aicssegmentation
0.5.2
Contents:
Overview
Installation
Stable release
From sources
Package modules
aicssegmentation package
Subpackages
aicssegmentation.bin package
aicssegmentation.cli package
aicssegmentation.core package
aicssegmentation.structure_wrapper package
aicssegmentation.structure_wrapper_config package
aicssegmentation.util package
aicssegmentation.workflow package
Submodules
aicssegmentation.exceptions module
Module contents
Contributing
Get Started!
Adding a new workflow
Deploying
aicssegmentation
Index
Index
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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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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V
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W
A
absolute_3d_hessian_eigenvalues() (in module aicssegmentation.core.hessian)
absolute_eigenvaluesh() (in module aicssegmentation.core.utils)
aicssegmentation (module)
aicssegmentation.bin (module)
aicssegmentation.bin.batch_processing (module)
aicssegmentation.cli (module)
aicssegmentation.cli.to_analysis (module)
aicssegmentation.core (module)
aicssegmentation.core.hessian (module)
aicssegmentation.core.MO_threshold (module)
aicssegmentation.core.output_utils (module)
aicssegmentation.core.pre_processing_utils (module)
aicssegmentation.core.seg_dot (module)
aicssegmentation.core.utils (module)
aicssegmentation.core.vessel (module)
aicssegmentation.core.visual (module)
aicssegmentation.exceptions (module)
aicssegmentation.structure_wrapper (module)
aicssegmentation.structure_wrapper.seg_actb (module)
aicssegmentation.structure_wrapper.seg_actn1 (module)
aicssegmentation.structure_wrapper.seg_atp2a2 (module)
aicssegmentation.structure_wrapper.seg_cardio_actn2 (module)
aicssegmentation.structure_wrapper.seg_cardio_atp2a2 (module)
aicssegmentation.structure_wrapper.seg_cardio_fbl (module)
aicssegmentation.structure_wrapper.seg_cardio_fbl_100x (module)
aicssegmentation.structure_wrapper.seg_cardio_myl7 (module)
aicssegmentation.structure_wrapper.seg_cardio_npm1 (module)
aicssegmentation.structure_wrapper.seg_cardio_npm1_100x (module)
aicssegmentation.structure_wrapper.seg_cardio_tnni1 (module)
aicssegmentation.structure_wrapper.seg_cardio_ttn (module)
aicssegmentation.structure_wrapper.seg_cetn2 (module)
aicssegmentation.structure_wrapper.seg_ctnnb1 (module)
aicssegmentation.structure_wrapper.seg_drug_npm1 (module)
aicssegmentation.structure_wrapper.seg_dsp (module)
aicssegmentation.structure_wrapper.seg_fbl (module)
aicssegmentation.structure_wrapper.seg_fbl_labelfree_4dn (module)
aicssegmentation.structure_wrapper.seg_gja1 (module)
aicssegmentation.structure_wrapper.seg_h2b_interphase (module)
aicssegmentation.structure_wrapper.seg_lamp1 (module)
aicssegmentation.structure_wrapper.seg_lmnb1_interphase (module)
aicssegmentation.structure_wrapper.seg_lmnb1_mitotic (module)
aicssegmentation.structure_wrapper.seg_myh10 (module)
aicssegmentation.structure_wrapper.seg_npm1 (module)
aicssegmentation.structure_wrapper.seg_npm1_SR (module)
aicssegmentation.structure_wrapper.seg_npm_labelfree_4dn (module)
aicssegmentation.structure_wrapper.seg_nup153 (module)
aicssegmentation.structure_wrapper.seg_PCNA_earlyS_midS (module)
aicssegmentation.structure_wrapper.seg_PCNA_lateS (module)
aicssegmentation.structure_wrapper.seg_PCNA_lateS_hole_fill (module)
aicssegmentation.structure_wrapper.seg_polr2a (module)
aicssegmentation.structure_wrapper.seg_pxn (module)
aicssegmentation.structure_wrapper.seg_rab5a (module)
aicssegmentation.structure_wrapper.seg_sec61b (module)
aicssegmentation.structure_wrapper.seg_sec61b_dual (module)
aicssegmentation.structure_wrapper.seg_slc25a17 (module)
aicssegmentation.structure_wrapper.seg_smc1a (module)
aicssegmentation.structure_wrapper.seg_son (module)
