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Index
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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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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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Q
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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
A
active (molyso.debugging.debugplot.DebugPlot attribute)
add() (molyso.generic.etc.QuickTableDumper method)
add_child() (molyso.mm.tracking_infrastructure.TrackedCell method)
add_children() (molyso.mm.tracking_infrastructure.TrackedCell method)
add_observation() (molyso.mm.tracking_infrastructure.TrackedCell method)
add_outcome() (molyso.mm.tracking_infrastructure.CellCrossingCheckingGlobalDuoOptimizerQueue method)
align_channels() (molyso.mm.tracking.TrackedPosition method)
align_with_and_return_indices() (molyso.mm.channel_detection.Channels method)
all_tracked_cells (molyso.mm.tracking_infrastructure.CellTracker attribute)
alternate_vertical_channel_region_detection() (in module molyso.mm.channel_detection)
analyse_cell_fates() (in module molyso.mm.tracking)
analyze_tracking() (in module molyso.mm.tracking_output)
average_cells (molyso.mm.tracking_infrastructure.CellTracker attribute)
B
BaseCache (class in molyso.generic.etc)
bits_to_numpy_type() (in module molyso.generic.etc)
bottom (molyso.mm.cell_detection.Cell attribute)
(molyso.mm.channel_detection.Channel attribute)
build_cache_filename() (molyso.generic.etc.FileCache method)
C
Cache (in module molyso.generic.etc)
catch_attribute_error() (in module molyso.mm.tracking_output)
catch_index_error() (in module molyso.mm.tracking_output)
Cell (class in molyso.mm.cell_detection)
cell_image (molyso.mm.cell_detection.Cell attribute)
cell_type (molyso.mm.cell_detection.Cells attribute)
CellCrossingCheckingGlobalDuoOptimizerQueue (class in molyso.mm.tracking_infrastructure)
Cells (class in molyso.mm.cell_detection)
cells (molyso.mm.channel_detection.Channel attribute)
cells_list (molyso.mm.cell_detection.Cells attribute)
cells_type (molyso.mm.channel_detection.Channel attribute)
CellTracker (class in molyso.mm.tracking_infrastructure)
centroid (molyso.mm.cell_detection.Cell attribute)
(molyso.mm.channel_detection.Channel attribute)
centroid_1d (molyso.mm.cell_detection.Cell attribute)
centroids (molyso.mm.cell_detection.Cells attribute)
(molyso.mm.channel_detection.Channels attribute)
Channel (class in molyso.mm.channel_detection)
channel (molyso.mm.cell_detection.Cell attribute)
(molyso.mm.cell_detection.Cells attribute)
channel_image (molyso.mm.channel_detection.Channel attribute)
channel_type (molyso.mm.channel_detection.Channels attribute)
Channels (class in molyso.mm.channel_detection)
channels_list (molyso.mm.channel_detection.Channels attribute)
children (molyso.mm.tracking_infrastructure.TrackedCell attribute)
clean() (molyso.mm.cell_detection.Cells method)
(molyso.mm.channel_detection.Channel method)
(molyso.mm.channel_detection.Channels method)
contains() (molyso.generic.etc.BaseCache method)
(molyso.generic.etc.FileCache method)
(molyso.generic.etc.Sqlite3Cache method)
context (molyso.debugging.debugplot.DebugPlot attribute)
correct_windows_signal_handlers() (in module molyso.generic.etc)
crop_out_of_channel_image() (molyso.mm.cell_detection.Cell method)
crop_out_of_image() (molyso.mm.channel_detection.Channel method)
current (molyso.generic.tunable.TunableManager attribute)
D
debug_init() (in module molyso.generic.etc)
DebugPlot (class in molyso.debugging.debugplot)
DebugPlotInterruptException
DebugPlotInterruptThrower (class in molyso.debugging.debugplot)
default_config (molyso.debugging.debugplot.DebugPlot attribute)
defaults (molyso.generic.tunable.TunableManager attribute)
delimiter (molyso.generic.etc.QuickTableDumper attribute)
descriptions (molyso.generic.tunable.TunableManager attribute)
deserialize() (molyso.generic.etc.BaseCache static method)
detect_cells() (molyso.mm.channel_detection.Channel method)
diverted_outputs (molyso.debugging.debugplot.DebugPlot attribute)
dummy_progress_indicator() (in module molyso.generic.etc)
E
each_image_slice() (in module molyso.generic.signal)
each_k_tracking_tracker_channels_in_results() (in module molyso.mm.tracking)
each_pos_k_tracking_tracker_channels_in_results() (in module molyso.mm.tracking)
elongation_rates (molyso.mm.tracking_infrastructure.TrackedCell attribute)
