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agora
extraction
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logfile_parser
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
_
__init__() (align method)
(alignParameters method)
(Argo method)
(autoreg method)
(autoregParameters method)
(BabyParameters method)
(BabyRunner method)
(BaseLocalImage method)
(BasePlotter method)
(BridgeH5 method)
(BridgeOmero method)
(butter method)
(butterParameters method)
(Cache method)
(catch22 method)
(catch22Parameters method)
(CellBenchmarker method)
(Cells method)
(CellTracker method)
(Chainer method)
(crosscorr method)
(crosscorrParameters method)
(Dataset method)
(DatasetLocalABC method)
(DatasetLocalDir method)
(DatasetLocalOME method)
(detrend method)
(detrendParameters method)
(dsignal method)
(dsignalParameters method)
(DynamicReader method)
(DynamicWriter method)
(Extractor method)
(ExtractorParameters method)
(FeatureCalculator method)
(fft method)
(fftParameters method)
(findpeaks method)
(findpeaksParameters method)
(gpsignal method)
(gpsignalParameters method)
(hollowExtractor method)
(Image method)
(ImageDir method)
(ImageDummy method)
(ImageLocalOME method)
(interpolate method)
(interpolateParameters method)
(knngraph method)
(knngraphParameters method)
(leiden method)
(leidenParameters method)
(LineageProcess method)
(LineageProcessParameters method)
(LinearBabyWriter method)
(MetaData method)
(mi method)
(miParameters method)
(ModelPredictor method)
(ModelPredictorWriter method)
(OmeroExplorer method)
(ParametersABC method)
(Parser method)
(Pipeline method)
(PipelineParameters method)
(PostProcessABC method)
(PostProcessor method)
(PostProcessorParameters method)
(ProcessABC method)
(savgol method)
(savgolParameters method)
(Signal method)
(standardscaler method)
(standardscalerParameters method)
(StateReader method)
(StateWriter method)
(StepABC method)
(Template method)
(TemplateParameters method)
(Tiler method)
(TilerParameters method)
(TilerWriter method)
(Trap method)
(TrapLocations method)
(UnsafeImage method)
(Writer method)
A
accumulate() (in module agora.io.utils)
add_file_as_annotation() (BridgeOmero method)
(Dataset method)
(Image method)
(UnsafeImage method)
add_index_levels() (in module agora.utils.kymograph)
add_name() (Chainer static method)
(Signal static method)
add_to_collection() (in module agora.abc)
agora
module
agora.abc
module
agora.io
module
agora.io.bridge
module
agora.io.cells
module
agora.io.decorators
module
agora.io.metadata
module
agora.io.reader
module
agora.io.signal
module
agora.io.utils
module
agora.io.writer
module
agora.logging
module
agora.track_abc
module
agora.utils
module
agora.utils.association
module
agora.utils.kymograph
module
agora.utils.lineage
module
agora.utils.merge
module
aliby
module
aliby.baby_client
module
aliby.bin
module
aliby.bin.run
module
aliby.haystack
module
aliby.io
module
aliby.io.dataset
module
aliby.io.image
module
aliby.io.omero
module
aliby.lineage
module
aliby.pipeline
module
aliby.tile
module
aliby.tile.tiler
module
aliby.tile.traps
module
aliby.track
module
aliby.track.benchmark
module
aliby.track.cell_tracker
module
aliby.track.utils
module
aliby.utils
module
aliby.utils.argo
module
align (class in postprocessor.core.multisignal.align)
alignParameters (class in postprocessor.core.multisignal.align)
annot_from_dset() (in module aliby.utils.argo)
apply_chain() (Chainer method)
apply_merges() (in module agora.utils.merge)
apply_prepost() (Chainer method)
(Signal method)
area() (in module extraction.core.functions.cell)
Argo (class in aliby.utils.argo)
as_function() (LineageProcess class method)
as_range() (Trap method)
as_tile() (Trap method)
assign_lbls() (CellTracker method)
at_time() (Trap method)