aicssegmentation.structure_wrapper.seg_st6gal1 (module)
aicssegmentation.structure_wrapper.seg_template (module)
aicssegmentation.structure_wrapper.seg_terf2 (module)
aicssegmentation.structure_wrapper.seg_tjp1 (module)
aicssegmentation.structure_wrapper.seg_tomm20 (module)
aicssegmentation.structure_wrapper.seg_tuba1b (module)
aicssegmentation.structure_wrapper.seg_ubtf (module)
aicssegmentation.structure_wrapper.structure_segmenter (module)
aicssegmentation.structure_wrapper_config (module)
aicssegmentation.util (module)
aicssegmentation.util.directories (module)
aicssegmentation.util.filesystem (module)
aicssegmentation.util.lazy (module)
aicssegmentation.workflow (module)
aicssegmentation.workflow.batch_workflow (module)
aicssegmentation.workflow.segmenter_function (module)
aicssegmentation.workflow.workflow (module)
aicssegmentation.workflow.workflow_config (module)
aicssegmentation.workflow.workflow_definition (module)
aicssegmentation.workflow.workflow_engine (module)
aicssegmentation.workflow.workflow_step (module)
Args (class in aicssegmentation.bin.batch_processing)
ArgumentNullError
B
BatchWorkflow (class in aicssegmentation.workflow.batch_workflow)
blob2dExplorer_single() (in module aicssegmentation.core.visual)
C
category (aicssegmentation.workflow.workflow_step.WorkflowStep attribute)
cell_local_adaptive_threshold() (in module aicssegmentation.core.utils)
compute_3d_hessian_matrix() (in module aicssegmentation.core.hessian)
compute_vesselness2D() (in module aicssegmentation.core.vessel)
compute_vesselness3D() (in module aicssegmentation.core.vessel)
ConfigurationException
CORE (aicssegmentation.workflow.workflow_step.WorkflowStepCategory attribute)
create_directory() (aicssegmentation.util.filesystem.FileSystemUtilities static method)
D
data_type (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
diagram_image() (aicssegmentation.workflow.workflow_definition.PrebuiltWorkflowDefinition property)
Directories (class in aicssegmentation.util.directories)
display_name (aicssegmentation.workflow.segmenter_function.SegmenterFunction attribute)
divide_nonzero() (in module aicssegmentation.core.utils)
dot_2d() (in module aicssegmentation.core.seg_dot)
dot_2d_slice_by_slice_wrapper() (in module aicssegmentation.core.seg_dot)
dot_3d() (in module aicssegmentation.core.seg_dot)
dot_3d_wrapper() (in module aicssegmentation.core.seg_dot)
dot_slice_by_slice() (in module aicssegmentation.core.seg_dot)
DROPDOWN (aicssegmentation.workflow.segmenter_function.WidgetType attribute)
E
edge_preserving_smoothing_3d() (in module aicssegmentation.core.pre_processing_utils)
execute() (aicssegmentation.bin.batch_processing.Executor method)
(aicssegmentation.workflow.workflow_step.WorkflowStep method)
execute_all() (aicssegmentation.workflow.batch_workflow.BatchWorkflow method)
(aicssegmentation.workflow.workflow.Workflow method)
execute_next() (aicssegmentation.workflow.batch_workflow.BatchWorkflow method)
(aicssegmentation.workflow.workflow.Workflow method)
execute_step() (aicssegmentation.workflow.workflow.Workflow method)
Executor (class in aicssegmentation.bin.batch_processing)
F
failed_files() (aicssegmentation.workflow.batch_workflow.BatchWorkflow property)
fila2dExplorer_single() (in module aicssegmentation.core.visual)
filament_2d_wrapper() (in module aicssegmentation.core.vessel)
filament_3d_wrapper() (in module aicssegmentation.core.vessel)
FileSystemUtilities (class in aicssegmentation.util.filesystem)
from_str() (aicssegmentation.workflow.segmenter_function.WidgetType static method)
(aicssegmentation.workflow.workflow_step.WorkflowStepCategory static method)
function (aicssegmentation.workflow.segmenter_function.SegmenterFunction attribute)
(aicssegmentation.workflow.workflow_step.WorkflowStep attribute)
FunctionParameter (class in aicssegmentation.workflow.segmenter_function)
G
