Index

A

active (library.database_model.animal.Animal attribute) (library.database_model.atlas_model.AtlasModel attribute) (library.database_model.elastix_transformation.ElastixTransformation attribute) (library.database_model.histology.Histology attribute) (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.Section attribute) (library.database_model.slide.Slide attribute) (library.database_model.slide.SlideCziTif attribute) add_downsampled_volumes() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) add_elastix_row() (library.controller.elastix_controller.ElastixController method) add_rechunking() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) add_row() (library.controller.sql_controller.SqlController method) add_segment_properties() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) add_segmentation_mesh() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) alias (library.database_model.animal.Animal attribute) align() (library.image_manipulation.pipeline_process.Pipeline method)

align_downsampled_images() (library.image_manipulation.elastix_manager.ElastixManager method) align_elastix() (in module library.utilities.utilities_registration) (in module pipeline.scripts.create_alignment_metrics) align_full_size_image() (library.image_manipulation.elastix_manager.ElastixManager method) align_image_to_affine() (in module library.utilities.utilities_registration) align_images() (library.image_manipulation.elastix_manager.ElastixManager method) align_section_masks() (library.image_manipulation.elastix_manager.ElastixManager method) all_slide_meta_data_exists_in_database() (library.image_manipulation.meta_manager.MetaUtilities method) anesthesia (library.database_model.histology.Histology attribute) Animal (class in library.database_model.animal) animal_exists() (library.controller.animal_controller.AnimalController method) AnimalController (class in library.controller.animal_controller) apply_full_transformations() (library.image_manipulation.elastix_manager.ElastixManager method) apply_mask() (in module library.utilities.utilities_mask) apply_QC() (library.image_manipulation.prep_manager.PrepCreater method) apply_user_mask_edits() (library.image_manipulation.mask_manager.MaskManager method) AtlasModel (class in library.database_model.atlas_model)

B

block (library.database_model.histology.Histology attribute)

C

calculate_chunks() (in module library.image_manipulation.neuroglancer_manager) calculate_elastix_channels() (library.image_manipulation.elastix_manager.ElastixManager method) calculate_elastix_transformation() (library.image_manipulation.elastix_manager.ElastixManager method) calculate_factors() (in module library.image_manipulation.neuroglancer_manager) call_alignment_metrics() (library.image_manipulation.elastix_manager.ElastixManager method) ch_1_filter_set (library.database_model.scan_run.ScanRun attribute) ch_2_filter_set (library.database_model.scan_run.ScanRun attribute) ch_3_filter_set (library.database_model.scan_run.ScanRun attribute) ch_4_filter_set (library.database_model.scan_run.ScanRun attribute) channel (library.database_model.slide.Section attribute) (library.database_model.slide.SlideCziTif attribute) channel_index (library.database_model.slide.Section attribute) channels_per_scene (library.database_model.scan_run.ScanRun attribute) check_czi_file_exists() (library.image_manipulation.meta_manager.MetaUtilities method) check_elastix_metric_row() (library.controller.elastix_controller.ElastixController method) check_elastix_row() (library.controller.elastix_controller.ElastixController method) check_programs() (library.image_manipulation.pipeline_process.Pipeline static method) check_status() (library.image_manipulation.pipeline_process.Pipeline method) clean() (library.image_manipulation.pipeline_process.Pipeline method) clean_and_rotate_image() (in module library.utilities.utilities_mask) combine_dims() (in module library.utilities.utilities_mask) comments (library.database_model.animal.Animal attribute) (library.database_model.histology.Histology attribute) (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.Slide attribute) (library.database_model.slide.SlideCziTif attribute) convert() (in module library.utilities.utilities_process) convert_2d_transform_forms() (in module library.utilities.utilities_registration) convert_size() (in module library.utilities.utilities_process) converted_status (library.database_model.scan_run.ScanRun attribute) correct_multiples() (library.image_manipulation.meta_manager.MetaUtilities method) counterstain (library.database_model.histology.Histology attribute)