attrs_from_h5() (in module agora.io.bridge)
autoreg (class in postprocessor.core.processes.autoreg)
autoreg_periodogram() (autoreg method)
autoregParameters (class in postprocessor.core.processes.autoreg)
available (Chainer property)
(Signal property)
B
BabyParameters (class in aliby.baby_client)
BabyRunner (class in aliby.baby_client)
background_max5() (in module extraction.core.functions.trap)
BaseLocalImage (class in aliby.io.image)
BasePlotter (class in postprocessor.routines.plottingabc)
bidirectional_retainment_filter() (in module agora.utils.kymograph)
BridgeH5 (class in agora.io.bridge)
BridgeOmero (class in aliby.io.omero)
butter (class in postprocessor.core.processes.butter)
butterfilter() (butter method)
butterParameters (class in postprocessor.core.processes.butter)
C
Cache (class in agora.io.utils)
calc_baryangles() (in module aliby.track.utils)
calc_barycentre() (in module aliby.track.utils)
calc_barydists() (in module aliby.track.utils)
calc_dtfeats() (CellTracker method)
calc_feat_ndarray() (CellTracker method)
calc_feats_from_mask() (CellTracker method)
(FeatureCalculator method)
calc_trapfeats() (CellTracker method)
(FeatureCalculator method)
calculate_errsum() (CellBenchmarker method)
catch22 (class in postprocessor.core.processes.catch22)
catch22Parameters (class in postprocessor.core.processes.catch22)
CellBenchmarker (class in aliby.track.benchmark)
Cells (class in agora.io.cells)
CellTracker (class in aliby.track.cell_tracker)
Chainer (class in postprocessor.chainer)
channels (Chainer property)
(Extractor property)
(hollowExtractor property)
(Signal property)
channels() (Argo method)
(OmeroExplorer method)
check_channels() (in module aliby.utils.argo)
check_type_recursive() (in module agora.abc)
choose_model_from_params() (in module aliby.baby_client)
classical_periodogram() (fft method)
clean_tracks() (in module postprocessor.core.functions.tracks)
close() (BridgeH5 method)
(Chainer method)
(Signal method)
(Writer method)
cluster_kymograph() (in module agora.utils.kymograph)
compare_pred_truth_lols() (in module aliby.track.utils)
compare_traps() (CellBenchmarker method)
conical_volume() (in module extraction.core.functions.cell)
convert_to_hours() (in module aliby.utils.argo)
crosscorr (class in postprocessor.core.multisignal.crosscorr)
crosscorrParameters (class in postprocessor.core.multisignal.crosscorr)
D
Dataset (class in aliby.io.omero)
dataset_to_df() (Chainer method)
(Signal method)
DatasetLocalABC (class in aliby.io.dataset)
DatasetLocalDir (class in aliby.io.dataset)
DatasetLocalOME (class in aliby.io.dataset)
datasets (Chainer property)
(Signal property)
datetime_to_timestamp() (in module agora.io.metadata)
default() (BabyParameters class method)
detrend (class in postprocessor.core.processes.detrend)
detrendParameters (class in postprocessor.core.processes.detrend)
df_extend_nan() (in module postprocessor.core.multisignal.align)
df_shift() (in module postprocessor.core.multisignal.align)
dimorder (ImageLocalOME property)
dir_to_meta() (in module agora.io.metadata)
dispatch_dataset() (in module aliby.io.dataset)
dispatch_metadata_parser() (in module agora.io.metadata)
div0() (in module extraction.core.functions.math_utils)
drop_level() (in module agora.utils.kymograph)
dsignal (class in postprocessor.core.processes.dsignal)
dsignalParameters (class in postprocessor.core.processes.dsignal)
dummy() (Tiler class method)
DynamicReader (class in agora.io.reader)
DynamicWriter (class in agora.io.writer)
E
eccentricity() (in module extraction.core.functions.cell)
estimate_gr() (in module postprocessor.core.processes.gpsignal)
exparams_from_meta() (in module extraction.core.functions.defaults)
extract_funs() (Extractor method)
(hollowExtractor method)
extract_header() (in module logfile_parser.swainlab_parser)
