ByoTrack
v0.4.2
Install
Installation
Getting started
ByoTrack fundamental features
Detectors
API
Video
Detections
Tracks
Tracker
Detector
Linker
Refiner
Parameters
API implementations
Detectors
Linkers
Refiners
Icy support
Icy
Fiji support
Fiji
Visualization
ByoTrack ViZ
ByoTrack
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
_
__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)