create_cleaned_images() (library.image_manipulation.image_cleaner.ImageCleaner method) create_cleaned_images_full_resolution() (library.image_manipulation.image_cleaner.ImageCleaner method) create_cleaned_images_thumbnail() (library.image_manipulation.image_cleaner.ImageCleaner method) create_dir2dir_transformations() (library.image_manipulation.elastix_manager.ElastixManager method) create_downsample() (in module library.utilities.utilities_process) create_downsampled_mask() (library.image_manipulation.mask_manager.MaskManager method) create_downsampled_transforms() (in module library.utilities.utilities_registration) create_downsamples() (library.image_manipulation.precomputed_manager.NgPrecomputedMaker method) create_full_resolution_mask() (library.image_manipulation.mask_manager.MaskManager method) create_image() (in module pipeline.scripts.create_alignment_metrics) create_mask() (library.image_manipulation.mask_manager.MaskManager method) create_mesh() (in module pipeline.scripts.create_neuroglancer_mesh) (in module pipeline.scripts.create_neuroglancer_mesh_from_volume) create_metrics() (library.image_manipulation.pipeline_process.Pipeline method) create_neuroglancer() (library.image_manipulation.precomputed_manager.NgPrecomputedMaker method) create_neuroglancer_normalization() (library.image_manipulation.precomputed_manager.NgPrecomputedMaker method) create_normalized_image() (library.image_manipulation.normalizer_manager.Normalizer method) create_rigid_parameters() (in module library.utilities.utilities_registration) create_scaled_transform() (in module library.utilities.utilities_registration) create_web_friendly_image() (library.image_manipulation.tiff_extractor_manager.TiffExtractor method) create_web_friendly_sections() (library.image_manipulation.elastix_manager.ElastixManager method) create_within_stack_transformations() (library.image_manipulation.elastix_manager.ElastixManager method) created (library.database_model.animal.Animal attribute) (library.database_model.atlas_model.AtlasModel attribute) (library.database_model.elastix_transformation.ElastixTransformation attribute) (library.database_model.histology.Histology attribute) (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.Section attribute) (library.database_model.slide.Slide attribute) (library.database_model.slide.SlideCziTif attribute) crop_image() (in module library.utilities.utilities_mask) czi_file (library.database_model.slide.Section attribute) CZIManager (class in library.image_manipulation.czi_manager)

D

date_of_birth (library.database_model.animal.Animal attribute)

date_sectioned (library.database_model.histology.Histology attribute) delete_row() (library.controller.sql_controller.SqlController method)

E

ElastixController (class in library.controller.elastix_controller) ElastixManager (class in library.image_manipulation.elastix_manager) ElastixTransformation (class in library.database_model.elastix_transformation) equalized() (in module library.utilities.utilities_mask) exsangination_method (library.database_model.histology.Histology attribute) extra_channel() (library.image_manipulation.pipeline_process.Pipeline method)

extract() (library.image_manipulation.pipeline_process.Pipeline method) extract_metadata_from_czi_file() (library.image_manipulation.czi_manager.CZIManager method) extract_png_from_czi() (in module library.image_manipulation.czi_manager) extract_slide_meta_data_and_insert_to_database() (library.image_manipulation.meta_manager.MetaUtilities method) extract_tiff_from_czi() (in module library.image_manipulation.czi_manager) extract_tiffs_from_czi() (library.image_manipulation.tiff_extractor_manager.TiffExtractor method)

F

file_name (library.database_model.slide.Section attribute) (library.database_model.slide.Slide attribute) (library.database_model.slide.SlideCziTif attribute) file_size (library.database_model.slide.Slide attribute) (library.database_model.slide.SlideCziTif attribute) file_type (library.database_model.scan_run.ScanRun attribute) file_validation() (library.image_manipulation.meta_manager.MetaUtilities method)

FileLocationManager (class in library.image_manipulation.filelocation_manager) fixative_method (library.database_model.histology.Histology attribute) FK_prep_id (library.database_model.elastix_transformation.ElastixTransformation attribute) (library.database_model.histology.Histology attribute) (library.database_model.scan_run.ScanRun attribute) FK_slide_id (library.database_model.slide.Section attribute) (library.database_model.slide.SlideCziTif attribute) flip (library.database_model.scan_run.ScanRun attribute)

G

genotype (library.database_model.animal.Animal attribute) get_alignment_directories() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_and_correct_multiples() (library.controller.slide_tif_controller.SlideCZIToTifController method) get_animal() (library.controller.animal_controller.AnimalController method) get_cpus() (in module library.utilities.utilities_process) get_czi() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_elastix_row() (library.controller.elastix_controller.ElastixController method) get_file_information() (library.image_manipulation.precomputed_manager.NgPrecomputedMaker method) get_full() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_full_aligned() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_full_aligned_iteration_0() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_full_cleaned() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_full_colored() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_full_masked() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_histogram() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_histology() (library.controller.histology_controller.HistologyController method) get_hostname() (in module library.utilities.utilities_process) get_ids_from_csv() (in module pipeline.scripts.create_neuroglancer_mesh_from_volume) get_image_size() (in module library.utilities.utilities_process) get_logdir() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_model_instance_segmentation() (library.image_manipulation.mask_manager.MaskManager method) get_neuroglancer() (library.image_manipulation.filelocation_manager.FileLocationManager method)

