Index

A

add_image_features (pycytominer.cyto_utils.cells.SingleCells attribute) aggregate() (in module pycytominer.aggregate) aggregate_compartment() (pycytominer.cyto_utils.cells.SingleCells method)

aggregate_profiles() (pycytominer.cyto_utils.cells.SingleCells method) aggregation_operation (pycytominer.cyto_utils.cells.SingleCells attribute) annotate() (in module pycytominer.annotate)

C

calculate_frequency() (in module pycytominer.operations.variance_threshold) center (pycytominer.operations.transform.Spherize attribute) check_aggregate_operation() (in module pycytominer.cyto_utils.util) check_compartments() (in module pycytominer.cyto_utils.util) check_compression_method() (in module pycytominer.cyto_utils.output) check_consensus_operation() (in module pycytominer.cyto_utils.util) check_correlation_method() (in module pycytominer.cyto_utils.util) check_fields_of_view() (in module pycytominer.cyto_utils.util) check_fields_of_view_format() (in module pycytominer.cyto_utils.util)

check_image_features() (in module pycytominer.cyto_utils.util) collate() (in module pycytominer.cyto_utils.collate) compartment_linking_cols (pycytominer.cyto_utils.cells.SingleCells attribute) compartments (pycytominer.cyto_utils.cells.SingleCells attribute) consensus() (in module pycytominer.consensus) convert_compartment_format_to_list() (in module pycytominer.cyto_utils.features) correlation_threshold() (in module pycytominer.operations.correlation_threshold) count_cells() (pycytominer.cyto_utils.cells.SingleCells method) count_na_features() (in module pycytominer.cyto_utils.features) count_sql_table_rows() (pycytominer.cyto_utils.cells.SingleCells method)

D

default_datatype_float (pycytominer.cyto_utils.cells.SingleCells attribute)

determine_high_cor_pair() (in module pycytominer.operations.correlation_threshold) drop_outlier_features() (in module pycytominer.cyto_utils.features)

E

epsilon (pycytominer.operations.transform.RobustMAD attribute) (pycytominer.operations.transform.Spherize attribute)

extract_image_features() (in module pycytominer.cyto_utils.util)

F

feature_select() (in module pycytominer.feature_select) features (pycytominer.cyto_utils.cells.SingleCells attribute) fields_of_view (pycytominer.cyto_utils.cells.SingleCells attribute)

fields_of_view_feature (pycytominer.cyto_utils.cells.SingleCells attribute) fit() (pycytominer.operations.transform.RobustMAD method) (pycytominer.operations.transform.Spherize method)

G

get_blocklist_features() (in module pycytominer.cyto_utils.features) get_default_compartments() (in module pycytominer.cyto_utils.util) get_na_columns() (in module pycytominer.operations.get_na_columns)

get_pairwise_correlation() (in module pycytominer.cyto_utils.util) get_sql_table_col_names() (pycytominer.cyto_utils.cells.SingleCells method) get_subsample() (pycytominer.cyto_utils.cells.SingleCells method)

I

image_cols (pycytominer.cyto_utils.cells.SingleCells attribute) image_feature_categories (pycytominer.cyto_utils.cells.SingleCells attribute) image_table_name (pycytominer.cyto_utils.cells.SingleCells attribute)

infer_cp_features() (in module pycytominer.cyto_utils.features) infer_delim() (in module pycytominer.cyto_utils.load) is_path_a_parquet_file() (in module pycytominer.cyto_utils.load)

L

label_compartment() (in module pycytominer.cyto_utils.features) load_compartment() (pycytominer.cyto_utils.cells.SingleCells method) load_image() (pycytominer.cyto_utils.cells.SingleCells method) load_image_data (pycytominer.cyto_utils.cells.SingleCells attribute)

load_known_metadata_dictionary() (in module pycytominer.cyto_utils.util) load_npz_features() (in module pycytominer.cyto_utils.load) load_npz_locations() (in module pycytominer.cyto_utils.load) load_platemap() (in module pycytominer.cyto_utils.load) load_profiles() (in module pycytominer.cyto_utils.load)

M

merge_cols (pycytominer.cyto_utils.cells.SingleCells attribute) merge_single_cells() (pycytominer.cyto_utils.cells.SingleCells method) method (pycytominer.operations.transform.Spherize attribute) module pycytominer pycytominer.aggregate pycytominer.annotate pycytominer.consensus pycytominer.cyto_utils pycytominer.cyto_utils.cells pycytominer.cyto_utils.collate pycytominer.cyto_utils.features pycytominer.cyto_utils.load pycytominer.cyto_utils.modz pycytominer.cyto_utils.output pycytominer.cyto_utils.util pycytominer.cyto_utils.write_gct pycytominer.feature_select pycytominer.normalize pycytominer.operations pycytominer.operations.correlation_threshold pycytominer.operations.get_na_columns pycytominer.operations.transform pycytominer.operations.variance_threshold

modz() (in module pycytominer.cyto_utils.modz) modz_base() (in module pycytominer.cyto_utils.modz)

N

normalize() (in module pycytominer.normalize)

O

object_feature (pycytominer.cyto_utils.cells.SingleCells attribute)

output() (in module pycytominer.cyto_utils.output) output_file (pycytominer.cyto_utils.cells.SingleCells attribute)

P

pycytominer module pycytominer.aggregate module pycytominer.annotate module pycytominer.consensus module pycytominer.cyto_utils module pycytominer.cyto_utils.cells module pycytominer.cyto_utils.collate module pycytominer.cyto_utils.features module pycytominer.cyto_utils.load module pycytominer.cyto_utils.modz module

pycytominer.cyto_utils.output module pycytominer.cyto_utils.util module pycytominer.cyto_utils.write_gct module pycytominer.feature_select module pycytominer.normalize module pycytominer.operations module pycytominer.operations.correlation_threshold module pycytominer.operations.get_na_columns module pycytominer.operations.transform module pycytominer.operations.variance_threshold module

R

RobustMAD (class in pycytominer.operations.transform)

run_check_errors() (in module pycytominer.cyto_utils.collate)

S

set_compression_method() (in module pycytominer.cyto_utils.output) set_output_file() (pycytominer.cyto_utils.cells.SingleCells method) set_subsample_frac() (pycytominer.cyto_utils.cells.SingleCells method) set_subsample_n() (pycytominer.cyto_utils.cells.SingleCells method) set_subsample_random_state() (pycytominer.cyto_utils.cells.SingleCells method) set_transform_request() (pycytominer.operations.transform.RobustMAD method) SingleCells (class in pycytominer.cyto_utils.cells)

Spherize (class in pycytominer.operations.transform) split_column_categories() (pycytominer.cyto_utils.cells.SingleCells method) sql_file (pycytominer.cyto_utils.cells.SingleCells attribute) strata (pycytominer.cyto_utils.cells.SingleCells attribute) subsample_frac (pycytominer.cyto_utils.cells.SingleCells attribute) subsample_n (pycytominer.cyto_utils.cells.SingleCells attribute) subsample_profiles() (pycytominer.cyto_utils.cells.SingleCells method) subsampling_random_state (pycytominer.cyto_utils.cells.SingleCells attribute)

T

transform() (pycytominer.operations.transform.RobustMAD method) (pycytominer.operations.transform.Spherize method)

V

variance_threshold() (in module pycytominer.operations.variance_threshold)

W

write_gct() (in module pycytominer.cyto_utils.write_gct)