Index

A

add_coords_to_experimental_metadata (module) add_coords_to_experimental_metadata() (in module add_coords_to_experimental_metadata) add_coords_to_yaml() (in module pysmFISH.utils) align_single_compress_pic() (in module pysmFISH.stitching_package.pairwisesingle) align_single_pair() (in module pysmFISH.stitching_package.pairwisesingle) align_single_pair_npy() (in module pysmFISH.stitching_package.pairwisesingle)

align_sub_region() (in module pysmFISH.stitching_package.hybregistration) all_dots_removal() (in module pysmFISH.dots_coords_calculations) apply_IJ_corners() (in module pysmFISH.stitching_package.tilejoining) apply_stitching (module) apply_stitching() (in module apply_stitching) assess_overlap() (in module pysmFISH.stitching_package.tilejoining) assess_performance() (in module pysmFISH.stitching_package.stitching)

C

calc_corners_coord() (in module pysmFISH.stitching_package.tilejoining) calc_translated_pics() (in module pysmFISH.stitching_package.pairwisehelper) calc_translated_pics_3D() (in module pysmFISH.stitching_package.pairwisehelper) calculate_PCM() (in module pysmFISH.stitching_package.pairwisehelper) calculate_PCM_method2() (in module pysmFISH.stitching_package.pairwisehelper) calculate_pos_shifts() (in module pysmFISH.stitching_package.pairwisesingle) catch_duplicated_dots() (in module pysmFISH.dots_coords_calculations) check_corner_blending() (in module pysmFISH.stitching_package.tilejoining) check_tile_set() (pysmFISH.stitching_package.MicroscopeData.MicroscopeData method)

check_trailing_slash() (in module pysmFISH.utils) combine_gene_pos() (in module pysmFISH.utils) correct_trans_and_size() (in module pysmFISH.stitching_package.hybregistration) counting_only() (in module pysmFISH.counting) create_loompy_raw_counting() (in module pysmFISH.hdf5_utils) create_single_directory() (in module pysmFISH.utils) create_structures_hdf5_files() (in module pysmFISH.stitching_package.hdf5preparation) create_structures_hdf5_stitched_ref_gene_file_npy() (in module pysmFISH.stitching_package.hdf5preparation) create_subdirectory_tree() (in module pysmFISH.utils)

D

determine_os() (in module pysmFISH.utils) determine_overlap() (in module pysmFISH.stitching_package.pairwisesingle) display_overlap() (in module pysmFISH.stitching_package.pairwisehelper) display_tiles() (in module pysmFISH.stitching_package.inout)

divide_final_image() (in module pysmFISH.stitching_package.hdf5preparation) dots_coords_correction (module) dots_coords_correction() (in module dots_coords_correction) dots_removing() (in module pysmFISH.dots_coords_calculations)

E

experimental_metadata_parser() (in module pysmFISH.utils)

extract_hdf5_refs() (in module pysmFISH.stitching_package.inout)

F

fill_hdf5_files() (in module pysmFISH.stitching_package.hdf5preparation) fill_hdf5_MPI() (in module pysmFISH.stitching_package.hdf5preparation) filtering_and_counting() (in module pysmFISH.counting) filtering_and_counting_experiment() (in module pysmFISH.counting) filtering_and_counting_ill_correction() (in module pysmFISH.counting)

filtering_raw_counting_config_parser() (in module pysmFISH.utils) find_best_trans() (in module pysmFISH.stitching_package.pairwisesingle) find_reg_final_image() (in module pysmFISH.stitching_package.hybregistration) free_hdf5_space() (in module pysmFISH.stitching_package.inout) function_to_run_dots_removal_parallel() (in module pysmFISH.dots_coords_calculations)

G

general_yaml_parser() (in module pysmFISH.utils) generate_blended_tile() (in module pysmFISH.stitching_package.tilejoining) generate_blended_tile_npy() (in module pysmFISH.stitching_package.tilejoining) get_image_names() (in module pysmFISH.stitching_package.inout) get_overlapping_region() (in module pysmFISH.stitching_package.pairwisehelper) get_pairwise_alignments() (in module pysmFISH.stitching_package.stitching) get_pairwise_input() (in module pysmFISH.stitching_package.stitching)

get_pairwise_input_npy() (in module pysmFISH.stitching_package.stitching) get_place_tile_input() (in module pysmFISH.stitching_package.stitching) get_place_tile_input_apply() (in module pysmFISH.stitching_package.stitching) get_place_tile_input_apply_npy() (in module pysmFISH.stitching_package.stitching) get_refine_pairwise_input() (in module pysmFISH.stitching_package.stitching) get_single_relative_trans() (in module pysmFISH.stitching_package.hybregistration) get_single_trans() (in module pysmFISH.stitching_package.hybregistration) GlobalOptimization (class in pysmFISH.stitching_package.GlobalOptimization)