get_neuroglancer_progress() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_normalized() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_nworkers() (library.image_manipulation.parallel_manager.ParallelManager method) get_resolution() (library.controller.sql_controller.SqlController method) get_rotation_center() (library.image_manipulation.elastix_manager.ElastixManager method) get_row() (library.controller.sql_controller.SqlController method) get_scales() (library.image_manipulation.precomputed_manager.NgPrecomputedMaker method) get_scan_run() (library.controller.scan_run_controller.ScanRunController method) get_scene() (library.image_manipulation.czi_manager.CZIManager method) get_scene_dimension() (library.image_manipulation.czi_manager.CZIManager method) get_section_count() (library.controller.sections_controller.SectionsController method) get_sections() (library.controller.sections_controller.SectionsController method) get_segment_ids() (in module library.image_manipulation.neuroglancer_manager) get_slide() (library.controller.slide_tif_controller.SlideCZIToTifController method) get_thumbnail() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_thumbnail_aligned() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_thumbnail_aligned_iteration() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_thumbnail_cleaned() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_thumbnail_colored() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_thumbnail_masked() (library.image_manipulation.filelocation_manager.FileLocationManager method) get_transformations() (library.image_manipulation.elastix_manager.ElastixManager method) get_user_entered_scan_id() (library.image_manipulation.meta_manager.MetaUtilities method) getMetricValue() (in module pipeline.scripts.create_alignment_metrics)

H

height (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.SlideCziTif attribute) histogram() (library.image_manipulation.pipeline_process.Pipeline method)

HistogramMaker (class in library.image_manipulation.histogram_maker) Histology (class in library.database_model.histology) HistologyController (class in library.controller.histology_controller)

I

id (library.database_model.elastix_transformation.ElastixTransformation attribute) (library.database_model.histology.Histology attribute) (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.Section attribute) (library.database_model.slide.Slide attribute) (library.database_model.slide.SlideCziTif attribute) ImageCleaner (class in library.image_manipulation.image_cleaner) init_precomputed() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method)

init_volume() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) insert_before_one (library.database_model.slide.Slide attribute) insert_between_five_six (library.database_model.slide.Slide attribute) insert_between_four_five (library.database_model.slide.Slide attribute) insert_between_one_two (library.database_model.slide.Slide attribute) insert_between_three_four (library.database_model.slide.Slide attribute) insert_between_two_three (library.database_model.slide.Slide attribute) iteration (library.database_model.elastix_transformation.ElastixTransformation attribute)

L

library.controller.animal_controller module library.controller.elastix_controller module library.controller.histology_controller module library.controller.scan_run_controller module library.controller.sections_controller module library.controller.slide_tif_controller module library.controller.sql_controller module library.database_model.animal module library.database_model.atlas_model module library.database_model.elastix_transformation module library.database_model.histology module library.database_model.scan_run module library.database_model.slide module library.image_manipulation.czi_manager module library.image_manipulation.elastix_manager module library.image_manipulation.filelocation_manager module

library.image_manipulation.histogram_maker module library.image_manipulation.image_cleaner module library.image_manipulation.mask_manager module library.image_manipulation.meta_manager module library.image_manipulation.neuroglancer_manager module library.image_manipulation.normalizer_manager module library.image_manipulation.parallel_manager module library.image_manipulation.pipeline_process module library.image_manipulation.precomputed_manager module library.image_manipulation.prep_manager module library.image_manipulation.tiff_extractor_manager module library.utilities.utilities_mask module library.utilities.utilities_process module library.utilities.utilities_registration module lines_that_start_with() (in module pipeline.scripts.create_alignment_metrics) load_elastix_transformation() (library.image_manipulation.elastix_manager.ElastixManager method) load_machine_learning_model() (library.image_manipulation.mask_manager.MaskManager method)