exit_handler_registered (molyso.debugging.debugplot.DebugPlot attribute)
exit_handlers (molyso.debugging.debugplot.DebugPlot attribute)
exp_plot_debugging (molyso.debugging.debugplot.DebugPlot attribute)
ExtremeAndProminence (class in molyso.generic.signal)
F
fancy_progress_bar() (in module molyso.generic.etc)
file_prefix (molyso.debugging.debugplot.DebugPlot attribute)
file_suffix (molyso.debugging.debugplot.DebugPlot attribute)
FileCache (class in molyso.generic.etc)
files_to_merge (molyso.debugging.debugplot.DebugPlot attribute)
find_cells_in_channel() (in module molyso.mm.cell_detection)
find_cells_in_channel_classic() (in module molyso.mm.cell_detection)
find_channels() (in module molyso.mm.channel_detection)
find_extrema_and_prominence() (in module molyso.generic.signal)
find_first_valid_time() (molyso.mm.tracking.TrackedPosition method)
find_insides() (in module molyso.generic.signal)
find_nearest() (molyso.mm.channel_detection.Channels method)
find_phase() (in module molyso.generic.signal)
fit_to_type() (in module molyso.generic.signal)
force_active (molyso.debugging.debugplot.DebugPlot attribute)
force_default (molyso.generic.tunable.TunableManager attribute)
G
get() (molyso.generic.etc.BaseCache method)
(molyso.generic.etc.FileCache method)
(molyso.generic.etc.Sqlite3Cache method)
get_cell_by_observation() (molyso.mm.tracking_infrastructure.CellTracker method)
get_context() (molyso.debugging.debugplot.DebugPlot class method)
get_coordinates() (molyso.mm.channel_detection.Channel method)
get_defaults() (molyso.generic.tunable.TunableManager class method)
get_descriptions() (molyso.generic.tunable.TunableManager class method)
get_file_for_merge() (molyso.debugging.debugplot.DebugPlot class method)
get_object_unique_id() (in module molyso.mm.tracking_output)
get_table() (molyso.generic.tunable.TunableManager class method)
get_tracking_work_size() (molyso.mm.tracking.TrackedPosition method)
get_tunable() (molyso.generic.tunable.TunableManager class method)
guess_channel_orientation() (molyso.mm.tracking.TrackedPosition method)
H
hamming_smooth() (in module molyso.generic.smoothing)
hires_power_spectrum() (in module molyso.generic.fft)
histogram() (in module molyso.generic.otsu)
horizontal_channel_detection() (in module molyso.mm.channel_detection)
horizontal_mean() (in module molyso.generic.signal)
I
ignorant_next() (in module molyso.generic.etc)
image (molyso.mm.channel_detection.Channel attribute)
(molyso.mm.channel_detection.Channels attribute)
individual_and_merge (molyso.debugging.debugplot.DebugPlot attribute)
individual_file_prefix (molyso.debugging.debugplot.DebugPlot attribute)
individual_files (molyso.debugging.debugplot.DebugPlot attribute)
inject_poly_drawing_helper() (in module molyso.debugging.debugplot)
interactive_ground_truth_main() (in module molyso.mm.highlevel_interactive_ground_truth)
interactive_main() (in module molyso.mm.highlevel_interactive_viewer)
is_tracked() (molyso.mm.tracking_infrastructure.CellTracker method)
iter_time() (in module molyso.generic.etc)
iterate_over_cells() (in module molyso.mm.tracking_output)
K
keys() (molyso.generic.etc.Sqlite3Cache method)
L
left (molyso.mm.channel_detection.Channel attribute)
length (molyso.mm.cell_detection.Cell attribute)
line_end (molyso.generic.etc.QuickTableDumper attribute)
load_tunables() (molyso.generic.tunable.TunableManager class method)
local_bottom (molyso.mm.cell_detection.Cell attribute)
local_top (molyso.mm.cell_detection.Cell attribute)
logger (molyso.generic.tunable.TunableManager attribute)
(molyso.mm.tracking.TrackedPosition attribute)
M
molyso (module)
molyso.debugging (module)
molyso.debugging.debugplot (module)
molyso.generic (module)
molyso.generic.etc (module)
molyso.generic.fft (module)
molyso.generic.otsu (module)
molyso.generic.registration (module)
molyso.generic.signal (module)
molyso.generic.smoothing (module)
molyso.generic.tunable (module)
molyso.mm (module)
molyso.mm.cell_detection (module)
molyso.mm.channel_detection (module)
molyso.mm.highlevel_interactive_ground_truth (module)
molyso.mm.highlevel_interactive_viewer (module)
molyso.mm.tracking (module)
molyso.mm.tracking_infrastructure (module)
molyso.mm.tracking_output (module)
N
nearest_tree (molyso.mm.cell_detection.Cells attribute)
(molyso.mm.channel_detection.Channels attribute)
new_cell() (molyso.mm.tracking_infrastructure.CellTracker method)
new_observed_cell() (molyso.mm.tracking_infrastructure.CellTracker method)
