Index

A

add_info() (linumpy.metrics.PipelineMetrics method) add_metric() (linumpy.metrics.PipelineMetrics method) add_overwrite_arg() (in module linumpy.cli.args) add_processes_arg() (in module linumpy.cli.args) add_verbose_arg() (in module linumpy.cli.args) add_volume_to_mosaic() (in module linumpy.mosaic.grid) add_z_slice_labels() (in module linumpy.imaging.visualization) affine_transform() (in module linumpy.gpu.interpolation) aggregate_metrics() (in module linumpy.metrics) align_images_sitk() (in module linumpy.registration.sitk) AnalysisOmeZarrWriter (class in linumpy.io) (class in linumpy.io.zarr) apply_2d_transform() (in module linumpy.mosaic.stacking) apply_bias_field() (in module linumpy.intensity.bias_field) apply_bias_field_gpu() (in module linumpy.gpu.bias_field) apply_blend_shift_refinement() (in module linumpy.mosaic.motor) apply_displacement_field() (in module linumpy.gpu.interpolation) apply_flatfield_correction() (in module linumpy.gpu.array_ops) apply_hanning_window() (in module linumpy.registration.phase_correlation) apply_histogram_matching() (in module linumpy.intensity.normalization) apply_interface_correction() (in module linumpy.geometry.crop)

apply_orientation_transform() (in module linumpy.imaging.orientation) apply_scaling() (in module linumpy.registration.manual) (linumpy.registration.manual.ManualImageCorrection method) apply_transform() (in module linumpy.registration.manual) (in module linumpy.registration.sitk) apply_transform_gpu() (in module linumpy.gpu.registration) apply_transform_to_volume() (in module linumpy.mosaic.stacking) apply_xy_shift() (in module linumpy.gpu.array_ops) (in module linumpy.imaging.transform) (in module linumpy.mosaic.stacking) apply_zprofile_smoothing() (in module linumpy.intensity.normalization) ascan_averaging_value (linumpy.io.thorlabs.ThorOCT attribute) assert_output_exists() (in module linumpy.cli.args) assess_slice_quality() (in module linumpy.metrics.image_quality) assess_slice_quality_gpu() (in module linumpy.gpu.image_quality) AVAILABLE_RESOLUTIONS (in module linumpy.reference.allen) axes (linumpy.io.OmeZarrWriter attribute) (linumpy.io.zarr.OmeZarrWriter attribute) axim_a (linumpy.registration.manual.ManualImageCorrection attribute) axim_b (linumpy.registration.manual.ManualImageCorrection attribute) axim_c (linumpy.registration.manual.ManualImageCorrection attribute)

B

binary_closing() (in module linumpy.gpu.morphology) binary_dilation() (in module linumpy.gpu.morphology) binary_erosion() (in module linumpy.gpu.morphology) binary_fill_holes() (in module linumpy.gpu.morphology) binary_opening() (in module linumpy.gpu.morphology) blend_overlap_xy() (in module linumpy.mosaic.stacking)

blend_overlap_z() (in module linumpy.mosaic.stacking) blending_method (linumpy.mosaic.grid.MosaicGrid attribute) bspline_evaluate() (in module linumpy.gpu.bspline) bspline_fit() (in module linumpy.gpu.bspline) bspline_fit_precompute() (in module linumpy.gpu.bspline) build_cumulative_shifts() (in module linumpy.stack_alignment.io)