extract_tp() (Extractor method)
(hollowExtractor method)
extract_traps() (Extractor method)
(hollowExtractor method)
extraction
module
extraction.core
module
extraction.core.extractor
module
extraction.core.functions
module
extraction.core.functions.cell
module
extraction.core.functions.custom
module
extraction.core.functions.custom.localisation
module
extraction.core.functions.defaults
module
extraction.core.functions.distributors
module
extraction.core.functions.loaders
module
extraction.core.functions.math_utils
module
extraction.core.functions.trap
module
extraction.core.functions.versioning
module
extraction.local_data_loaders
module
Extractor (class in extraction.core.extractor)
ExtractorParameters (class in extraction.core.extractor)
F
FeatureCalculator (class in agora.track_abc)
fft (class in postprocessor.core.processes.fft)
fftParameters (class in postprocessor.core.processes.fft)
fields_to_dict_or_table() (in module logfile_parser.swainlab_parser)
filename_to_dict_indices() (in module agora.io.metadata)
filt_cluster() (in module agora.utils.kymograph)
find_channel_index() (in module aliby.tile.tiler)
find_channel_name() (in module aliby.tile.tiler)
find_drift() (Tiler method)
find_file() (in module agora.io.metadata)
find_ids() (Writer static method)
findpeaks (class in postprocessor.core.processes.findpeaks)
findpeaksParameters (class in postprocessor.core.processes.findpeaks)
fit_autoreg() (autoreg method)
flatten() (in module agora.io.bridge)
flatten_dict() (in module agora.io.metadata)
flatten_nesteddict() (in module extraction.core.extractor)
format_field() (StateWriter static method)
format_segmentation() (in module aliby.baby_client)
format_states() (StateWriter method)
format_values_tpback() (StateWriter static method)
format_values_traps() (StateWriter static method)
from_existing_h5() (Pipeline class method)
from_folder() (Pipeline class method)
from_h5() (Dataset class method)
(Image class method)
(Tiler class method)
(UnsafeImage class method)
from_image() (Tiler class method)
from_img() (Extractor class method)
(hollowExtractor class method)
from_tiler() (Extractor class method)
(hollowExtractor class method)
from_tiler_init() (TrapLocations class method)
from_yaml() (alignParameters class method)
(autoregParameters class method)
(BabyParameters class method)
(butterParameters class method)
(catch22Parameters class method)
(crosscorrParameters class method)
(detrendParameters class method)
(dsignalParameters class method)
(ExtractorParameters class method)
(fftParameters class method)
(findpeaksParameters class method)
(gpsignalParameters class method)
(interpolateParameters class method)
(knngraphParameters class method)
(leidenParameters class method)
(LineageProcessParameters class method)
(miParameters class method)
(ParametersABC class method)
(PipelineParameters class method)
(PostProcessorParameters class method)
(savgolParameters class method)
(standardscalerParameters class method)
(TemplateParameters class method)
(TilerParameters class method)
G
gauss3D() (in module extraction.core.functions.custom.localisation)
gen_boolmat_from_clabs() (in module aliby.track.benchmark)
gen_cm_stats() (CellBenchmarker method)
gen_errorplots() (CellBenchmarker method)
gen_stats_dict() (in module aliby.track.benchmark)
generate_palette_map() (in module postprocessor.routines.plot_utils)
get() (Chainer method)
get_annot() (in module aliby.utils.argo)
get_annotsets() (in module aliby.utils.argo)
get_avg_gr() (in module postprocessor.core.functions.tracks)
get_avg_grs() (in module postprocessor.core.functions.tracks)
get_balanced_acc() (in module aliby.track.benchmark)
get_channel_index() (Tiler method)
get_chs() (in module aliby.utils.argo)
