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Get Started

  • Usage
    • Installation
    • Step-by-step Guide
      • 1- Pipeline Parameter Configuration
        • Step 1: Import Modules and Configure Logger
        • Step 2: Initialize Configuration Object
        • Step 3: Mandatory Configuration
        • Step 4: Raw Data Directory Structure
        • Step 5: Optional Configuration
        • Step 6: Set Parameters
        • Next Steps
      • 2- Volume Alignment
        • Load the Configuration
        • Execute Volumetric Alignment
        • Next Steps
      • 3- Alignment Evaluation
        • Step 1: Load Configuration Settings
        • Step 2: Additional Configuration for Alignment Evaluation
        • Step 3: Alignment Measurement
        • Step 4: Alignment Evaluation and Confidence Interval Calculation
        • Next Steps
      • 4- Puncta Extraction
        • Step 1: Load Configuration Settings
        • Step 2: Puncta Extraction
        • Step 3: Channel Consolidation
        • Step 4: Code Consolidation
        • Next Steps
      • 5- Puncta Basecalling
        • Step 1: Load Configuration Settings
        • Step 2: Assign Genes to Detected Puncta for All FOVs
        • Step 3: Assign Puncta to Nuclei for All FOVs
        • Conclusion

Package Reference

  • Args Module
    • Pipeline Parameters
      • Args
        • Args.create_directroy_structure()
        • Args.get_memory_config()
        • Args.get_processing_recommendations()
        • Args.load_config_yaml()
        • Args.load_params()
        • Args.print()
        • Args.save_config_yaml()
        • Args.save_params()
        • Args.set_params()
        • Args.set_permissions()
  • Align Module
    • Volumes Alignment
      • execute_volumetric_alignment_bigstream()
      • transform_ref_code()
      • volumetric_alignment()
    • Volumes Alignment Evaluation
      • calculate_alignment_evaluation_ci()
      • measure_round_alignment_NCC()
      • plot_alignment_evaluation()
      • alignment_NCC()
      • template_matching()
  • Puncta Module
    • Puncta Extraction
      • calculate_coords_cpu()
      • calculate_coords_gpu()
      • extract()
      • puncta_extraction_cpu()
      • puncta_extraction_gpu()
    • Puncta Consolidation
      • consolidate_channels()
      • consolidate_channels_function()
      • consolidate_codes()
      • consolidate_codes_function()
    • Puncta Inspection
      • in_region()
      • inspect_across_rounds_plotly()
      • inspect_between_rounds_plotly()
      • inspect_localmaximum_matplotlib()
      • inspect_localmaximum_plotly()
      • inspect_puncta_ROI_matplotlib()
      • inspect_puncta_ROI_plotly()
      • inspect_puncta_improvement_matplotlib()
      • inspect_puncta_individual_matplotlib()
      • inspect_puncta_individual_plotly()
      • inspect_raw_matplotlib()
      • inspect_raw_plotly()
      • plot_genes_global()
      • plot_genes_global_zstep()
    • Puncta Improve Detection
      • find_nearest_points()
      • find_nearest_puncta()
      • improve_nearest()
      • puncta_all_nearest_points()
      • puncta_nearest_points()
    • Puncta Base-Calling
      • puncta_assign_gene()
      • puncta_assign_nuclei()
    • Puncta Benchmark
      • aggregate_puncta_analysis()
      • plot_benchmark_data()
      • puncta_analysis()
  • Segmentation Module
    • Segmentation [Cellpose]
      • display_3d_masks()
      • segment_3d()
  • Stitching Module
    • Stitching
      • apply_new_ids()
      • blend()
      • blend2()
      • deduplicate_blob_ids()
      • find_overlapping_blobs()
      • get_all_blobs()
      • get_bottom_surface()
      • get_contact_surface()
      • get_offsets()
      • get_offsets_nd2()
      • get_tiles_overlaps()
      • get_top_surface()
      • make_stitched_dedup_h5()
      • make_stitched_h5()
      • overlapping()
    • Tileset
      • Tileset
        • Tileset.create_blank_h5bdv()
        • Tileset.dedup_segmentation_ids()
        • Tileset.find_intensity_scale()
        • Tileset.get_centroids()
        • Tileset.get_slice()
        • Tileset.init_from_bdv()
        • Tileset.init_from_h5()
        • Tileset.init_from_jp2()
        • Tileset.init_from_nd2()
        • Tileset.init_from_tiff_files()
        • Tileset.load_all()
        • Tileset.load_tile()
        • Tileset.local_to_global()
        • Tileset.preview_nd2()
        • Tileset.produce_output_volume()
        • Tileset.scale_intensity()
        • Tileset.scale_offset()
        • Tileset.show_slice()
        • Tileset.update_offsets()
        • Tileset.write_into_h5bdv()
    • Tiles
      • Tile
        • Tile.apply_mask()
        • Tile.fast_nd2_read_downscale()
        • Tile.find_intensity_scale()
        • Tile.from_array()
        • Tile.from_jp2()
        • Tile.from_nd2()
        • Tile.from_tiff()
        • Tile.save_as_jp2()
        • Tile.save_as_tiff()
        • Tile.scale_intensity()
  • Utils Module
    • Utility Functions
      • chmod()
      • display_img()
      • downsample_volume()
      • enhance_and_filter_volume()
      • gene_barcode_mapping()
      • generate_debug_candidate()
      • get_offsets()
      • retrieve_all_puncta()
      • retrieve_complete()
      • retrieve_digit()
      • retrieve_gene()
      • retrieve_img()
      • retrieve_one_puncta()
      • retrieve_summary()
      • retrieve_vol()
      • subtract_background_rolling_ball()
      • subtract_background_top_hat()
      • visualize_progress()
    • Package Logger
      • configure_logger()
  • I/O Module
    • I/O Functions
      • create_folder_structure()
      • downsample()
      • imsToVol()
      • nd2ToChunk()
      • nd2ToSlice()
      • nd2ToVol()
      • parse_sitk_log()
      • readNd2()
      • readXlsx()
      • save_gif()
      • tiff2H5()
  • Beta Module
    • Beta functions
      • algin_channels()
      • algin_channels_function()
      • algin_channels_function_new()
      • algin_channels_new()
      • blend_ind()
      • foreground_segmentation()
      • foreground_segmentation_new()
      • quantile_normalization()
  • Overview: module code

All modules for which code is available

  • exm.align.align
  • exm.align.align_eval
  • exm.align.align_utils
  • exm.args.args
  • exm.beta.beta
  • exm.io.io
  • exm.puncta.basecalling
  • exm.puncta.benchmark
  • exm.puncta.consolidate
  • exm.puncta.extract
  • exm.puncta.improve
  • exm.puncta.inspect
  • exm.segmentation.segmentation
  • exm.stitching.stitching
  • exm.stitching.tileset
  • exm.utils.log
  • exm.utils.utils

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