C

CANONICAL_COLUMNS (in module linumpy.io.slice_config) center_shifts() (in module linumpy.stack_alignment.units) centre_of_mass_offset() (in module linumpy.registration.refinement) clear_gpu_memory() (in module linumpy.gpu.image_quality) clip_percentile() (in module linumpy.gpu.array_ops) collect_interface_crop_metrics() (in module linumpy.metrics) collect_normalization_metrics() (in module linumpy.metrics) collect_pairwise_registration_metrics() (in module linumpy.metrics) collect_psf_compensation_metrics() (in module linumpy.metrics) collect_stack_metrics() (in module linumpy.metrics) collect_stitch_3d_metrics() (in module linumpy.metrics) collect_xy_transform_metrics() (in module linumpy.metrics) command_iteration() (in module linumpy.registration.sitk) compare_motor_vs_registration() (in module linumpy.mosaic.motor) compressed_data (linumpy.io.thorlabs.ThorOCT attribute) compute_affine_output_shape() (in module linumpy.mosaic.motor) compute_affine_positions() (in module linumpy.mosaic.motor) compute_edge_score() (in module linumpy.metrics.image_quality) compute_edge_score_gpu() (in module linumpy.gpu.image_quality) compute_metric() (linumpy.gpu.registration.GPUAcceleratedRegistration method) compute_mosaic_shape() (linumpy.mosaic.grid.MosaicGrid method) compute_motor_positions() (in module linumpy.mosaic.motor) compute_motor_transform() (in module linumpy.registration.transforms) compute_nonzero_percentile_memory_efficient() (in module linumpy.gpu.array_ops) compute_percentiles_memory_efficient() (in module linumpy.gpu.array_ops) compute_quality_report() (in module linumpy.metrics.image_quality) compute_registration_refinements() (in module linumpy.mosaic.motor) compute_scale_factors() (in module linumpy.intensity.normalization) compute_ssim_2d() (in module linumpy.metrics.image_quality) compute_ssim_2d_gpu() (in module linumpy.gpu.image_quality) compute_ssim_3d() (in module linumpy.metrics.image_quality) compute_ssim_3d_gpu() (in module linumpy.gpu.image_quality)

compute_std_projection() (in module linumpy.gpu.array_ops) compute_summary_statistics() (in module linumpy.metrics) compute_tissue_mask() (in module linumpy.intensity.bias_field) compute_variance_score() (in module linumpy.metrics.image_quality) compute_variance_score_gpu() (in module linumpy.gpu.image_quality) config (linumpy.io.thorlabs.ThorOCT attribute) confocal_psf() (in module linumpy.intensity.psf_model) convert_shifts_to_pixels() (in module linumpy.stack_alignment.units) convert_to_8bit() (in module linumpy.intensity.convert) correct_tile_offset_shifts() (in module linumpy.stack_alignment.filter) cp (in module linumpy.gpu.image_quality) create_directory() (in module linumpy.io) (in module linumpy.io.zarr) create_tempstore() (in module linumpy.io) (in module linumpy.io.zarr) create_tissue_mask() (in module linumpy.gpu.morphology) create_transform() (in module linumpy.registration.transforms) create_transformation_dict() (in module linumpy.io) (in module linumpy.io.zarr) crop_below_interface() (in module linumpy.geometry.crop) crop_first_index (linumpy.io.thorlabs.PreprocessingConfig attribute) crop_second_index (linumpy.io.thorlabs.PreprocessingConfig attribute) crop_tiles() (linumpy.mosaic.grid.MosaicGrid method) crop_volume() (in module linumpy.geometry.crop) crop_z0_whole_slice() (in module linumpy.geometry.crop) cross_correlation() (in module linumpy.registration.phase_correlation) CUPY_AVAILABLE (in module linumpy.gpu) current_x (linumpy.registration.manual.ManualImageCorrection attribute) current_y (linumpy.registration.manual.ManualImageCorrection attribute) current_z (linumpy.registration.manual.ManualImageCorrection attribute) CustomScaler (class in linumpy.io) (class in linumpy.io.zarr)

D

default() (linumpy.metrics.MetricsEncoder method) DEFAULT_N_CPUS (in module linumpy.cli.args) DEFAULT_THRESHOLDS (linumpy.metrics.PipelineMetrics attribute) DEFAULT_TILE_FILE_PATTERN (in module linumpy.mosaic.discovery) (in module linumpy.mosaic.quick_stitch) detect_and_fix_galvo_shift() (in module linumpy.gpu.corrections) detect_calibration_slice() (in module linumpy.metrics.image_quality) detect_galvo_band_in_tile() (in module linumpy.geometry.galvo) detect_galvo_for_slice() (in module linumpy.geometry.galvo) detect_galvo_shift() (in module linumpy.geometry.galvo) detect_interface_z() (in module linumpy.geometry.interface) detect_mosaic() (in module linumpy.mosaic.quick_stitch) detect_shift_units() (in module linumpy.cli.args) (in module linumpy.stack_alignment.units)

