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) alpha (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher 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) bbox (byotrack.api.detector.detections.Detections attribute) blocking_value (byotrack.implementation.linker.trackmate.trackmate.TrackMateParameters attribute) byotrack.api.detector.detections module byotrack.api.detector.detector module byotrack.api.linker 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.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) ChannelSelect (class in byotrack.video.transforms) clean_tracks() (byotrack.implementation.refiner.cleaner.Cleaner static method)

Cleaner (class in byotrack.implementation.refiner.cleaner) compute_dist() (byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher method) 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) 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.MultiStepTracker attribute) Detector (class in byotrack.api.detector.detector) device (byotrack.implementation.detector.wavelet.WaveletDetector attribute) display_lifetime() (in module byotrack.visualize) dist (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher attribute) DistStitcher (class in byotrack.implementation.refiner.stitching.dist_stitcher)

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) 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) 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)

H

handle_actions() (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) 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)

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.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.refiner.interpolater.ForwardBackwardInterpolater 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.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.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)

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

O

open() (byotrack.video.reader.VideoReader static method)

OpenCVVideoReader (class in byotrack.video.reader) 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)

parametrized (byotrack.api.parameters.ParametrizedObjectMixin attribute) ParametrizedObjectMixin (class in byotrack.api.parameters) path (byotrack.video.reader.VideoReader attribute) points (byotrack.api.tracks.Track attribute) position (byotrack.api.detector.detections.Detections 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.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) 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.refiner.Refiner 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.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) skip_computation() (byotrack.implementation.refiner.stitching.dist_stitcher.DistStitcher static method) 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) 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.video.video.Video method) tree_depth (byotrack.implementation.linker.icy_emht.icy_emht.EMHTParameters attribute)

U

update_stats() (byotrack.video.transforms.ScaleAndNormalize method)

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

V

video (byotrack.visualize.InteractiveVisualizer attribute) Video (class in byotrack.video.video)

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

W

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