Get Started
Package Reference
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()
execute_volumetric_alignment_bigstream()
transform_ref_code()
volumetric_alignment()
calculate_alignment_evaluation_ci()
measure_round_alignment_NCC()
plot_alignment_evaluation()
alignment_NCC()
template_matching()
calculate_coords_cpu()
calculate_coords_gpu()
extract()
puncta_extraction_cpu()
puncta_extraction_gpu()
consolidate_channels()
consolidate_channels_function()
consolidate_codes()
consolidate_codes_function()
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()
find_nearest_points()
find_nearest_puncta()
improve_nearest()
puncta_all_nearest_points()
puncta_nearest_points()
puncta_assign_gene()
puncta_assign_nuclei()
aggregate_puncta_analysis()
plot_benchmark_data()
puncta_analysis()
display_3d_masks()
segment_3d()
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.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()
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()
chmod()
display_img()
downsample_volume()
enhance_and_filter_volume()
gene_barcode_mapping()
generate_debug_candidate()
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()
configure_logger()
create_folder_structure()
downsample()
imsToVol()
nd2ToChunk()
nd2ToSlice()
nd2ToVol()
parse_sitk_log()
readNd2()
readXlsx()
save_gif()
tiff2H5()
algin_channels()
algin_channels_function()
algin_channels_function_new()
algin_channels_new()
blend_ind()
foreground_segmentation()
foreground_segmentation_new()
quantile_normalization()
To use exm-toolbox, first install it using pip:
(.venv) $ pip install git+https://github.com/RuihanZhang2015/ExSeq-Toolbox