dimension (linumpy.microscope.oct.OCT property) directory (linumpy.microscope.oct.OCT attribute) display_overlap() (in module linumpy.imaging.overlay) download_template() (in module linumpy.reference.allen) download_template_ras_aligned() (in module linumpy.reference.allen) downsample (linumpy.registration.manual.ManualImageCorrection attribute) downsample_gpu() (in module linumpy.gpu.bias_field) downscale_factor (linumpy.io.OmeZarrWriter attribute) (linumpy.io.zarr.OmeZarrWriter attribute) draw_cursor() (linumpy.registration.manual.ManualImageCorrection method) dtype (linumpy.io.OmeZarrWriter property) (linumpy.io.zarr.OmeZarrWriter property) (linumpy.mosaic.grid.MosaicGrid attribute)

E

enforce_z_consistency() (in module linumpy.mosaic.stacking) eqhist() (in module linumpy.intensity.normalize) erase_polarization_1 (linumpy.io.thorlabs.PreprocessingConfig attribute) erase_polarization_2 (linumpy.io.thorlabs.PreprocessingConfig attribute) erase_raw_data (linumpy.io.thorlabs.PreprocessingConfig attribute) errors (linumpy.metrics.PipelineMetrics attribute)

estimate_affine_from_pairs() (in module linumpy.mosaic.motor) estimate_lh_profile_parameters() (in module linumpy.geometry.interface) estimate_mosaic_transform() (in module linumpy.registration.transforms) estimate_n_slices_from_zarr() (in module linumpy.imaging.visualization) estimate_psf() (in module linumpy.intensity.psf_model) extract_positions_from_scan() (linumpy.io.thorlabs.ThorOCT static method) extract_psf_parameters_from_mosaic() (in module linumpy.psf.extract)

F

f_r() (in module linumpy.intensity.psf_model) FALSE_STRINGS (in module linumpy.io.slice_config) fft2() (in module linumpy.gpu.fft_ops) fill_holes_2d_and_3d() (in module linumpy.segmentation.brain) filter_outlier_shifts() (in module linumpy.stack_alignment.filter) filter_slices_to_use() (in module linumpy.io.slice_config) filter_step_outliers() (in module linumpy.stack_alignment.filter) finalize() (linumpy.io.AnalysisOmeZarrWriter method) (linumpy.io.OmeZarrWriter method) (linumpy.io.zarr.AnalysisOmeZarrWriter method) (linumpy.io.zarr.OmeZarrWriter method) find_best_overlap_planes() (in module linumpy.mosaic.interpolation) find_best_z() (in module linumpy.registration.refinement)

find_cutting_plane() (in module linumpy.geometry.interface) find_focal_depth() (in module linumpy.intensity.psf_model) find_interface_from_gradient() (in module linumpy.intensity.attenuation) find_tissue_depth() (in module linumpy.geometry.interface) find_tissue_interface() (in module linumpy.geometry.interface) find_z_overlap() (in module linumpy.mosaic.stacking) first_polarization (linumpy.io.thorlabs.ThorOCT attribute) fit_interface() (in module linumpy.geometry.interface) fit_tissue_confocal_model() (in module linumpy.intensity.psf_model) fix_galvo_shift() (in module linumpy.geometry.galvo) (in module linumpy.gpu.corrections) fmt (linumpy.io.OmeZarrWriter attribute) (linumpy.io.zarr.OmeZarrWriter attribute) force_skip_slices() (in module linumpy.io.slice_config)