new_observed_origin() (molyso.mm.tracking_infrastructure.CellTracker method)
new_origin() (molyso.mm.tracking_infrastructure.CellTracker method)
new_pdf_output() (molyso.debugging.debugplot.DebugPlot class method)
next_free_filename() (in module molyso.debugging.debugplot)
normalize() (in module molyso.generic.signal)
NotReallyATree (class in molyso.generic.etc)
O
one_every_n() (in module molyso.generic.signal)
origins (molyso.mm.tracking_infrastructure.CellTracker attribute)
outliers() (in module molyso.generic.signal)
P
parent (molyso.mm.tracking_infrastructure.TrackedCell attribute)
parse_range() (in module molyso.generic.etc)
pdfopener() (molyso.debugging.debugplot.DebugPlot class method)
perform_everything() (molyso.mm.tracking.TrackedPosition method)
perform_optimal() (molyso.mm.tracking_infrastructure.CellCrossingCheckingGlobalDuoOptimizerQueue method)
perform_tracking() (molyso.mm.tracking.TrackedPosition method)
plot_timeline() (in module molyso.mm.tracking_output)
poly_drawing_helper() (in module molyso.debugging.debugplot)
post_figure (molyso.debugging.debugplot.DebugPlot attribute)
power_spectrum() (in module molyso.generic.fft)
pp (molyso.debugging.debugplot.DebugPlot attribute)
precision (molyso.generic.etc.QuickTableDumper attribute)
prepare_key() (molyso.generic.etc.BaseCache static method)
prettify_numpy_array() (in module molyso.generic.etc)
putative_orientation (molyso.mm.channel_detection.Channel attribute)
Q
query() (molyso.generic.etc.NotReallyATree method)
QuickTableDumper (class in molyso.generic.etc)
R
raw_elongation_rates (molyso.mm.tracking_infrastructure.TrackedCell attribute)
raw_trajectories (molyso.mm.tracking_infrastructure.TrackedCell attribute)
real_bottom (molyso.mm.channel_detection.Channel attribute)
real_top (molyso.mm.channel_detection.Channel attribute)
relative_maxima() (in module molyso.generic.signal)
relative_minima() (in module molyso.generic.signal)
remove_empty_channels() (molyso.mm.tracking.TrackedPosition method)
remove_empty_channels_post_tracking() (molyso.mm.tracking.TrackedPosition method)
remove_outliers() (in module molyso.generic.signal)
right (molyso.mm.channel_detection.Channel attribute)
S
s_to_h() (in module molyso.mm.tracking_output)
s_to_h_str() (in module molyso.mm.tracking_output)
seen_as (molyso.mm.tracking_infrastructure.TrackedCell attribute)
serialize() (molyso.generic.etc.BaseCache static method)
set() (molyso.generic.etc.BaseCache method)
(molyso.generic.etc.FileCache method)
(molyso.generic.etc.Sqlite3Cache method)
set_context() (molyso.debugging.debugplot.DebugPlot class method)
set_description() (molyso.generic.tunable.TunableManager class method)
set_times() (molyso.mm.tracking.TrackedPosition method)
shift_image() (in module molyso.generic.registration)
signals() (in module molyso.generic.smoothing)
silent_progress_bar() (in module molyso.generic.etc)
simple_baseline_correction() (in module molyso.generic.signal)
smooth() (in module molyso.generic.smoothing)
spectrum() (in module molyso.generic.fft)
spectrum_bins() (in module molyso.generic.fft)
spectrum_bins_by_length() (in module molyso.generic.fft)
spectrum_fourier() (in module molyso.generic.fft)
Sqlite3Cache (class in molyso.generic.etc)
stringify() (molyso.generic.etc.QuickTableDumper method)
T
threshold_otsu() (in module molyso.generic.otsu)
threshold_outliers() (in module molyso.generic.signal)
throw_on_anything (molyso.debugging.debugplot.DebugPlot attribute)
tick() (molyso.mm.tracking_infrastructure.CellTracker method)
timepoints (molyso.mm.tracking_infrastructure.CellTracker attribute)
to_list() (in module molyso.mm.tracking_infrastructure)
top (molyso.mm.cell_detection.Cell attribute)
(molyso.mm.channel_detection.Channel attribute)
TrackedCell (class in molyso.mm.tracking_infrastructure)
TrackedPosition (class in molyso.mm.tracking)
tracker (molyso.mm.tracking_infrastructure.TrackedCell attribute)
tracker_to_cell_list() (in module molyso.mm.tracking_output)
trajectories (molyso.mm.tracking_infrastructure.TrackedCell attribute)
translation_2x1d() (in module molyso.generic.registration)
tunable() (in module molyso.generic.tunable)
TunableManager (class in molyso.generic.tunable)
U
ultimate_parent (molyso.mm.tracking_infrastructure.TrackedCell attribute)
V
vertical_channel_region_detection() (in module molyso.mm.channel_detection)
vertical_mean() (in module molyso.generic.signal)
W
write_list() (molyso.generic.etc.QuickTableDumper method)
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