H

hdf5_create_preprocessing_file() (in module pysmFISH.hdf5_utils)

hood_creation() (in module pysmFISH.dots_coords_calculations)

I

identify_nodes() (in module pysmFISH.utils) image_chunking() (in module pysmFISH.object_based_segmentation) image_chunks_calculator() (in module pysmFISH.object_based_segmentation)

init_console_logger() (in module pysmFISH.utils) init_file_logger() (in module pysmFISH.utils) IntersectionCouples() (in module pysmFISH.object_based_segmentation)

L

list_chunking() (in module pysmFISH.utils) load_stitching_coord() (in module pysmFISH.stitching_package.inout)

load_tile() (in module pysmFISH.stitching_package.inout) load_tile_3D() (in module pysmFISH.stitching_package.inout)

M

make_final_image() (in module pysmFISH.stitching_package.tilejoining) make_final_image_npy() (in module pysmFISH.stitching_package.tilejoining)

make_mask() (in module pysmFISH.stitching_package.tilejoining) make_tile_set() (pysmFISH.stitching_package.MicroscopeData.MicroscopeData method) MicroscopeData (class in pysmFISH.stitching_package.MicroscopeData)

N

nd2_to_npy() (in module pysmFISH.io) non_linear_blending() (in module pysmFISH.stitching_package.tilejoining)

non_linear_blending_corner() (in module pysmFISH.stitching_package.tilejoining) normalize_coords() (pysmFISH.stitching_package.MicroscopeData.MicroscopeData method) nuclei_filtering() (in module pysmFISH.filtering)

O

obj_properties_calculator() (in module pysmFISH.object_based_segmentation)

overlapping_images_grid() (in module pysmFISH.dots_coords_calculations) OverlappingCouples() (in module pysmFISH.object_based_segmentation)

P

partial_image_mean() (in module pysmFISH.utils) paste_in_final_image_MPI() (in module pysmFISH.stitching_package.tilejoining) perform_blending_par_proof() (in module pysmFISH.stitching_package.tilejoining) performOptimization() (pysmFISH.stitching_package.GlobalOptimization.GlobalOptimization method) plot_coordinates() (in module pysmFISH.stitching_package.inout) plot_final_image() (in module pysmFISH.stitching_package.stitching) plot_overlaps() (in module pysmFISH.stitching_package.pairwisesingle) plot_stitched_coordinates() (in module pysmFISH.stitching_package.inout) polyT_segmentation() (in module pysmFISH.object_based_segmentation) prepare_for_comparing() (in module pysmFISH.stitching_package.hybregistration) preprocessing_script (module) preprocessing_script() (in module preprocessing_script) process_standalone_experiment (module) process_standalone_experiment() (in module process_standalone_experiment) processing_combinations() (in module pysmFISH.dots_coords_calculations) pysmFISH.counting (module)

pysmFISH.dots_calling (module) pysmFISH.dots_coords_calculations (module) pysmFISH.filtering (module) pysmFISH.hdf5_utils (module) pysmFISH.io (module) pysmFISH.object_based_segmentation (module) pysmFISH.stitching_package.GlobalOptimization (module) pysmFISH.stitching_package.hdf5preparation (module) pysmFISH.stitching_package.hybregistration (module) pysmFISH.stitching_package.inout (module) pysmFISH.stitching_package.MicroscopeData (module) pysmFISH.stitching_package.pairwisehelper (module) pysmFISH.stitching_package.pairwisesingle (module) pysmFISH.stitching_package.stitching (module) pysmFISH.stitching_package.tilejoining (module) pysmFISH.utils (module)

R

read_IJ_corners() (in module pysmFISH.stitching_package.inout) reference_registration (module) reference_registration() (in module reference_registration) refine_pairwise_alignments() (in module pysmFISH.stitching_package.stitching)

refine_single_pair() (in module pysmFISH.stitching_package.pairwisesingle) register_dots_coords() (in module pysmFISH.dots_coords_calculations) register_final_images() (in module pysmFISH.stitching_package.hybregistration) register_final_images_old() (in module pysmFISH.stitching_package.hybregistration) register_final_images_reg_data_only() (in module pysmFISH.stitching_package.hybregistration)

S

save_as_tiff() (in module pysmFISH.stitching_package.stitching) save_image() (in module pysmFISH.stitching_package.inout) save_to_file() (in module pysmFISH.stitching_package.inout)

smFISH_filtering() (in module pysmFISH.filtering) staining_segmentation (module) staining_segmentation() (in module staining_segmentation)

T

thr_calculator() (in module pysmFISH.dots_calling)

transform_data_file() (in module pysmFISH.stitching_package.hybregistration) transform_final_image() (in module pysmFISH.stitching_package.hybregistration)

X

xcov_nd() (in module pysmFISH.stitching_package.pairwisehelper)