G

gaussian_filter() (in module linumpy.gpu.morphology) generate_axes_dict() (in module linumpy.io) (in module linumpy.io.zarr) get_3d_psf() (in module linumpy.intensity.psf_model) get_agarose_mask() (in module linumpy.intensity.normalization) get_aline_attenuation() (in module linumpy.intensity.attenuation) get_array_module() (in module linumpy.gpu) get_attenuation_faber2004() (in module linumpy.intensity.attenuation) get_attenuation_vermeer2013() (in module linumpy.intensity.attenuation) get_available_cpus() (in module linumpy.cli.args) get_average_blending_weights() (in module linumpy.mosaic.grid) get_average_volume() (in module linumpy.intensity.psf_model) get_data() (in module linumpy.io.test_data) get_diffusion_blending_weights() (in module linumpy.mosaic.grid) get_extended_attenuation_vermeer2013() (in module linumpy.intensity.attenuation) get_flag() (in module linumpy.io.slice_config) get_flat_agarose_profile() (in module linumpy.intensity.attenuation) get_gradient_attenuation() (in module linumpy.intensity.attenuation) get_heterogeneous_attenuation() (in module linumpy.intensity.attenuation) get_home() (in module linumpy) get_image() (linumpy.mosaic.grid.MosaicGrid method) get_interface_depth_from_mask() (in module linumpy.geometry.interface) get_interface_mask() (in module linumpy.intensity.attenuation) get_largest_cc() (in module linumpy.mosaic.discovery) (in module linumpy.mosaic.quick_stitch) get_largest_component() (in module linumpy.gpu.morphology) get_mosaic_info() (in module linumpy.mosaic.discovery) (in module linumpy.mosaic.quick_stitch) get_neighbor_overlap() (linumpy.mosaic.grid.MosaicGrid method) get_neighbor_overlap_from_pos() (linumpy.mosaic.grid.MosaicGrid method) get_neighbor_tiles() (linumpy.mosaic.grid.MosaicGrid method)

get_neighbors_around_tile() (linumpy.mosaic.grid.MosaicGrid method) get_neighbors_list() (linumpy.mosaic.grid.MosaicGrid method) get_overall_status() (linumpy.metrics.PipelineMetrics method) get_overlap() (in module linumpy.mosaic.overlap) get_overlay_as_rgb() (in module linumpy.imaging.overlay) get_position() (linumpy.mosaic.grid.MosaicGrid method) get_psoct_tiles_ids() (linumpy.io.thorlabs.ThorOCT static method) get_quadratic_interface() (in module linumpy.geometry.interface) get_root() (in module linumpy) get_signal_from_attenuation() (in module linumpy.intensity.attenuation) get_slice_resolutions_from_psf() (in module linumpy.intensity.psf_model) get_smooth_intensity_transition() (in module linumpy.intensity.normalize) get_stitched_image() (linumpy.mosaic.grid.MosaicGrid method) get_tile() (linumpy.mosaic.grid.MosaicGrid method) get_tiles() (linumpy.mosaic.grid.MosaicGrid method) get_tiles_ids() (in module linumpy.mosaic.discovery) (in module linumpy.mosaic.quick_stitch) get_tiles_ids_from_list() (in module linumpy.mosaic.discovery) (in module linumpy.mosaic.quick_stitch) get_view_a() (linumpy.registration.manual.ManualImageCorrection method) get_view_b() (linumpy.registration.manual.ManualImageCorrection method) get_view_c() (linumpy.registration.manual.ManualImageCorrection method) get_vignette() (in module linumpy.intensity.vignette) glm_volume_normalization() (in module linumpy.intensity.psf_model) global_overlap_similarity() (linumpy.mosaic.grid.MosaicGrid method) GPU_AVAILABLE (in module linumpy.gpu) GPU_DEVICE_NAME (in module linumpy.gpu) gpu_info() (in module linumpy.gpu) GPU_MEMORY_GB (in module linumpy.gpu) GPUAcceleratedRegistration (class in linumpy.gpu.registration) gradient_magnitude_alignment() (in module linumpy.registration.refinement) grid_coordinates (linumpy.registration.manual.ManualImageCorrection attribute)

H

header (linumpy.io.thorlabs.ThorOCT attribute)

I

i_profile_piece_wise_model() (in module linumpy.intensity.psf_model) ifft2() (in module linumpy.gpu.fft_ops) image (linumpy.mosaic.grid.MosaicGrid attribute) image_interpolator (linumpy.registration.manual.ManualImageCorrection attribute) imax (linumpy.mosaic.grid.MosaicGrid attribute) imin (linumpy.mosaic.grid.MosaicGrid attribute)

info (linumpy.microscope.oct.OCT attribute) info_filename (linumpy.microscope.oct.OCT attribute) interpolate_average() (in module linumpy.mosaic.interpolation) interpolate_weighted() (in module linumpy.mosaic.interpolation) interpolate_z_morph() (in module linumpy.mosaic.interpolation) is_interpolated() (in module linumpy.io.slice_config) itk_registration() (in module linumpy.registration.sitk)

