Index

_

_get_focus_function() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method)

A

adaptive_fft_focus() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method) add_step() (ezstitcher.core.pipeline.Pipeline method) apply_mask() (ezstitcher.core.image_processor.ImageProcessor static method)

Ashlar assemble_image() (ezstitcher.core.stitcher.Stitcher method) auto_detect_patterns() (ezstitcher.core.microscope_interfaces.FilenameParser method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method)

B

Best Focus

blur() (ezstitcher.core.image_processor.ImageProcessor static method)

C

can_parse() (ezstitcher.core.microscope_interfaces.FilenameParser class method) (ezstitcher.microscopes.imagexpress.ImageXpressFilenameParser class method) (ezstitcher.microscopes.opera_phenix.OperaPhenixFilenameParser class method) Channel clean_temp_folders() (ezstitcher.core.file_system_manager.FileSystemManager static method) cleanup_processed_files() (ezstitcher.core.file_system_manager.FileSystemManager static method) combined_focus_measure() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method) Composite Image CompositeStep (class in ezstitcher.core.steps) compute_focus_metrics() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method)

config (ezstitcher.core.pipeline.ProcessingContext attribute) construct_filename() (ezstitcher.core.microscope_interfaces.FilenameParser method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method) (ezstitcher.microscopes.imagexpress.ImageXpressFilenameParser method) (ezstitcher.microscopes.opera_phenix.OperaPhenixFilenameParser method) copy_file() (ezstitcher.core.file_system_manager.FileSystemManager static method) create_composite() (ezstitcher.core.image_processor.ImageProcessor static method) create_microscope_handler() (in module ezstitcher.core.microscope_interfaces) create_output_directories() (ezstitcher.core.file_system_manager.FileSystemManager static method) create_projection() (ezstitcher.core.image_processor.ImageProcessor static method) create_weight_mask() (ezstitcher.core.image_processor.ImageProcessor static method)

D

default_extensions (ezstitcher.core.file_system_manager.FileSystemManager attribute) DEFAULT_MICROSCOPE (ezstitcher.core.microscope_interfaces.MicroscopeHandler attribute)

DEFAULT_WEIGHTS (ezstitcher.core.focus_analyzer.FocusAnalyzer attribute) detect_plate_structure() (ezstitcher.core.pipeline_orchestrator.PipelineOrchestrator method) detect_zstack_folders() (ezstitcher.core.file_system_manager.FileSystemManager static method)

E

ensure_directory() (ezstitcher.core.file_system_manager.FileSystemManager static method) EZStitcher (class in ezstitcher.ez) ezstitcher.core module ezstitcher.core.config module ezstitcher.core.file_system_manager module ezstitcher.core.focus_analyzer module ezstitcher.core.image_processor module ezstitcher.core.microscope_interfaces module

ezstitcher.core.pipeline module ezstitcher.core.pipeline_orchestrator module ezstitcher.core.steps module ezstitcher.core.stitcher module ezstitcher.ez module ezstitcher.microscopes.imagexpress module ezstitcher.microscopes.opera_phenix module

F

FILENAME_COMPONENTS (ezstitcher.core.microscope_interfaces.FilenameParser attribute) FileSystemManager (class in ezstitcher.core.file_system_manager) find_best_focus() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method) find_file_recursive() (ezstitcher.core.file_system_manager.FileSystemManager static method) find_image_directory() (ezstitcher.core.file_system_manager.FileSystemManager static method) find_metadata_file() (ezstitcher.core.microscope_interfaces.MetadataHandler method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method) (ezstitcher.microscopes.imagexpress.ImageXpressMetadataHandler method) (ezstitcher.microscopes.opera_phenix.OperaPhenixMetadataHandler method)

find_z_stack_dirs() (ezstitcher.core.file_system_manager.FileSystemManager static method) Focus Metric FocusAnalyzer (class in ezstitcher.core.focus_analyzer) FocusStep (class in ezstitcher.core.steps)

G

generate_positions() (ezstitcher.core.pipeline_orchestrator.PipelineOrchestrator method) (ezstitcher.core.stitcher.Stitcher method) generate_positions_df() (ezstitcher.core.stitcher.Stitcher method) get_grid_dimensions() (ezstitcher.core.microscope_interfaces.MetadataHandler method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method) (ezstitcher.microscopes.imagexpress.ImageXpressMetadataHandler method) (ezstitcher.microscopes.opera_phenix.OperaPhenixMetadataHandler method)

get_pixel_size() (ezstitcher.core.microscope_interfaces.MetadataHandler method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method) (ezstitcher.microscopes.imagexpress.ImageXpressMetadataHandler method) (ezstitcher.microscopes.opera_phenix.OperaPhenixMetadataHandler method) Grid Size group_patterns_by_component() (ezstitcher.core.microscope_interfaces.FilenameParser method)

I

ImageProcessor (class in ezstitcher.core.image_processor) ImageStitchingStep (class in ezstitcher.core.steps) ImageXpress

ImageXpressFilenameParser (class in ezstitcher.microscopes.imagexpress) ImageXpressMetadataHandler (class in ezstitcher.microscopes.imagexpress) input_dir (ezstitcher.core.pipeline.Pipeline attribute) (ezstitcher.core.pipeline.ProcessingContext attribute)

L

laplacian_energy() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method)

list_image_files() (ezstitcher.core.file_system_manager.FileSystemManager static method) load_image() (ezstitcher.core.file_system_manager.FileSystemManager static method)