generate_segmentation_contour() (in module aicssegmentation.core.output_utils)
get_3dseed_from_mid_frame() (in module aicssegmentation.core.utils)
get_all_functions() (aicssegmentation.workflow.workflow_config.WorkflowConfig method)
get_assets_dir() (aicssegmentation.util.directories.Directories class method)
get_available_workflows() (aicssegmentation.workflow.workflow_config.WorkflowConfig method)
get_executable_batch_workflow() (aicssegmentation.workflow.workflow_engine.WorkflowEngine method)
get_executable_batch_workflow_from_config_file() (aicssegmentation.workflow.workflow_engine.WorkflowEngine method)
get_executable_workflow() (aicssegmentation.workflow.workflow_engine.WorkflowEngine method)
get_executable_workflow_from_config_file() (aicssegmentation.workflow.workflow_engine.WorkflowEngine method)
get_middle_frame() (in module aicssegmentation.core.utils)
get_module_version() (in module aicssegmentation)
get_most_recent_result() (aicssegmentation.workflow.workflow.Workflow method)
get_next_step() (aicssegmentation.workflow.workflow.Workflow method)
get_result() (aicssegmentation.workflow.workflow.Workflow method)
get_seed_for_objects() (in module aicssegmentation.core.utils)
get_structure_config_dir() (aicssegmentation.util.directories.Directories class method)
get_workflow_definition() (aicssegmentation.workflow.workflow_config.WorkflowConfig method)
get_workflow_definition_from_config_file() (aicssegmentation.workflow.workflow_config.WorkflowConfig method)
H
hierachical_builder() (in module aicssegmentation.cli.to_analysis)
histogram_otsu() (in module aicssegmentation.core.utils)
hole_filling() (in module aicssegmentation.core.utils)
I
image_smoothing_gaussian_3d() (in module aicssegmentation.core.pre_processing_utils)
image_smoothing_gaussian_slice_by_slice() (in module aicssegmentation.core.pre_processing_utils)
img_seg_combine() (in module aicssegmentation.core.visual)
increment (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
input_dir() (aicssegmentation.workflow.batch_workflow.BatchWorkflow property)
intensity_normalization() (in module aicssegmentation.core.pre_processing_utils)
invert_mask() (in module aicssegmentation.core.utils)
is_done() (aicssegmentation.workflow.batch_workflow.BatchWorkflow method)
(aicssegmentation.workflow.workflow.Workflow method)
L
lazy_property() (in module aicssegmentation.util.lazy)
logSlice() (in module aicssegmentation.core.seg_dot)
M
main() (in module aicssegmentation.bin.batch_processing)
mask_image() (in module aicssegmentation.core.utils)
masked_builder() (in module aicssegmentation.cli.to_analysis)
max_value (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
min_value (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
mipView() (in module aicssegmentation.core.visual)
MO() (in module aicssegmentation.core.MO_threshold)
MO_high_level() (in module aicssegmentation.core.MO_threshold)
MO_low_level() (in module aicssegmentation.core.MO_threshold)
module (aicssegmentation.workflow.segmenter_function.SegmenterFunction attribute)
N
name (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
(aicssegmentation.workflow.segmenter_function.SegmenterFunction attribute)
(aicssegmentation.workflow.workflow_definition.PrebuiltWorkflowDefinition attribute)
(aicssegmentation.workflow.workflow_definition.WorkflowDefinition attribute)
name() (aicssegmentation.workflow.workflow_step.WorkflowStep property)
O
options (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
output_dir() (aicssegmentation.workflow.batch_workflow.BatchWorkflow property)
output_hook() (in module aicssegmentation.core.output_utils)
P
parameter_values (aicssegmentation.workflow.workflow_step.WorkflowStep attribute)
parameters (aicssegmentation.workflow.segmenter_function.SegmenterFunction attribute)
parent (aicssegmentation.workflow.workflow_step.WorkflowStep attribute)
