Index

A

adjust_spatial_coordinates() (in module mftools.cellgene)

assign_to_cells() (in module mftools.barcodes)

B

block() (mftools.fileio.DaxFile method)

block_range() (mftools.fileio.DaxFile method)

C

calculate_drift() (in module mftools.util) calculate_global_coordinates() (in module mftools.barcodes) cell_volume_histogram() (in module mftools.plotting) CellSegmentation (class in mftools.segmentation) channel() (mftools.fileio.DaxFile method) check_drift() (in module mftools.plotting) cluster_cells() (in module mftools.cellgene)

confidence_ratios() (in module mftools.plotting) count_raw_barcodes() (mftools.fileio.MerlinOutput method) count_unfiltered_barcodes() (in module mftools.barcodes) counts_per_cell_histogram() (in module mftools.plotting) create_cell_by_gene_table() (in module mftools.barcodes) create_color_image() (in module mftools.plotting) create_scanpy_object() (in module mftools.cellgene)

D

DaxFile (class in mftools.fileio)

drift_histogram() (in module mftools.plotting)

E

exact_vs_corrected() (in module mftools.plotting)

expand_codebook() (in module mftools.barcodes)

F

fileinfo() (mftools.fileio.DaxFile method) filename() (mftools.fileio.ImageDataset method) filter_by_volume() (in module mftools.segmentation) find_cell_communities() (in module mftools.cellgene) find_fov_overlaps() (mftools.images.FOVPositions method) find_overlapping_cells() (mftools.segmentation.CellSegmentation method)

flat_field_correct() (in module mftools.images) fov (mftools.images.Overlap attribute) fov_error_bar() (in module mftools.plotting) fov_error_spatial() (in module mftools.plotting) fov_number_map() (in module mftools.plotting) FOVPositions (class in mftools.images) frame() (mftools.fileio.DaxFile method)

G

genes_detected_per_cell_histogram() (in module mftools.plotting) get() (in module mftools.config) (in module mftools.stats) get_entire_image() (mftools.fileio.DaxFile method)

get_median_image() (in module mftools.images) get_overlap_volume() (mftools.segmentation.CellSegmentation method) get_per_bit_stats() (in module mftools.barcodes) get_slice() (in module mftools.images)

H

has() (in module mftools.config) has_cell_metadata() (mftools.fileio.MerfishAnalysis method)

has_positions() (mftools.fileio.ImageDataset method) highpass_filter() (in module mftools.images)

I

ImageDataset (class in mftools.fileio)

L

label_clusters() (in module mftools.cellgene) link_cell_ids() (in module mftools.barcodes) linked_cells (mftools.segmentation.CellSegmentation property) load() (in module mftools.config) load_barcode_table() (mftools.fileio.MerfishAnalysis method) load_cell_by_gene_table() (mftools.fileio.MerfishAnalysis method) load_cell_metadata() (mftools.fileio.MerfishAnalysis method) load_codebook() (mftools.fileio.MerlinOutput method) load_data_organization() (in module mftools.fileio) (mftools.fileio.MerlinOutput method) load_drift_transformations() (mftools.fileio.MerlinOutput method) load_exported_barcodes() (mftools.fileio.MerlinOutput method) load_fileinfo() (mftools.fileio.DaxFile method)

load_filtered_barcodes() (mftools.fileio.MerlinOutput method) load_fov_positions() (in module mftools.fileio) (mftools.fileio.ImageDataset method) (mftools.fileio.MerlinOutput method) load_from_file() (in module mftools.config) load_hyb_drifts() (mftools.fileio.MerlinOutput method) load_image() (mftools.fileio.ImageDataset method) load_linked_cells() (mftools.fileio.MerfishAnalysis method) load_mask() (in module mftools.fileio) load_raw_barcodes() (mftools.fileio.MerlinOutput method) load_stats() (in module mftools.fileio) local_to_global_coordinates() (mftools.images.FOVPositions method) lowpass_filter() (in module mftools.images)

M

make_metadata_table() (mftools.segmentation.CellSegmentation method) make_table() (in module mftools.barcodes) match_cells_in_overlap() (in module mftools.segmentation) max_projection() (mftools.fileio.DaxFile method) MerfishAnalysis (class in mftools.fileio) MerlinOutput (class in mftools.fileio) metadata (mftools.segmentation.CellSegmentation property) mftools module mftools.barcodes module mftools.cellgene module mftools.config module mftools.fileio module mftools.images module

mftools.plotting module mftools.segmentation module mftools.stats module mftools.util module module mftools mftools.barcodes mftools.cellgene mftools.config mftools.fileio mftools.images mftools.plotting mftools.segmentation mftools.stats mftools.util

N

n_fovs() (mftools.fileio.ImageDataset method) (mftools.fileio.MerlinOutput method)

normalize() (in module mftools.cellgene) normalize_codebook() (in module mftools.barcodes)

O

optimize_number_PCs() (in module mftools.cellgene)

Overlap (class in mftools.images) overlaps (mftools.images.FOVPositions property)

P

path() (in module mftools.config) per_bit_error() (in module mftools.barcodes) per_bit_error_bar() (in module mftools.plotting) per_bit_error_line() (in module mftools.plotting) per_color_error() (in module mftools.plotting)

per_fov_error() (in module mftools.barcodes) per_gene_error() (in module mftools.barcodes) per_hyb_error() (in module mftools.plotting) plot() (in module mftools.plotting) plot_mask() (in module mftools.plotting) process_merlin_barcodes() (in module mftools.barcodes)

R

reference_gene_counts() (in module mftools.util)

remove_small_cells_from_mask() (in module mftools.segmentation) rnaseq_correlation() (in module mftools.plotting)

S

save_barcode_table() (mftools.fileio.MerfishAnalysis method) save_cell_by_gene_table() (mftools.fileio.MerfishAnalysis method) save_cell_metadata() (mftools.fileio.MerfishAnalysis method) save_linked_cells() (mftools.fileio.MerfishAnalysis method) save_mask() (in module mftools.fileio) save_stats() (in module mftools.fileio)

search_for_mask_file() (in module mftools.fileio) segment_fov() (mftools.segmentation.CellSegmentation method) set() (in module mftools.config) (in module mftools.stats) set_barcode_stats() (in module mftools.barcodes) spatial_cell_clusters() (in module mftools.plotting) spatial_transcripts_per_fov() (in module mftools.plotting)

T

transcripts_per_gene_scatterplot() (in module mftools.plotting)

transfer_labels() (in module mftools.cellgene) trim_barcodes_in_overlaps() (in module mftools.barcodes)

U

umap_clusters() (in module mftools.plotting)

update() (in module mftools.config)

X

xslice (mftools.images.Overlap attribute)

Y

yslice (mftools.images.Overlap attribute)

Z

zslice() (mftools.fileio.DaxFile method)