get_closest_pairs() (in module postprocessor.core.functions.tracks)
get_consecutives() (BridgeH5 static method)
(Chainer static method)
(Signal static method)
(Writer static method)
get_contiguous_pairs() (in module postprocessor.core.functions.tracks)
get_data_lazy() (ImageDir method)
(ImageDummy method)
(ImageLocalOME method)
(in module aliby.io.omero)
get_dMetric() (in module postprocessor.core.functions.tracks)
get_dMetric_wrap() (in module postprocessor.core.functions.tracks)
get_examples_dir() (in module aliby.io.image)
(in module logfile_parser.legacy)
get_existing_ids() (Writer static method)
get_feats2use() (CellTracker method)
get_frac_error_df() (CellBenchmarker method)
get_image_class() (in module aliby.io.image)
get_imgs() (Extractor method)
(hollowExtractor method)
get_info_tree() (BridgeH5 method)
(Chainer method)
(Signal method)
(Writer method)
get_joinable() (in module postprocessor.core.functions.tracks)
get_joint_ids() (in module postprocessor.core.functions.tracks)
get_last_i() (in module postprocessor.core.functions.tracks)
get_legacy_log_example_interface() (in module logfile_parser.legacy)
get_logfile() (in module aliby.utils.argo)
get_logfile_grammars_dir() (in module logfile_parser.legacy)
get_means() (in module postprocessor.core.functions.tracks)
get_merged() (Chainer method)
(Signal method)
get_merges() (Chainer method)
(Signal method)
get_meta_from_legacy() (in module agora.io.metadata)
get_meta_swainlab() (in module agora.io.metadata)
get_mother_ilocs_from_daughters() (in module agora.utils.kymograph)
get_mothers_from_another_df() (in module agora.utils.kymograph)
get_new_lbls() (CellTracker method)
get_nfeats_from_model() (in module aliby.track.cell_tracker)
get_parameters() (in module postprocessor.core.abc)
get_picks() (Chainer method)
(Signal method)
get_precision() (in module aliby.track.benchmark)
get_process() (in module postprocessor.core.abc)
get_raw() (Chainer method)
(Signal method)
get_recall() (in module aliby.track.benchmark)
get_retained() (Chainer static method)
(Signal static method)
get_sha() (in module extraction.core.functions.versioning)
get_store_path() (in module agora.io.utils)
get_tc() (Tiler method)
get_tiles() (Extractor method)
(hollowExtractor method)
get_tiles_timepoint() (Tiler method)
get_tnr() (in module aliby.track.benchmark)
get_tp_data() (Tiler method)
get_tracks_ntps() (in module postprocessor.core.functions.tracks)
get_trap_data() (Tiler method)
get_truth_matrix_from_pair() (CellBenchmarker method)
get_val() (in module postprocessor.core.functions.tracks)
get_vec_closest_pairs() (in module postprocessor.core.functions.tracks)
gpsignal (class in postprocessor.core.processes.gpsignal)
gpsignalParameters (class in postprocessor.core.processes.gpsignal)
GrammarNotFound
graph_prune() (in module postprocessor.core.processes.knngraph)
group_by_traps() (Cells method)
groupsort() (in module agora.io.bridge)
guess_from_meta() (ExtractorParameters static method)
H
half_ceil() (in module aliby.tile.traps)
half_floor() (in module aliby.tile.traps)
has_channels() (in module aliby.utils.argo)
HeaderEndNotFound
heatmap() (in module postprocessor.routines.heatmap)
histogram() (in module postprocessor.routines.histogram)
hollowExtractor (class in extraction.core.extractor)
I
identify_trap_locations() (in module aliby.tile.traps)
ifoob_pad() (Tiler static method)
Image (class in aliby.io.omero)
image_creds_from_h5() (in module agora.io.bridge)
ImageDir (class in aliby.io.image)
ImageDummy (class in aliby.io.image)
ImageLocalOME (class in aliby.io.image)
imBackground() (in module extraction.core.functions.trap)
imread() (in module agora.io.utils)
initialise_tf() (in module aliby.haystack)
initialise_traps() (Tiler method)
interpolate (class in postprocessor.core.processes.interpolate)