M

machine (library.database_model.scan_run.ScanRun attribute) make_combined_histogram() (library.image_manipulation.histogram_maker.HistogramMaker method) make_histogram() (library.image_manipulation.histogram_maker.HistogramMaker method) make_single_histogram() (in module library.image_manipulation.histogram_maker) mask() (library.image_manipulation.pipeline_process.Pipeline method) MaskManager (class in library.image_manipulation.mask_manager) merge_mask() (in module library.utilities.utilities_mask) MetaUtilities (class in library.image_manipulation.meta_manager) metric (library.database_model.elastix_transformation.ElastixTransformation attribute) module library.controller.animal_controller library.controller.elastix_controller library.controller.histology_controller library.controller.scan_run_controller library.controller.sections_controller library.controller.slide_tif_controller library.controller.sql_controller library.database_model.animal library.database_model.atlas_model library.database_model.elastix_transformation library.database_model.histology library.database_model.scan_run library.database_model.slide library.image_manipulation.czi_manager library.image_manipulation.elastix_manager library.image_manipulation.filelocation_manager library.image_manipulation.histogram_maker library.image_manipulation.image_cleaner library.image_manipulation.mask_manager library.image_manipulation.meta_manager library.image_manipulation.neuroglancer_manager library.image_manipulation.normalizer_manager library.image_manipulation.parallel_manager library.image_manipulation.pipeline_process library.image_manipulation.precomputed_manager library.image_manipulation.prep_manager library.image_manipulation.tiff_extractor_manager library.utilities.utilities_mask library.utilities.utilities_process library.utilities.utilities_registration pipeline.scripts.create_alignment_metrics pipeline.scripts.create_neuroglancer_mesh pipeline.scripts.create_neuroglancer_mesh_from_volume pipeline.scripts.create_pipeline

mounting (library.database_model.histology.Histology attribute)

N

neuroglancer() (library.image_manipulation.pipeline_process.Pipeline method) NgPrecomputedMaker (class in library.image_manipulation.precomputed_manager) normalize16() (in module library.utilities.utilities_mask) normalize8() (in module library.utilities.utilities_mask)

normalize_image() (in module library.utilities.utilities_mask) normalize_stack() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) Normalizer (class in library.image_manipulation.normalizer_manager) number_of_slides (library.database_model.scan_run.ScanRun attribute) NumpyToNeuroglancer (class in library.image_manipulation.neuroglancer_manager)

O

objective (library.database_model.scan_run.ScanRun attribute)

oblique_notes (library.database_model.histology.Histology attribute) orientation (library.database_model.histology.Histology attribute)

P

parallel_create_cleaned() (library.image_manipulation.image_cleaner.ImageCleaner method) parallel_extract_slide_meta_data_and_insert_to_database() (library.image_manipulation.meta_manager.MetaUtilities method) ParallelManager (class in library.image_manipulation.parallel_manager) parameter_elastix_parameter_file_to_dict() (library.image_manipulation.elastix_manager.ElastixManager static method) parameters_to_rigid_transform() (in module library.utilities.utilities_registration) perfusion_age_in_days (library.database_model.histology.Histology attribute) perfusion_date (library.database_model.histology.Histology attribute) Pipeline (class in library.image_manipulation.pipeline_process) pipeline.scripts.create_alignment_metrics module pipeline.scripts.create_neuroglancer_mesh module

pipeline.scripts.create_neuroglancer_mesh_from_volume module pipeline.scripts.create_pipeline module place_image() (in module library.utilities.utilities_mask) post_fixation_period (library.database_model.histology.Histology attribute) prep_id (library.database_model.animal.Animal attribute) (library.database_model.slide.Section attribute) PrepCreater (class in library.image_manipulation.prep_manager) process_image() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) process_image_mesh() (library.image_manipulation.neuroglancer_manager.NumpyToNeuroglancer method) processed (library.database_model.slide.Slide attribute) processing_duration (library.database_model.slide.SlideCziTif attribute)

Q

query_table() (library.controller.sql_controller.SqlController method)

R

read_image() (in module library.utilities.utilities_process) rescan_number (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.Section attribute) resize_tif() (library.image_manipulation.mask_manager.MaskManager static method) resolution (library.database_model.scan_run.ScanRun attribute) rigid_transform_to_parmeters() (in module library.utilities.utilities_registration)

rotate_image() (in module library.utilities.utilities_mask) rotation (library.database_model.elastix_transformation.ElastixTransformation attribute) (library.database_model.scan_run.ScanRun attribute) row_exists() (library.controller.sql_controller.SqlController method) run_commands_concurrently() (library.image_manipulation.parallel_manager.ParallelManager method) run_commands_with_threads() (library.image_manipulation.parallel_manager.ParallelManager method)