M

margin_ratio (ezstitcher.core.config.StitcherConfig attribute) (ezstitcher.core.stitcher.StitcherConfig attribute) Max Projection max_projection() (ezstitcher.core.image_processor.ImageProcessor static method) max_shift (ezstitcher.core.config.StitcherConfig attribute) (ezstitcher.core.stitcher.StitcherConfig attribute) Mean Projection mean_projection() (ezstitcher.core.image_processor.ImageProcessor static method) Metadata Microscope Handler MicroscopeHandler (class in ezstitcher.core.microscope_interfaces) module ezstitcher.core ezstitcher.core.config ezstitcher.core.file_system_manager ezstitcher.core.focus_analyzer ezstitcher.core.image_processor ezstitcher.core.microscope_interfaces ezstitcher.core.pipeline ezstitcher.core.pipeline_orchestrator ezstitcher.core.steps ezstitcher.core.stitcher ezstitcher.ez ezstitcher.microscopes.imagexpress ezstitcher.microscopes.opera_phenix

N

normalize() (ezstitcher.core.image_processor.ImageProcessor static method)

normalized_variance() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method) num_workers (ezstitcher.core.config.PipelineConfig attribute)

O

Opera Phenix OperaPhenixFilenameParser (class in ezstitcher.microscopes.opera_phenix) OperaPhenixMetadataHandler (class in ezstitcher.microscopes.opera_phenix)

organize_zstack_folders() (ezstitcher.core.file_system_manager.FileSystemManager static method) out_dir_suffix (ezstitcher.core.config.PipelineConfig attribute) output_dir (ezstitcher.core.pipeline.Pipeline attribute) (ezstitcher.core.pipeline.ProcessingContext attribute)

P

parse_filename() (ezstitcher.core.microscope_interfaces.FilenameParser method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method) (ezstitcher.microscopes.imagexpress.ImageXpressFilenameParser method) (ezstitcher.microscopes.opera_phenix.OperaPhenixFilenameParser method) parse_positions_csv() (ezstitcher.core.stitcher.Stitcher static method) path_list_from_pattern() (ezstitcher.core.microscope_interfaces.FilenameParser method) (ezstitcher.core.microscope_interfaces.MicroscopeHandler method) percentile_normalize() (ezstitcher.core.image_processor.ImageProcessor static method) Pipeline (class in ezstitcher.core.pipeline) PipelineConfig (class in ezstitcher.core.config) PipelineOrchestrator (class in ezstitcher.core.pipeline_orchestrator) Pixel Size pixel_size (ezstitcher.core.config.StitcherConfig attribute) (ezstitcher.core.stitcher.StitcherConfig attribute)

PLACEHOLDER_PATTERN (ezstitcher.core.microscope_interfaces.FilenameParser attribute) Plate Position Generation PositionGenerationStep (class in ezstitcher.core.steps) positions_dir_suffix (ezstitcher.core.config.PipelineConfig attribute) preprocess() (ezstitcher.core.image_processor.ImageProcessor static method) Preprocessing process() (ezstitcher.core.steps.ImageStitchingStep method) (ezstitcher.core.steps.PositionGenerationStep method) (ezstitcher.core.steps.Step method) process_well() (ezstitcher.core.pipeline_orchestrator.PipelineOrchestrator method) ProcessingContext (class in ezstitcher.core.pipeline)

R

Reference Channel remove_directory() (ezstitcher.core.file_system_manager.FileSystemManager static method) rename_files_with_consistent_padding() (ezstitcher.core.file_system_manager.FileSystemManager static method)

results (ezstitcher.core.pipeline.ProcessingContext attribute) run() (ezstitcher.core.pipeline.Pipeline method) (ezstitcher.core.pipeline_orchestrator.PipelineOrchestrator method)

S

save_image() (ezstitcher.core.file_system_manager.FileSystemManager static method) save_positions_df() (ezstitcher.core.stitcher.Stitcher static method) select_best_focus() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method) set_options() (ezstitcher.ez.EZStitcher method) sharpen() (ezstitcher.core.image_processor.ImageProcessor static method) Site stack_equalize_histogram() (ezstitcher.core.image_processor.ImageProcessor static method) stack_percentile_normalize() (ezstitcher.core.image_processor.ImageProcessor static method) Step (class in ezstitcher.core.steps)

stitch() (ezstitcher.ez.EZStitcher method) stitch_images() (ezstitcher.core.pipeline_orchestrator.PipelineOrchestrator method) stitch_plate() (in module ezstitcher.ez) stitched_dir_suffix (ezstitcher.core.config.PipelineConfig attribute) Stitcher (class in ezstitcher.core.stitcher) stitcher (ezstitcher.core.config.PipelineConfig attribute) StitcherConfig (class in ezstitcher.core.config) (class in ezstitcher.core.stitcher) Stitching Subpixel Precision

T

tenengrad_variance() (ezstitcher.core.focus_analyzer.FocusAnalyzer static method) Tile Tile Overlap

tile_overlap (ezstitcher.core.config.StitcherConfig attribute) (ezstitcher.core.stitcher.StitcherConfig attribute) tophat() (ezstitcher.core.image_processor.ImageProcessor static method)

W

Well	well_filter (ezstitcher.core.config.PipelineConfig attribute) (ezstitcher.core.pipeline.ProcessingContext attribute)

Z

Z-Index

Z-Stack ZFlatStep (class in ezstitcher.core.steps)