interpolateParameters (class in postprocessor.core.processes.interpolate)
intersection_matrix() (in module agora.utils.kymograph)
J
join_track_pair() (in module postprocessor.core.functions.tracks)
join_tracks() (in module postprocessor.core.functions.tracks)
join_tracks_pair() (in module agora.utils.merge)
K
knngraph (class in postprocessor.core.processes.knngraph)
knngraphParameters (class in postprocessor.core.processes.knngraph)
L
labelled_in_frame() (Cells method)
labels (Cells property)
legacy_get_last_tp() (Pipeline static method)
leiden (class in postprocessor.core.processes.leiden)
leidenParameters (class in postprocessor.core.processes.leiden)
lineage() (Chainer method)
(Signal method)
LineageProcess (class in postprocessor.core.lineageprocess)
LineageProcessParameters (class in postprocessor.core.lineageprocess)
LinearBabyWriter (class in agora.io.writer)
load() (Argo method)
(in module extraction.local_data_loaders)
(OmeroExplorer method)
load_1z() (in module extraction.local_data_loaders)
load_acq() (in module aliby.utils.argo)
load_annot_from_cache() (in module aliby.utils.argo)
load_attributes() (in module agora.io.writer)
(in module extraction.core.functions.defaults)
load_cellfuns() (in module extraction.core.functions.loaders)
load_cellfuns_core() (in module extraction.core.functions.loaders)
load_custom_args() (in module extraction.core.functions.loaders)
load_custom_funs() (Extractor method)
(hollowExtractor method)
load_funs() (in module extraction.core.functions.loaders)
load_lineage() (LineageProcess method)
load_meta() (Extractor method)
(hollowExtractor method)
load_paired_images() (in module extraction.local_data_loaders)
load_redfuns() (in module extraction.core.functions.loaders)
load_test_dset() (in module postprocessor.core.functions.tracks)
load_tiled_image() (in module extraction.local_data_loaders)
load_trapfuns() (in module extraction.core.functions.loaders)
localid_to_idx() (in module postprocessor.core.functions.tracks)
locate_indices() (in module agora.io.writer)
logfile_parser
module
logfile_parser.legacy
module
logfile_parser.logfile_parser
module
logfile_parser.swainlab_parser
module
lol_to_adj() (in module aliby.track.utils)
M
matlab_style_gauss2D() (in module extraction.core.functions.custom.localisation)
matrix_trap_tp_where() (Cells method)
max2p5pc() (in module extraction.core.functions.cell)
max5px() (in module extraction.core.functions.cell)
max_nonstop_ntps() (in module postprocessor.core.functions.tracks)
max_ntps() (in module postprocessor.core.functions.tracks)
mb_array_to_dict() (in module agora.utils.lineage)
mean() (in module extraction.core.functions.cell)
mean_plot() (in module postprocessor.routines.mean_plot)
median() (in module extraction.core.functions.cell)
median_plot() (in module postprocessor.routines.median_plot)
melt_reset() (in module agora.utils.kymograph)
merge_tracks() (in module postprocessor.core.functions.tracks)
merges (Chainer property)
(Signal property)
meta_h5 (BridgeH5 property)
(Chainer property)
(Signal property)
(Writer property)
MetaData (class in agora.io.metadata)
metadata (Image property)
(UnsafeImage property)
mi (class in postprocessor.core.multisignal.mi)
min_maj_approximation() (in module extraction.core.functions.cell)
miParameters (class in postprocessor.core.multisignal.mi)
ModelPredictor (class in aliby.haystack)
ModelPredictorWriter (class in aliby.haystack)
module
agora
agora.abc
agora.io
agora.io.bridge
agora.io.cells
agora.io.decorators
agora.io.metadata
agora.io.reader
agora.io.signal
agora.io.utils
agora.io.writer
agora.logging
agora.track_abc
agora.utils
agora.utils.association
agora.utils.kymograph
agora.utils.lineage
agora.utils.merge
aliby
aliby.baby_client
aliby.bin
aliby.bin.run
aliby.haystack