S

scaled() (in module library.utilities.utilities_mask) scaledXXX() (in module library.utilities.utilities_mask) scan_date (library.database_model.scan_run.ScanRun attribute) scan_run_id (library.database_model.slide.Slide attribute) scan_runs (library.database_model.animal.Animal attribute) ScanRun (class in library.database_model.scan_run) ScanRunController (class in library.controller.scan_run_controller) scene_index (library.database_model.slide.Section attribute) (library.database_model.slide.SlideCziTif attribute) scene_number (library.database_model.slide.Section attribute) (library.database_model.slide.SlideCziTif attribute) scene_order (library.database_model.histology.Histology attribute) scene_qc_1 (library.database_model.slide.Slide attribute) scene_qc_2 (library.database_model.slide.Slide attribute) scene_qc_3 (library.database_model.slide.Slide attribute) scene_qc_4 (library.database_model.slide.Slide attribute) scene_qc_5 (library.database_model.slide.Slide attribute) scene_qc_6 (library.database_model.slide.Slide attribute) scenes (library.database_model.slide.Slide attribute) scenes_per_slide (library.database_model.scan_run.ScanRun attribute) Section (class in library.database_model.slide) section (library.database_model.elastix_transformation.ElastixTransformation attribute)

section_schema (library.database_model.scan_run.ScanRun attribute) section_thickness (library.database_model.histology.Histology attribute) sectioning_method (library.database_model.histology.Histology attribute) SectionsController (class in library.controller.sections_controller) sex (library.database_model.animal.Animal attribute) ship_date (library.database_model.animal.Animal attribute) shipper (library.database_model.animal.Animal attribute) side_sectioned_first (library.database_model.histology.Histology attribute) Slide (class in library.database_model.slide) slide_folder_path (library.database_model.scan_run.ScanRun attribute) slide_physical_id (library.database_model.slide.Section attribute) (library.database_model.slide.Slide attribute) slide_status (library.database_model.slide.Slide attribute) SlideCziTif (class in library.database_model.slide) SlideCZIToTifController (class in library.controller.slide_tif_controller) slides (library.database_model.scan_run.ScanRun attribute) smooth_image() (in module library.utilities.utilities_mask) special_perfusion_notes (library.database_model.histology.Histology attribute) species (library.database_model.animal.Animal attribute) SqlController (class in library.controller.sql_controller) stock_number (library.database_model.animal.Animal attribute) strain (library.database_model.animal.Animal attribute)

T

TASK_ALIGN (library.image_manipulation.pipeline_process.Pipeline attribute) TASK_CLEAN (library.image_manipulation.pipeline_process.Pipeline attribute) TASK_CREATE_METRICS (library.image_manipulation.pipeline_process.Pipeline attribute) TASK_EXTRA_CHANNEL (library.image_manipulation.pipeline_process.Pipeline attribute) TASK_EXTRACT (library.image_manipulation.pipeline_process.Pipeline attribute) TASK_HISTOGRAM (library.image_manipulation.pipeline_process.Pipeline attribute) TASK_MASK (library.image_manipulation.pipeline_process.Pipeline attribute)

TASK_NEUROGLANCER (library.image_manipulation.pipeline_process.Pipeline attribute) test_dir() (in module library.utilities.utilities_process) tif_id (library.database_model.slide.Section attribute) tif_to_png() (in module library.utilities.utilities_registration) TiffExtractor (class in library.image_manipulation.tiff_extractor_manager) tissue_source (library.database_model.animal.Animal attribute) tracking_number (library.database_model.animal.Animal attribute) transform_image() (library.image_manipulation.elastix_manager.ElastixManager method)

U

update_elastix_row() (library.controller.elastix_controller.ElastixController method) update_row() (library.controller.sql_controller.SqlController method)

update_scanrun() (library.controller.scan_run_controller.ScanRunController method) (library.image_manipulation.prep_manager.PrepCreater method) update_tif() (library.controller.slide_tif_controller.SlideCZIToTifController method)

V

vender (library.database_model.animal.Animal attribute)

virus_id (library.database_model.histology.Histology attribute)

W

whole_brain (library.database_model.histology.Histology attribute) width (library.database_model.scan_run.ScanRun attribute) (library.database_model.slide.SlideCziTif attribute)

write_image() (in module library.utilities.utilities_process)

X

xshift (library.database_model.elastix_transformation.ElastixTransformation attribute)

Y

yshift (library.database_model.elastix_transformation.ElastixTransformation attribute)

Z

zresolution (library.database_model.scan_run.ScanRun attribute)