peak_local_max_wrapper() (in module aicssegmentation.core.utils)
POST_PROCESSING (aicssegmentation.workflow.workflow_step.WorkflowStepCategory attribute)
PRE_PROCESSING (aicssegmentation.workflow.workflow_step.WorkflowStepCategory attribute)
PrebuiltWorkflowDefinition (class in aicssegmentation.workflow.workflow_definition)
process_img() (aicssegmentation.structure_wrapper.structure_segmenter.StructureSegmenter method)
processed_files() (aicssegmentation.workflow.batch_workflow.BatchWorkflow property)
prune_z_slices() (in module aicssegmentation.core.utils)
R
random_colormap() (in module aicssegmentation.core.visual)
remove_hot_pixel() (in module aicssegmentation.core.utils)
remove_index_object() (in module aicssegmentation.core.utils)
reset() (aicssegmentation.workflow.workflow.Workflow method)
S
save_segmentation() (in module aicssegmentation.core.output_utils)
save_workflow_definition() (aicssegmentation.workflow.workflow_engine.WorkflowEngine method)
save_workflow_definition_as_json() (aicssegmentation.workflow.workflow_config.WorkflowConfig method)
seg_fluo_side_by_side() (in module aicssegmentation.core.visual)
segment() (aicssegmentation.bin.batch_processing.Executor method)
segmentation_intersection() (in module aicssegmentation.core.utils)
segmentation_quick_view() (in module aicssegmentation.core.visual)
segmentation_union() (in module aicssegmentation.core.utils)
segmentation_xor() (in module aicssegmentation.core.utils)
SegmenterFunction (class in aicssegmentation.workflow.segmenter_function)
show_info() (aicssegmentation.bin.batch_processing.Args method)
simple_builder() (in module aicssegmentation.cli.to_analysis)
single_fluorescent_view() (in module aicssegmentation.core.visual)
size_filter() (in module aicssegmentation.core.utils)
sliceViewer() (in module aicssegmentation.core.visual)
SLIDER (aicssegmentation.workflow.segmenter_function.WidgetType attribute)
sortbyabs() (in module aicssegmentation.core.utils)
step_number (aicssegmentation.workflow.workflow_step.WorkflowStep attribute)
steps (aicssegmentation.workflow.workflow_definition.PrebuiltWorkflowDefinition attribute)
(aicssegmentation.workflow.workflow_definition.WorkflowDefinition attribute)
StructureSegmenter (class in aicssegmentation.structure_wrapper.structure_segmenter)
suggest_normalization_param() (in module aicssegmentation.core.pre_processing_utils)
T
thumbnail_post() (aicssegmentation.workflow.workflow_definition.PrebuiltWorkflowDefinition property)
thumbnail_pre() (aicssegmentation.workflow.workflow_definition.PrebuiltWorkflowDefinition property)
topology_preserving_thinning() (in module aicssegmentation.core.utils)
total_files() (aicssegmentation.workflow.batch_workflow.BatchWorkflow property)
V
vesselness2D() (in module aicssegmentation.core.vessel)
vesselness2D_single_slice() (in module aicssegmentation.core.vessel)
vesselness3D() (in module aicssegmentation.core.vessel)
vesselnessSliceBySlice() (in module aicssegmentation.core.vessel)
W
watershed_wrapper() (in module aicssegmentation.core.utils)
widget_type (aicssegmentation.workflow.segmenter_function.FunctionParameter attribute)
WidgetType (class in aicssegmentation.workflow.segmenter_function)
Workflow (class in aicssegmentation.workflow.workflow)
Workflow_actb() (in module aicssegmentation.structure_wrapper.seg_actb)
Workflow_actn1() (in module aicssegmentation.structure_wrapper.seg_actn1)
Workflow_atcn1() (in module aicssegmentation.structure_wrapper.seg_actn1)
Workflow_atp2a2() (in module aicssegmentation.structure_wrapper.seg_atp2a2)
Workflow_cardio_actn2() (in module aicssegmentation.structure_wrapper.seg_cardio_actn2)
Workflow_cardio_atp2a2() (in module aicssegmentation.structure_wrapper.seg_cardio_atp2a2)
Workflow_cardio_fbl() (in module aicssegmentation.structure_wrapper.seg_cardio_fbl)