aliby.io
aliby.io.dataset
aliby.io.image
aliby.io.omero
aliby.lineage
aliby.pipeline
aliby.tile
aliby.tile.tiler
aliby.tile.traps
aliby.track
aliby.track.benchmark
aliby.track.cell_tracker
aliby.track.utils
aliby.utils
aliby.utils.argo
extraction
extraction.core
extraction.core.extractor
extraction.core.functions
extraction.core.functions.cell
extraction.core.functions.custom
extraction.core.functions.custom.localisation
extraction.core.functions.defaults
extraction.core.functions.distributors
extraction.core.functions.loaders
extraction.core.functions.math_utils
extraction.core.functions.trap
extraction.core.functions.versioning
extraction.local_data_loaders
logfile_parser
logfile_parser.legacy
logfile_parser.logfile_parser
logfile_parser.swainlab_parser
postprocessor
postprocessor.chainer
postprocessor.core
postprocessor.core.abc
postprocessor.core.functions
postprocessor.core.functions.tracks
postprocessor.core.lineageprocess
postprocessor.core.multisignal
postprocessor.core.multisignal.align
postprocessor.core.multisignal.crosscorr
postprocessor.core.multisignal.mi
postprocessor.core.processes
postprocessor.core.processes.autoreg
postprocessor.core.processes.butter
postprocessor.core.processes.catch22
postprocessor.core.processes.detrend
postprocessor.core.processes.dsignal
postprocessor.core.processes.fft
postprocessor.core.processes.findpeaks
postprocessor.core.processes.gpsignal
postprocessor.core.processes.interpolate
postprocessor.core.processes.knngraph
postprocessor.core.processes.leiden
postprocessor.core.processes.savgol
postprocessor.core.processes.standardscaler
postprocessor.core.processes.template
postprocessor.core.processor
postprocessor.routines
postprocessor.routines.heatmap
postprocessor.routines.histogram
postprocessor.routines.mean_plot
postprocessor.routines.median_plot
postprocessor.routines.plot_utils
postprocessor.routines.plottingabc
postprocessor.routines.single_birth_plot
postprocessor.routines.single_plot
mother_assign_from_dynamic() (Cells static method)
mothers (Cells property)
mothers_daughters (Cells property)
N
n_merges (Chainer property)
(Signal property)
n_processed (Tiler property)
n_traps (Tiler property)
non_uniform_savgol() (in module postprocessor.core.processes.savgol)
ntimepoints (Chainer property)
(Signal property)
ntps (Chainer property)
(Signal property)
nuc_conv_3d() (in module extraction.core.functions.custom.localisation)
nuc_est_conv() (in module extraction.core.functions.custom.localisation)
O
OmeroExplorer (class in aliby.utils.argo)
optimise_ar_order() (autoreg method)
P
p_available (Chainer property)
(Signal property)
pad_array() (ImageDummy static method)
pad_if_needed() (StateWriter static method)
ParametersABC (class in agora.abc)
parametrized() (in module agora.io.utils)
parse() (Parser method)
parse_annot() (in module aliby.utils.argo)
parse_fields() (in module logfile_parser.swainlab_parser)
parse_from_grammar() (in module logfile_parser.swainlab_parser)
parse_from_swainlab_grammar() (in module logfile_parser.swainlab_parser)
parse_logfiles() (in module agora.io.metadata)
parse_swainlab_metadata() (in module agora.io.metadata)
parse_table() (in module logfile_parser.swainlab_parser)
parse_x() (in module logfile_parser.swainlab_parser)
ParseError
Parser (class in logfile_parser.logfile_parser)
pick_baryfun() (in module aliby.track.utils)
pick_mother() (PostProcessor static method)
picks (Chainer property)
(Signal property)
Pipeline (class in aliby.pipeline)
PipelineParameters (class in aliby.pipeline)
plot() (BasePlotter method)
plot_joinable() (in module postprocessor.core.functions.tracks)
PostProcessABC (class in postprocessor.core.abc)
postprocessor
module
PostProcessor (class in postprocessor.core.processor)
postprocessor.chainer
module
