Index

A

analyze_flow() (in module merquaco.perfusion)

C

calculate_class_areas() (in module merquaco.pixel_classification) calculate_class_percentages() (in module merquaco.pixel_classification) classify_pixels() (in module merquaco.pixel_classification) compare_codebook_fov_genes() (merquaco.data_loss.FOVDropout static method)

compute_z_ratio() (in module merquaco.z_plane_detection) create_dapi_image() (in module merquaco.pixel_classification) create_transcripts_image() (in module merquaco.pixel_classification) create_ventricle_genes_image() (in module merquaco.pixel_classification)

D

detect_dropouts() (merquaco.data_loss.FOVDropout static method) detect_false_positives() (merquaco.data_loss.FOVDropout static method)

draw_genes_dropped_per_fov() (merquaco.data_loss.DropoutResult method) dropout_summary() (merquaco.data_loss.DropoutResult method)

F

find_fovs() (merquaco.experiment.Experiment static method)

find_on_tissue_fovs() (merquaco.data_loss.FOVDropout static method)

G

generate_damage_mask() (in module merquaco.pixel_classification) generate_dapi_mask() (in module merquaco.pixel_classification) generate_detachment_mask() (in module merquaco.pixel_classification) generate_mask() (in module merquaco.pixel_classification) generate_transcripts_mask() (in module merquaco.pixel_classification) generate_ventricle_mask() (in module merquaco.pixel_classification) get_chunk_values() (in module merquaco.periodicity) get_considered_fov_counts() (merquaco.data_loss.DropoutResult method) get_considered_fovs() (merquaco.data_loss.DropoutResult method) get_considered_gene_counts() (merquaco.data_loss.DropoutResult method) get_considered_genes() (merquaco.data_loss.DropoutResult method) get_dropout_count() (merquaco.data_loss.DropoutResult method)

get_dropped_fov_counts() (merquaco.data_loss.DropoutResult method) get_dropped_fovs() (merquaco.data_loss.DropoutResult method) get_dropped_gene_counts() (merquaco.data_loss.DropoutResult method) get_dropped_genes() (merquaco.data_loss.DropoutResult method) get_false_positive_fov_counts() (merquaco.data_loss.DropoutResult method) get_false_positive_fovs() (merquaco.data_loss.DropoutResult method) get_fov_neighbors() (merquaco.experiment.Experiment static method) get_fovs_dataframe() (merquaco.experiment.Experiment static method) get_image_dimensions() (in module merquaco.periodicity) get_periodicity_list() (in module merquaco.periodicity) get_periodicity_vals_all_z() (in module merquaco.periodicity) get_transcript_density() (merquaco.experiment.Experiment static method) get_transcripts_per_z() (in module merquaco.z_plane_detection)

M

merquaco module merquaco.data_loss module merquaco.experiment module merquaco.experiment.Experiment module merquaco.figures module merquaco.perfusion module merquaco.periodicity module

merquaco.pixel_classification module merquaco.z_plane_detection module module merquaco merquaco.data_loss merquaco.experiment merquaco.experiment.Experiment merquaco.figures merquaco.perfusion merquaco.periodicity merquaco.pixel_classification merquaco.z_plane_detection

P

plot_every_z_plane() (in module merquaco.figures) plot_full_pixel_fig() (in module merquaco.figures) plot_mask() (in module merquaco.figures) plot_masks() (in module merquaco.figures)

plot_perfusion_figure() (in module merquaco.figures) plot_periodicity_hist() (in module merquaco.figures) plot_pixel_classification() (in module merquaco.figures) plot_pixel_percentages() (in module merquaco.figures) plot_transcripts_per_z() (in module merquaco.figures)

R

read_codebook() (merquaco.experiment.Experiment static method) read_transcripts() (merquaco.experiment.Experiment static method) remove_blanks() (merquaco.experiment.Experiment static method)

run_all_qc() (merquaco.experiment.Experiment method) run_dropout_pipeline() (merquaco.experiment.Experiment method) run_full_pixel_classification() (merquaco.experiment.Experiment method)

S

save_fov_tsv() (merquaco.data_loss.FOVDropout static method)

scale_transcripts_xy() (merquaco.experiment.Experiment static method)

T

transcripts_overview() (in module merquaco.figures)