MERFISH Tools documentation

Note

This project is under active development.

Installation

To use, first install it using pip:

$ pip install git+https://github.com/epigen-UCSD/merfish_tools

Contents:

• Selecting genes for a MERFISH gene panel
• Using MERFISH Tools for downstream analysis of MERSCOPE data
• mftools package
  • Submodules
  • mftools.barcodes module
    • Functions
    • assign_to_cells()
    • calculate_global_coordinates()
    • count_unfiltered_barcodes()
    • create_cell_by_gene_table()
    • expand_codebook()
    • get_per_bit_stats()
    • link_cell_ids()
    • make_table()
    • normalize_codebook()
    • per_bit_error()
    • per_fov_error()
    • per_gene_error()
    • process_merlin_barcodes()
    • set_barcode_stats()
    • trim_barcodes_in_overlaps()
  • mftools.cellgene module
    • adjust_spatial_coordinates()
    • cluster_cells()
    • create_scanpy_object()
    • find_cell_communities()
    • label_clusters()
    • normalize()
    • optimize_number_PCs()
    • transfer_labels()
  • mftools.config module
    • Settings
    • get()
    • has()
    • load()
    • load_from_file()
    • path()
    • set()
    • update()
  • mftools.fileio module
    • DaxFile
      • DaxFile.block()
      • DaxFile.block_range()
      • DaxFile.channel()
      • DaxFile.fileinfo()
      • DaxFile.frame()
      • DaxFile.get_entire_image()
      • DaxFile.load_fileinfo()
      • DaxFile.max_projection()
      • DaxFile.zslice()
    • ImageDataset
      • ImageDataset.filename()
      • ImageDataset.has_positions()
      • ImageDataset.load_fov_positions()
      • ImageDataset.load_image()
      • ImageDataset.n_fovs()
    • MerfishAnalysis
      • MerfishAnalysis.has_cell_metadata()
      • MerfishAnalysis.load_barcode_table()
      • MerfishAnalysis.load_cell_by_gene_table()
      • MerfishAnalysis.load_cell_metadata()
      • MerfishAnalysis.load_linked_cells()
      • MerfishAnalysis.save_barcode_table()
      • MerfishAnalysis.save_cell_by_gene_table()
      • MerfishAnalysis.save_cell_metadata()
      • MerfishAnalysis.save_linked_cells()
    • MerlinOutput
      • MerlinOutput.count_raw_barcodes()
      • MerlinOutput.load_codebook()
      • MerlinOutput.load_data_organization()
      • MerlinOutput.load_drift_transformations()
      • MerlinOutput.load_exported_barcodes()
      • MerlinOutput.load_filtered_barcodes()
      • MerlinOutput.load_fov_positions()
      • MerlinOutput.load_hyb_drifts()
      • MerlinOutput.load_raw_barcodes()
      • MerlinOutput.n_fovs()
    • load_data_organization()
    • load_fov_positions()
    • load_mask()
    • load_stats()
    • save_mask()
    • save_stats()
    • search_for_mask_file()
  • mftools.images module
    • FOVPositions
      • FOVPositions.find_fov_overlaps()
      • FOVPositions.local_to_global_coordinates()
      • FOVPositions.overlaps
    • Overlap
      • Overlap.fov
      • Overlap.xslice
      • Overlap.yslice
    • flat_field_correct()
    • get_median_image()
    • get_slice()
    • highpass_filter()
    • lowpass_filter()
  • mftools.plotting module
    • cell_volume_histogram()
    • check_drift()
    • confidence_ratios()
    • counts_per_cell_histogram()
    • create_color_image()
    • drift_histogram()
    • exact_vs_corrected()
    • fov_error_bar()
    • fov_error_spatial()
    • fov_number_map()
    • genes_detected_per_cell_histogram()
    • per_bit_error_bar()
    • per_bit_error_line()
    • per_color_error()
    • per_hyb_error()
    • plot()
    • plot_mask()
    • rnaseq_correlation()
    • spatial_cell_clusters()
    • spatial_transcripts_per_fov()
    • transcripts_per_gene_scatterplot()
    • umap_clusters()
  • mftools.segmentation module
    • CellSegmentation
      • CellSegmentation.find_overlapping_cells()
      • CellSegmentation.get_overlap_volume()
      • CellSegmentation.linked_cells
      • CellSegmentation.make_metadata_table()
      • CellSegmentation.metadata
      • CellSegmentation.segment_fov()
    • filter_by_volume()
    • match_cells_in_overlap()
    • remove_small_cells_from_mask()
  • mftools.stats module
    • get()
    • set()
  • mftools.util module
    • calculate_drift()
    • reference_gene_counts()
  • Module contents
• Glossary