postprocessor.core
module
postprocessor.core.abc
module
postprocessor.core.functions
module
postprocessor.core.functions.tracks
module
postprocessor.core.lineageprocess
module
postprocessor.core.multisignal
module
postprocessor.core.multisignal.align
module
postprocessor.core.multisignal.crosscorr
module
postprocessor.core.multisignal.mi
module
postprocessor.core.processes
module
postprocessor.core.processes.autoreg
module
postprocessor.core.processes.butter
module
postprocessor.core.processes.catch22
module
postprocessor.core.processes.detrend
module
postprocessor.core.processes.dsignal
module
postprocessor.core.processes.fft
module
postprocessor.core.processes.findpeaks
module
postprocessor.core.processes.gpsignal
module
postprocessor.core.processes.interpolate
module
postprocessor.core.processes.knngraph
module
postprocessor.core.processes.leiden
module
postprocessor.core.processes.savgol
module
postprocessor.core.processes.standardscaler
module
postprocessor.core.processes.template
module
postprocessor.core.processor
module
postprocessor.routines
module
postprocessor.routines.heatmap
module
postprocessor.routines.histogram
module
postprocessor.routines.mean_plot
module
postprocessor.routines.median_plot
module
postprocessor.routines.plot_utils
module
postprocessor.routines.plottingabc
module
postprocessor.routines.single_birth_plot
module
postprocessor.routines.single_plot
module
PostProcessorParameters (class in postprocessor.core.processor)
predict_all() (CellBenchmarker method)
predict_proba_from_ndarray() (CellTracker method)
predict_set() (CellBenchmarker method)
probabilities_from_impair() (CellTracker method)
ProcessABC (class in agora.abc)
R
read_hdf5() (TrapLocations class method)
rec_bottom() (in module postprocessor.core.functions.tracks)
recursive_groupsort() (in module agora.io.bridge)
reduce_dims() (Extractor method)
(hollowExtractor method)
reduce_extract() (Extractor method)
(hollowExtractor method)
reduce_z() (in module extraction.core.functions.distributors)
repr_obj() (in module agora.io.utils)
retained() (Chainer method)
(Signal method)
run() (align method)
(autoreg method)
(butter method)
(crosscorr method)
(detrend method)
(fft method)
(findpeaks method)
(in module aliby.bin.run)
(knngraph method)
(mi method)
(Pipeline method)
(standardscaler method)
(Tiler method)
run_prepost() (PostProcessor method)
run_tp() (CellTracker method)
(ModelPredictor method)
S
save_to_hdf() (Extractor method)
(hollowExtractor method)
savgol (class in postprocessor.core.processes.savgol)
savgolParameters (class in postprocessor.core.processes.savgol)
scale_feats() (CellTracker method)
(FeatureCalculator method)
segment_traps() (in module aliby.tile.traps)
server_info_from_h5() (BridgeOmero class method)
(Dataset class method)
(Image class method)
(UnsafeImage class method)
shape (Tiler property)
(TrapLocations property)
Signal (class in agora.io.signal)
single_birth_plot() (in module postprocessor.routines.single_birth_plot)
single_plot() (in module postprocessor.routines.single_plot)
slices_from_spans() (in module agora.utils.kymograph)
small_peaks_conv() (in module extraction.core.functions.custom.localisation)
solve_matrices() (in module postprocessor.core.functions.tracks)
solve_matrices_wrap() (in module postprocessor.core.functions.tracks)
solve_matrix() (in module postprocessor.core.functions.tracks)
spherical_volume() (in module extraction.core.functions.cell)
split_df() (in module agora.utils.kymograph)
stack_masks_in_trap() (in module agora.io.cells)
stages (Chainer property)
(Signal property)
stages_span (Chainer property)
(Signal property)
standardscaler (class in postprocessor.core.processes.standardscaler)
standardscalerParameters (class in postprocessor.core.processes.standardscaler)
