CellTK
latest
Contents:
Quickstart Guide
Pipelines
Operations
Arrays
Plotting
Utilities
CellTK
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
_
__call__() (celltk.core.operation.Operation method)
A
adaptive_thres() (celltk.segment.Segment method)
add_derived_metric() (celltk.extract.Extract method)
add_extra_metric() (celltk.extract.Extract method)
add_filter() (celltk.extract.Extract method)
add_function() (celltk.core.operation.Operation method)
add_metric_slots() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
add_operations() (celltk.core.orchestrator.Orchestrator method)
(celltk.core.pipeline.Pipeline method)
agglomeration_segmentation() (celltk.segment.Segment method)
align_by_cross_correlation() (celltk.process.Process method)
amplitude() (celltk.utils.peak_utils.PeakHelper method)
any_nan() (in module celltk.utils.filter_utils)
any_negative() (in module celltk.utils.filter_utils)
apply_log_bias_field() (celltk.process.Process method)
apply_mask() (celltk.core.operation.Operation method)
area_under_curve() (celltk.utils.peak_utils.PeakHelper method)
B
bar_plot() (celltk.utils.plot_utils.PlotHelper method)
bayesian_tracker() (celltk.track.Track method)
binary_fill_holes() (celltk.segment.Segment method)
binary_threshold() (celltk.core.operation.Operation method)
binomial_blur() (celltk.process.Process method)
bootstrap_estimator() (in module celltk.utils.estimator_utils)
box_plot() (celltk.utils.plot_utils.PlotHelper method)
build_experiment_file() (celltk.core.orchestrator.Orchestrator method)
C
canny_edge_segmentation() (celltk.segment.Segment method)
cast_sitk() (in module celltk.utils.operation_utils)
celltk.core.arrays
module
celltk.core.orchestrator
module
celltk.core.pipeline
module
celltk.evaluate
module
celltk.extract
module
celltk.process
module
celltk.segment
module
celltk.track
module
celltk.utils.estimator_utils
module
celltk.utils.filter_utils
module
celltk.utils.metric_utils
module
celltk.utils.operation_utils
module
celltk.utils.peak_utils
module
celltk.utils.plot_utils
module
chan_vese_dense_levelset() (celltk.segment.Segment method)
channels (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
clean_labels() (celltk.segment.Segment method)
condition (celltk.core.arrays.ConditionArray property)
ConditionArray (class in celltk.core.arrays)
conditions (celltk.core.arrays.ExperimentArray property)
confidence_connected() (celltk.segment.Segment method)
confidence_interval() (in module celltk.utils.estimator_utils)
constant_thres() (celltk.segment.Segment method)
contour2d_plot() (celltk.utils.plot_utils.PlotHelper method)
convex_hull_object() (celltk.segment.Segment method)
coordinate_dimensions (celltk.core.arrays.ConditionArray property)
coordinates (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
crop_array() (in module celltk.utils.operation_utils)
crop_to_area() (celltk.process.Process method)
curvature_anisotropic_diffusion() (celltk.process.Process method)
D
data_from_regionprops_table() (in module celltk.utils.operation_utils)
detect_cell_division() (celltk.track.Track method)
detect_peak_tracts() (celltk.utils.peak_utils.PeakHelper method)
dilate_sitk() (in module celltk.utils.operation_utils)
dtype (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
E
Evaluate (class in celltk.evaluate)
expand_to_cytoring() (celltk.segment.Segment method)
ExperimentArray (class in celltk.core.arrays)
Extract (class in celltk.extract)
extract_data_from_image() (celltk.extract.Extract method)
F
fast_marching_level_set() (celltk.segment.Segment method)
filter_cells() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
filter_objects_by_props() (celltk.segment.Segment method)
filter_peaks() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
(celltk.utils.peak_utils.PeakHelper method)
find_boundaries() (celltk.segment.Segment method)
first_time() (celltk.utils.peak_utils.PeakHelper method)
fraction_of_total() (in module celltk.utils.estimator_utils)
G
gaussian_filter() (celltk.process.Process method)
gaussian_laplace_filter() (celltk.process.Process method)
generate_mask() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
get_binary_footprint() (in module celltk.utils.operation_utils)
get_bootstrap_population() (in module celltk.utils.estimator_utils)
get_cell_index() (in module celltk.utils.operation_utils)
get_image_pixel_type() (in module celltk.utils.operation_utils)
get_inputs_and_outputs() (celltk.core.operation.Operation method)
