pythologist
pythologist
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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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I
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K
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M
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N
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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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W
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Z
A
add_sample_path() (pythologist_reader.formats.inform.immunoprofile.CellProjectInFormImmunoProfile method)
append_sample() (pythologist_reader.CellProjectGeneric method)
B
binary_calls() (pythologist_reader.CellFrameGeneric method)
binary_image_dilation() (in module pythologist_image_utilities)
build_segmentation_image() (pythologist.interface.SegmentationImages method)
C
cartesian() (pythologist.CellDataFrame method)
cdf() (pythologist_reader.CellFrameGeneric property)
(pythologist_reader.CellProjectGeneric property)
(pythologist_reader.CellSampleGeneric property)
cell_map() (pythologist_reader.CellFrameGeneric method)
cell_map_image() (pythologist_reader.CellFrameGeneric method)
CellDataFrame (class in pythologist)
CellFrameGeneric (class in pythologist_reader)
CellProjectGeneric (class in pythologist_reader)
CellProjectInForm (class in pythologist_reader.formats.inform.sets)
CellProjectInFormCustomMask (class in pythologist_reader.formats.inform.custom)
CellProjectInFormImmunoProfile (class in pythologist_reader.formats.inform.immunoprofile)
CellProjectInFormLineArea (class in pythologist_reader.formats.inform.custom)
CellSampleGeneric (class in pythologist_reader)
CellSampleInFormImmunoProfile (class in pythologist_reader.formats.inform.immunoprofile)
channel_image_dataframe() (pythologist_reader.CellProjectGeneric property)
collapse_phenotypes() (pythologist.CellDataFrame method)
combine_regions() (pythologist.CellDataFrame method)
concat() (pythologist.CellDataFrame class method)
contacts() (pythologist.CellDataFrame method)
convert_cascading_scores_to_mutually_exclusive_ordinal_binary() (pythologist.CellDataFrame method)
counts() (pythologist.CellDataFrame method)
D
db() (pythologist.CellDataFrame property)
drop_scored_calls() (pythologist.CellDataFrame method)
E
edge_map() (pythologist_reader.CellFrameGeneric method)
edge_map_image() (pythologist_reader.CellFrameGeneric method)
F
fill_phenotype_calls() (pythologist.CellDataFrame method)
fill_phenotype_label() (pythologist.CellDataFrame method)
flood_fill() (in module pythologist_image_utilities)
frame_columns() (pythologist.CellDataFrame property)
frame_ids() (pythologist_reader.CellSampleGeneric property)
frame_iter() (pythologist_reader.CellProjectGeneric method)
(pythologist_reader.CellSampleGeneric method)
G
gates() (pythologist_reader.formats.inform.sets.CellProjectInForm property)
get_channels() (pythologist_reader.CellFrameGeneric method)
get_data() (pythologist_reader.CellFrameGeneric method)
get_frame() (pythologist_reader.CellSampleGeneric method)
get_image() (pythologist_reader.CellFrameGeneric method)
(pythologist_reader.CellProjectGeneric method)
get_labeled_raw() (pythologist_reader.CellFrameGeneric method)
(pythologist_reader.CellProjectGeneric method)
(pythologist_reader.CellSampleGeneric method)
get_measured_regions() (pythologist.CellDataFrame method)
get_raw() (pythologist_reader.CellFrameGeneric method)
get_sample() (pythologist_reader.CellProjectGeneric method)
get_valid_cell_indecies() (pythologist.CellDataFrame method)
I
id() (pythologist_reader.CellFrameGeneric property)
(pythologist_reader.CellProjectGeneric property)
(pythologist_reader.CellSampleGeneric property)
image_edges() (in module pythologist_image_utilities)
interaction_map() (pythologist_reader.CellFrameGeneric method)
is_uniform() (pythologist.CellDataFrame method)
K
key() (pythologist_reader.CellProjectGeneric property)
(pythologist_reader.CellSampleGeneric property)
M
make_binary_image_array() (in module pythologist_image_utilities)
map_image_ids() (in module pythologist_image_utilities)
median_id_coordinates() (in module pythologist_image_utilities)
merge_scores() (pythologist.CellDataFrame method)
microns_per_pixel() (pythologist.CellDataFrame property)
(pythologist_reader.CellProjectGeneric property)
N
NearestNeighbors (class in pythologist.measurements.spatial.nearestneighbors)
nearestneighbors() (pythologist.CellDataFrame method)
P
permute_phenotype_labels() (pythologist.CellDataFrame method)
phenotype_calls() (pythologist_reader.CellFrameGeneric method)
phenotypes() (pythologist.CellDataFrame property)
phenotypes_to_regions() (pythologist.CellDataFrame method)
phenotypes_to_scored() (pythologist.CellDataFrame method)
processed_image() (pythologist_reader.CellFrameGeneric property)
processed_image_id() (pythologist_reader.CellFrameGeneric property)
project_columns() (pythologist.CellDataFrame property)
project_name() (pythologist_reader.CellProjectGeneric property)
prune_neighbors() (pythologist.CellDataFrame method)
pythologist_image_utilities (module)
Q
qc() (pythologist.CellDataFrame method)
(pythologist_reader.CellProjectGeneric method)
(pythologist_reader.formats.inform.sets.CellProjectInForm method)
R
read_hdf() (pythologist.CellDataFrame class method)
read_path() (pythologist_reader.formats.inform.custom.CellProjectInFormCustomMask method)
(pythologist_reader.formats.inform.custom.CellProjectInFormLineArea method)
(pythologist_reader.formats.inform.immunoprofile.CellSampleInFormImmunoProfile method)
(pythologist_reader.formats.inform.sets.CellProjectInForm method)
read_tiff_stack() (in module pythologist_image_utilities)
regions() (pythologist.CellDataFrame property)
regions_to_scored() (pythologist.CellDataFrame method)
rename_phenotype() (pythologist.CellDataFrame method)
rename_region() (pythologist.CellDataFrame method)
rename_scored_calls() (pythologist.CellDataFrame method)
S
sample_columns() (pythologist.CellDataFrame property)
sample_ids() (pythologist_reader.CellProjectGeneric property)
sample_iter() (pythologist_reader.CellProjectGeneric method)
scored_names() (pythologist.CellDataFrame property)
scored_to_phenotype() (pythologist.CellDataFrame method)
segmentation_images() (pythologist.CellDataFrame method)
segmentation_info() (pythologist_reader.CellFrameGeneric method)
SegmentationImageOutput (class in pythologist.interface)
SegmentationImages (class in pythologist.interface)
serialize() (pythologist.CellDataFrame method)
set_data() (pythologist_reader.CellFrameGeneric method)
set_id() (pythologist_reader.CellProjectGeneric method)
set_interaction_map() (pythologist_reader.CellFrameGeneric method)
set_processed_image_id() (pythologist_reader.CellFrameGeneric method)
set_regions() (pythologist_reader.CellFrameGeneric method)
shape() (pythologist_reader.CellFrameGeneric property)
subset() (pythologist.CellDataFrame method)
T
table_names() (pythologist_reader.CellFrameGeneric property)
threshold() (pythologist.CellDataFrame method)
threshold_on_mutually_exclusive_ordinal_labels() (pythologist.CellDataFrame method)
to_hdf() (pythologist.CellDataFrame method)
W
watershed_image() (in module pythologist_image_utilities)
write_to_path() (pythologist.interface.SegmentationImageOutput method)
Z
zero_fill_missing_phenotypes() (pythologist.CellDataFrame method)
zero_fill_missing_scores() (pythologist.CellDataFrame method)