3SplineUWTApprox (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) 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.fiji.io module byotrack.fiji.run module byotrack.icy.io module

byotrack.icy.run module byotrack.implementation.detector.stardist module byotrack.implementation.detector.wavelet 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.video.reader module byotrack.video.transforms module byotrack.video.video module byotrack.visualize module

C

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) clean_tracks() (byotrack.implementation.refiner.cleaner.Cleaner static method) Cleaner (class in byotrack.implementation.refiner.cleaner) collect() (byotrack.api.linker.OnlineLinker 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) compute_dist() (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher method) compute_stats_on (byotrack.video.video.VideoTransformConfig attribute) compute_threshold() (byotrack.implementation.detector.wavelet.WaveletDetector method) confidence (byotrack.api.detector.detections.Detections attribute) constant_directed_propagate() (in module byotrack.implementation.refiner.propagation) 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.implementation.detector.stardist.StarDistDetector method) (byotrack.implementation.detector.wavelet.WaveletDetector method) detection_ids (byotrack.api.tracks.Track 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) 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) DummyOpticalFlow (class in byotrack.api.optical_flow.optical_flow)

E

EMC2Stitcher (class in byotrack.implementation.refiner.stitching.emc2) EMHTParameters (class in byotrack.implementation.linker.icy_emht.icy_emht) ensure_3d() (byotrack.video.reader.VideoReader static method) 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)

F

fiji_path (byotrack.fiji.run.FijiRunner attribute) FijiRunner (class in byotrack.fiji.run) flow_at() (byotrack.api.optical_flow.optical_flow.OpticalFlow method) forward() (byotrack.implementation.detector.wavelet.B3SplineUWT method) (byotrack.implementation.detector.wavelet.B3SplineUWTApprox 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.video.reader.VideoReader attribute) frame_shape (byotrack.visualize.InteractiveVisualizer attribute) from_pretrained() (byotrack.implementation.detector.stardist.StarDistDetector static method) from_trained() (byotrack.implementation.detector.stardist.StarDistDetector static method) 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) grab() (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader method)

grid_step (byotrack.visualize.InteractiveFlowVisualizer attribute)

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) inertia (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute)

InteractiveFlowVisualizer (class in byotrack.visualize) InteractiveVisualizer (class in byotrack.visualize) 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_search_radius (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute)

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) length (byotrack.api.detector.detections.Detections attribute) (byotrack.video.reader.VideoReader 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_multi_frames_detections() (byotrack.api.detector.detections.Detections static method) load_tracks() (in module byotrack.fiji.io) (in module byotrack.icy.io)

M

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) 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) model (byotrack.implementation.detector.stardist.StarDistDetector 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.fiji.io byotrack.fiji.run byotrack.icy.io byotrack.icy.run byotrack.implementation.detector.stardist byotrack.implementation.detector.wavelet 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.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) MultiStepTracker (class in byotrack.api.tracker)

N

n_frames (byotrack.visualize.InteractiveVisualizer attribute) nms_threshold (byotrack.implementation.detector.stardist.StarDistDetector attribute)

normalize (byotrack.video.video.VideoTransformConfig attribute) normalize() (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher static method)

O

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.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) 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)

path (byotrack.video.reader.VideoReader attribute) points (byotrack.api.tracks.Track attribute) (byotrack.visualize.InteractiveFlowVisualizer attribute) position (byotrack.api.detector.detections.Detections attribute) precompute (byotrack.visualize.InteractiveFlowVisualizer attribute) preprocess() (byotrack.api.optical_flow.optical_flow.OpticalFlow method) prob_threshold (byotrack.implementation.detector.stardist.StarDistDetector 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) relabel_consecutive() (in module byotrack.api.detector.detections) release() (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader method) released (byotrack.video.reader.VideoReader attribute) reset() (byotrack.api.linker.OnlineLinker method) retrieve() (byotrack.video.reader.OpenCVVideoReader method) (byotrack.video.reader.TiffVideoReader method) (byotrack.video.reader.VideoReader 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.visualize.InteractiveFlowVisualizer method) (byotrack.visualize.InteractiveVisualizer method)

runner (byotrack.implementation.linker.icy_emht.icy_emht.IcyEMHTLinker attribute) (byotrack.implementation.linker.trackmate.trackmate.TrackMateLinker attribute)

S

save() (byotrack.api.detector.detections.Detections method) (byotrack.api.tracks.Track static method) (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters method) save_detections() (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.icy.io) scale (byotrack.implementation.detector.wavelet.WaveletDetector attribute) ScaleAndNormalize (class in byotrack.video.transforms) seek() (byotrack.video.reader.OpenCVVideoReader 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.video) smooth_clip (byotrack.video.transforms.ScaleAndNormalize attribute) (byotrack.video.video.VideoTransformConfig attribute) sorted_alphanumeric() (in module byotrack.api.detector.detections) specs (byotrack.implementation.linker.trackmate.trackmate.TrackMateLinker attribute) splitting_max_distance (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) StarDistDetector (class in byotrack.implementation.detector.stardist) start (byotrack.api.tracks.Track attribute) supported_extensions (byotrack.video.reader.VideoReader 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) Tracker (class in byotrack.api.tracker) TrackMateLinker (class in byotrack.implementation.linker.trackmate.trackmate) TrackMateParameters (class in byotrack.implementation.linker.trackmate.trackmate) tracks (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

update() (byotrack.api.linker.OnlineLinker method) update_detection_ids() (in module byotrack.api.tracks)

update_stats() (byotrack.video.transforms.ScaleAndNormalize method) use_most_likely_model (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute)

V

video (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)