get_mask() (celltk.core.arrays.ConditionArray method)
get_split_idxs() (in module celltk.utils.operation_utils)
gray_fill_holes() (in module celltk.utils.operation_utils)
H
heatmap2d_plot() (celltk.utils.plot_utils.PlotHelper method)
heatmap_plot() (celltk.utils.plot_utils.PlotHelper method)
histogram_matching() (celltk.process.Process method)
histogram_plot() (celltk.utils.plot_utils.PlotHelper method)
I
image_to_mask() (celltk.core.operation.Operation method)
inside() (in module celltk.utils.filter_utils)
inside_percentile() (in module celltk.utils.filter_utils)
intensity_stdev() (in module celltk.utils.metric_utils)
intensity_variance() (in module celltk.utils.metric_utils)
interpolate_nans() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
inverse_gaussian_gradient() (celltk.process.Process method)
invert() (celltk.core.operation.Operation method)
items() (celltk.core.arrays.ExperimentArray method)
K
keys (celltk.core.arrays.ConditionArray property)
keys() (celltk.core.arrays.ExperimentArray method)
kit_sch_ge_tracker() (celltk.track.Track method)
L
label() (celltk.segment.Segment method)
label_by_parent() (in module celltk.utils.operation_utils)
label_by_voting() (celltk.segment.Segment method)
last_time() (celltk.utils.peak_utils.PeakHelper method)
length() (celltk.utils.peak_utils.PeakHelper method)
level_set_mask() (celltk.segment.Segment method)
li_thres() (celltk.segment.Segment method)
line_plot() (celltk.utils.plot_utils.PlotHelper method)
lineage_masks() (celltk.track.Track method)
lineage_to_track() (in module celltk.utils.operation_utils)
linear_tracker_w_properties() (celltk.track.Track method)
load() (celltk.core.arrays.ConditionArray class method)
(celltk.core.arrays.ExperimentArray class method)
load_condition() (celltk.core.arrays.ExperimentArray method)
load_from_yaml() (celltk.core.pipeline.Pipeline class method)
load_operations_from_yaml() (celltk.core.orchestrator.Orchestrator method)
M
make_boolean_mask() (celltk.core.operation.Operation method)
make_edge_potential_image() (celltk.process.Process method)
make_maurer_distance_map() (celltk.process.Process method)
make_single_cell_stack() (celltk.evaluate.Evaluate method)
mark_active_cells() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
mask_to_image() (celltk.core.operation.Operation method)
mask_to_seeds() (celltk.core.operation.Operation method)
(in module celltk.utils.operation_utils)
match_labels_linear() (celltk.core.operation.Operation method)
(in module celltk.utils.operation_utils)
max_time() (celltk.utils.peak_utils.PeakHelper method)
median_intensity() (in module celltk.utils.metric_utils)
merge_conditions() (celltk.core.arrays.ExperimentArray method)
metrics (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
misic_predict() (celltk.segment.Segment method)
module
celltk.core.arrays
celltk.core.orchestrator
celltk.core.pipeline
celltk.evaluate
celltk.extract
celltk.process
celltk.segment
celltk.track
celltk.utils.estimator_utils
celltk.utils.filter_utils
celltk.utils.metric_utils
celltk.utils.operation_utils
celltk.utils.peak_utils
celltk.utils.plot_utils
morphological_acwe() (celltk.segment.Segment method)
morphological_geodesic_active_contour() (celltk.segment.Segment method)
morphological_watershed() (celltk.segment.Segment method)
multiotsu_thres() (celltk.segment.Segment method)
N
n4_illumination_bias_correction() (celltk.process.Process method)
nan_helper_2d() (in module celltk.utils.operation_utils)
ncells (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
ndi_binary_fill_holes() (in module celltk.utils.operation_utils)
ndim (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
nonlinearity() (celltk.utils.peak_utils.PeakHelper method)
normal_approx() (in module celltk.utils.estimator_utils)
O
Operation (class in celltk.core.operation)
Orchestrator (class in celltk.core.orchestrator)
otsu_thres() (celltk.segment.Segment method)
outside() (in module celltk.utils.filter_utils)
outside_percentile() (in module celltk.utils.filter_utils)
overlay_tracks() (celltk.evaluate.Evaluate method)
P
PadHelper (class in celltk.utils.operation_utils)
paired_dot_distance() (in module celltk.utils.operation_utils)
parents_from_track() (in module celltk.utils.operation_utils)
PeakHelper (class in celltk.utils.peak_utils)
Pipeline (class in celltk.core.pipeline)
PlotHelper (class in celltk.utils.plot_utils)