Workflow_cardio_fbl_100x() (in module aicssegmentation.structure_wrapper.seg_cardio_fbl_100x)
Workflow_cardio_myl7() (in module aicssegmentation.structure_wrapper.seg_cardio_myl7)
Workflow_cardio_npm1() (in module aicssegmentation.structure_wrapper.seg_cardio_npm1)
Workflow_cardio_npm1_100x() (in module aicssegmentation.structure_wrapper.seg_cardio_npm1_100x)
Workflow_cardio_tnni1() (in module aicssegmentation.structure_wrapper.seg_cardio_tnni1)
Workflow_cardio_ttn() (in module aicssegmentation.structure_wrapper.seg_cardio_ttn)
Workflow_cetn2() (in module aicssegmentation.structure_wrapper.seg_cetn2)
Workflow_ctnnb1() (in module aicssegmentation.structure_wrapper.seg_ctnnb1)
workflow_definition() (aicssegmentation.workflow.workflow.Workflow property)
workflow_definitions() (aicssegmentation.workflow.workflow_engine.WorkflowEngine property)
Workflow_drug_npm1() (in module aicssegmentation.structure_wrapper.seg_drug_npm1)
Workflow_dsp() (in module aicssegmentation.structure_wrapper.seg_dsp)
Workflow_fbl() (in module aicssegmentation.structure_wrapper.seg_fbl)
Workflow_fbl_labelfree_4dn() (in module aicssegmentation.structure_wrapper.seg_fbl_labelfree_4dn)
Workflow_gja1() (in module aicssegmentation.structure_wrapper.seg_gja1)
Workflow_h2b_interphase() (in module aicssegmentation.structure_wrapper.seg_h2b_interphase)
Workflow_lamp1() (in module aicssegmentation.structure_wrapper.seg_lamp1)
Workflow_lmnb1_interphase() (in module aicssegmentation.structure_wrapper.seg_lmnb1_interphase)
Workflow_lmnb1_mitotic() (in module aicssegmentation.structure_wrapper.seg_lmnb1_mitotic)
Workflow_myh10() (in module aicssegmentation.structure_wrapper.seg_myh10)
Workflow_npm1() (in module aicssegmentation.structure_wrapper.seg_npm1)
Workflow_npm1_SR() (in module aicssegmentation.structure_wrapper.seg_npm1_SR)
Workflow_npm_labelfree_4dn() (in module aicssegmentation.structure_wrapper.seg_npm_labelfree_4dn)
Workflow_nup153() (in module aicssegmentation.structure_wrapper.seg_nup153)
Workflow_PCNA_earlyS_midS() (in module aicssegmentation.structure_wrapper.seg_PCNA_earlyS_midS)
Workflow_PCNA_lateS() (in module aicssegmentation.structure_wrapper.seg_PCNA_lateS)
Workflow_PCNA_lateS_hole_fill() (in module aicssegmentation.structure_wrapper.seg_PCNA_lateS_hole_fill)
Workflow_polr2a() (in module aicssegmentation.structure_wrapper.seg_polr2a)
Workflow_pxn() (in module aicssegmentation.structure_wrapper.seg_pxn)
Workflow_rab5a() (in module aicssegmentation.structure_wrapper.seg_rab5a)
Workflow_sec61b() (in module aicssegmentation.structure_wrapper.seg_sec61b)
Workflow_sec61b_dual() (in module aicssegmentation.structure_wrapper.seg_sec61b_dual)
Workflow_slc25a17() (in module aicssegmentation.structure_wrapper.seg_slc25a17)
Workflow_smc1a() (in module aicssegmentation.structure_wrapper.seg_smc1a)
Workflow_son() (in module aicssegmentation.structure_wrapper.seg_son)
Workflow_st6gal1() (in module aicssegmentation.structure_wrapper.seg_st6gal1)
Workflow_template() (in module aicssegmentation.structure_wrapper.seg_template)
Workflow_terf2() (in module aicssegmentation.structure_wrapper.seg_terf2)
Workflow_tjp1() (in module aicssegmentation.structure_wrapper.seg_tjp1)
Workflow_tomm20() (in module aicssegmentation.structure_wrapper.seg_tomm20)
Workflow_tuba1b() (in module aicssegmentation.structure_wrapper.seg_tuba1b)
Workflow_ubtf() (in module aicssegmentation.structure_wrapper.seg_ubtf)
WorkflowConfig (class in aicssegmentation.workflow.workflow_config)
WorkflowDefinition (class in aicssegmentation.workflow.workflow_definition)
WorkflowEngine (class in aicssegmentation.workflow.workflow_engine)
WorkflowStep (class in aicssegmentation.workflow.workflow_step)
WorkflowStepCategory (class in aicssegmentation.workflow.workflow_step)
write_log_file_summary() (aicssegmentation.workflow.batch_workflow.BatchWorkflow method)