StateReader (class in agora.io.reader)
StateWriter (class in agora.io.writer)
std() (in module extraction.core.functions.cell)
stem (Chainer property)
(Signal property)
StepABC (class in agora.abc)
store_signal_path() (Chainer method)
(Signal method)
stretch_image() (in module aliby.tile.traps)
switch_case_nfeats() (in module aliby.track.cell_tracker)
T
table_to_df() (in module logfile_parser.swainlab_parser)
tags() (Argo method)
(OmeroExplorer method)
Template (class in postprocessor.core.processes.template)
TemplateParameters (class in postprocessor.core.processes.template)
Tiler (class in aliby.tile.tiler)
TilerParameters (class in aliby.tile.tiler)
TilerWriter (class in agora.io.writer)
timed() (in module agora.io.utils)
timepoints() (Argo method)
(OmeroExplorer method)
timer() (in module agora.logging)
(in module aliby.haystack)
tinterval (Chainer property)
(Signal property)
to_dict() (alignParameters method)
(autoregParameters method)
(BabyParameters method)
(butterParameters method)
(catch22Parameters method)
(crosscorrParameters method)
(detrendParameters method)
(dsignalParameters method)
(ExtractorParameters method)
(fftParameters method)
(findpeaksParameters method)
(gpsignalParameters method)
(interpolateParameters method)
(knngraphParameters method)
(leidenParameters method)
(LineageProcessParameters method)
(miParameters method)
(ParametersABC method)
(PipelineParameters method)
(PostProcessorParameters method)
(savgolParameters method)
(standardscalerParameters method)
(TemplateParameters method)
(TilerParameters method)
(TrapLocations method)
to_legacy() (in module logfile_parser.legacy)
to_yaml() (alignParameters method)
(autoregParameters method)
(BabyParameters method)
(butterParameters method)
(catch22Parameters method)
(crosscorrParameters method)
(detrendParameters method)
(dsignalParameters method)
(ExtractorParameters method)
(fftParameters method)
(findpeaksParameters method)
(gpsignalParameters method)
(interpolateParameters method)
(knngraphParameters method)
(leidenParameters method)
(LineageProcessParameters method)
(miParameters method)
(ParametersABC method)
(PipelineParameters method)
(PostProcessorParameters method)
(savgolParameters method)
(standardscalerParameters method)
(TemplateParameters method)
(TilerParameters method)
Trap (class in aliby.tile.tiler)
trap_apply() (in module extraction.core.functions.distributors)
TrapLocations (class in aliby.tile.tiler)
traps_loc (CellBenchmarker property)
U
UnsafeImage (class in aliby.io.omero)
update() (alignParameters method)
(autoregParameters method)
(BabyParameters method)
(butterParameters method)
(catch22Parameters method)
(crosscorrParameters method)
(detrendParameters method)
(dsignalParameters method)
(ExtractorParameters method)
(fftParameters method)
(findpeaksParameters method)
(gpsignalParameters method)
(interpolateParameters method)
(knngraphParameters method)
(leidenParameters method)
(LineageProcessParameters method)
(miParameters method)
(ParametersABC method)
(PipelineParameters method)
(PostProcessorParameters method)
(savgolParameters method)
(standardscalerParameters method)
(TemplateParameters method)
(TilerParameters method)
update_baby_modelset() (BabyParameters method)
V
validate_association() (in module agora.utils.association)
volume() (in module extraction.core.functions.cell)
W
where() (Cells method)
write() (DynamicWriter method)
(LinearBabyWriter method)
(ModelPredictorWriter method)
(StateWriter method)
(TilerWriter method)
(Writer method)
write_arraylike() (Writer static method)
write_dset() (Writer method)
write_index() (Writer static method)
write_meta() (Writer method)
write_pd() (Writer method)
Writer (class in agora.io.writer)
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