predict_peaks() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
(in module celltk.utils.metric_utils)
Process (class in celltk.process)
prominence() (celltk.utils.peak_utils.PeakHelper method)
propagate_values() (celltk.core.arrays.ConditionArray method)
R
random_walk_segmentation() (celltk.segment.Segment method)
recurssive_gauss_gradient() (celltk.process.Process method)
recurssive_gauss_magnitude() (celltk.process.Process method)
regional_extrema() (celltk.segment.Segment method)
regions (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
regular_seeds() (celltk.core.operation.Operation method)
remove_empty_sites() (celltk.core.arrays.ExperimentArray method)
remove_nuc_from_cyto() (celltk.segment.Segment method)
remove_parents() (celltk.core.arrays.ConditionArray method)
remove_short_traces() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
reshape_mask() (celltk.core.arrays.ConditionArray method)
ridgeline_plot() (celltk.utils.plot_utils.PlotHelper method)
roberts_edge_detection() (celltk.process.Process method)
rolling_ball_background_subtract() (celltk.process.Process method)
run() (celltk.core.orchestrator.Orchestrator method)
(celltk.core.pipeline.Pipeline method)
run_operation() (celltk.core.operation.Operation method)
S
save() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
save_as_yaml() (celltk.core.pipeline.Pipeline method)
save_condition_map_as_yaml() (celltk.core.orchestrator.Orchestrator method)
save_kept_cells() (celltk.evaluate.Evaluate method)
save_operations_as_yaml() (celltk.core.orchestrator.Orchestrator method)
(celltk.core.pipeline.Pipeline method)
save_pipelines_as_yamls() (celltk.core.orchestrator.Orchestrator method)
scatter_plot() (celltk.utils.plot_utils.PlotHelper method)
Segment (class in celltk.segment)
segment_peaks_agglomeration() (in module celltk.utils.peak_utils)
set_condition() (celltk.core.arrays.ConditionArray method)
set_conditions() (celltk.core.arrays.ExperimentArray method)
set_logger() (celltk.core.operation.Operation method)
set_metric_list() (celltk.extract.Extract method)
set_position_id() (celltk.core.arrays.ConditionArray method)
set_time() (celltk.core.arrays.ConditionArray method)
(celltk.core.arrays.ExperimentArray method)
shape (celltk.core.arrays.ConditionArray property)
(celltk.core.arrays.ExperimentArray property)
shape_detection_level_set() (celltk.segment.Segment method)
shift_array() (in module celltk.utils.operation_utils)
simple_linear_tracker() (celltk.track.Track method)
simple_watershed_tracker() (celltk.track.Track method)
sitk_binary_fill_holes() (in module celltk.utils.operation_utils)
sitk_filter_pipeline() (celltk.segment.Segment method)
sitk_label() (celltk.segment.Segment method)
skimage_level_set() (in module celltk.utils.operation_utils)
sliding_window_generator() (in module celltk.utils.operation_utils)
sobel_edge_detection() (celltk.process.Process method)
sobel_edge_magnitude() (celltk.process.Process method)
split_array() (in module celltk.utils.operation_utils)
stack_pad() (in module celltk.utils.operation_utils)
T
threshold_level_set() (celltk.segment.Segment method)
tile_images() (celltk.process.Process method)
time (celltk.core.arrays.ExperimentArray property)
total_intensity() (in module celltk.utils.metric_utils)
trace_color_plot() (celltk.utils.plot_utils.PlotHelper method)
Track (class in celltk.track)
track_to_lineage() (in module celltk.utils.operation_utils)
track_to_mask() (in module celltk.utils.operation_utils)
U
unet_predict() (celltk.process.Process method)
(celltk.segment.Segment method)
uniform_filter() (celltk.process.Process method)
update_condition_map() (celltk.core.orchestrator.Orchestrator method)
V
values() (celltk.core.arrays.ExperimentArray method)
violin_plot() (celltk.utils.plot_utils.PlotHelper method)
voronoi_boundaries() (in module celltk.utils.operation_utils)
W
watershed_from_markers() (celltk.segment.Segment method)
watershed_ift_segmentation() (celltk.segment.Segment method)
wavelet_background_estimate() (in module celltk.utils.operation_utils)
wavelet_background_subtract() (celltk.process.Process method)
wavelet_noise_estimate() (in module celltk.utils.operation_utils)
wavelet_noise_subtract() (celltk.process.Process method)
width() (celltk.utils.peak_utils.PeakHelper method)
wilson_score() (in module celltk.utils.estimator_utils)
Read the Docs
v: latest
Versions
latest
stable
v043b3
Downloads
pdf
On Read the Docs
Project Home
Builds