L

label_connected_components() (in module linumpy.gpu.morphology) linear() (linumpy.io.CustomScaler method) (linumpy.io.zarr.CustomScaler method) linear_homogeneous_profile() (in module linumpy.geometry.interface) linumpy module linumpy.cli module linumpy.cli.args module linumpy.config module linumpy.geometry module linumpy.geometry.crop module linumpy.geometry.galvo module linumpy.geometry.interface module linumpy.geometry.resample module linumpy.geometry.resampling module linumpy.gpu module linumpy.gpu.array_ops module linumpy.gpu.bias_field module linumpy.gpu.bspline module linumpy.gpu.corrections module linumpy.gpu.fft_ops module linumpy.gpu.image_quality module linumpy.gpu.interpolation module linumpy.gpu.morphology module linumpy.gpu.n4 module linumpy.gpu.registration module linumpy.imaging module linumpy.imaging.orientation module linumpy.imaging.overlay module linumpy.imaging.transform module linumpy.imaging.visualization module linumpy.intensity module linumpy.intensity.artifact module linumpy.intensity.attenuation module linumpy.intensity.bias_field module linumpy.intensity.convert module linumpy.intensity.normalization module linumpy.intensity.normalize module linumpy.intensity.psf_model module linumpy.intensity.vignette module linumpy.io module linumpy.io.slice_config module

linumpy.io.test_data module linumpy.io.thorlabs module linumpy.io.zarr module linumpy.metrics module linumpy.metrics.image_quality module linumpy.microscope module linumpy.microscope.oct module linumpy.mosaic module linumpy.mosaic.discovery module linumpy.mosaic.grid module linumpy.mosaic.interpolation module linumpy.mosaic.motor module linumpy.mosaic.overlap module linumpy.mosaic.quick_stitch module linumpy.mosaic.stacking module linumpy.psf module linumpy.psf.extract module linumpy.psf.synthetic module linumpy.reference module linumpy.reference.allen module linumpy.registration module linumpy.registration.manual module linumpy.registration.phase_correlation module linumpy.registration.refinement module linumpy.registration.sitk module linumpy.registration.transforms module linumpy.segmentation module linumpy.segmentation.brain module linumpy.stack_alignment module linumpy.stack_alignment.filter module linumpy.stack_alignment.io module linumpy.stack_alignment.units module LINUMPY_HOME (in module linumpy) LINUMPY_ROOT (in module linumpy) list_gpus() (in module linumpy.gpu) load() (linumpy.io.thorlabs.ThorOCT method) load_and_process() (linumpy.io.thorlabs.ThorOCT method) load_image() (linumpy.microscope.oct.OCT method) load_metrics() (in module linumpy.metrics) load_shifts_csv() (in module linumpy.stack_alignment.io) log_issues() (linumpy.metrics.PipelineMetrics method) logger (in module linumpy.metrics) (in module linumpy.mosaic.interpolation) (in module linumpy.mosaic.motor) (in module linumpy.mosaic.stacking)

M

ManualImageCorrection (class in linumpy.registration.manual) map_coordinates() (in module linumpy.gpu.interpolation) mask_under_interface() (in module linumpy.geometry.crop) match_histogram() (in module linumpy.intensity.normalize) match_histogram_sequentially() (in module linumpy.intensity.normalize) match_shape() (in module linumpy.imaging.transform) max_z (linumpy.registration.manual.ManualImageCorrection attribute) median_filter() (in module linumpy.gpu.morphology) merge_fragments() (in module linumpy.io.slice_config) metric (linumpy.gpu.registration.GPUAcceleratedRegistration attribute) metrics (linumpy.metrics.PipelineMetrics attribute) MetricsEncoder (class in linumpy.metrics) module linumpy linumpy.cli linumpy.cli.args linumpy.config linumpy.geometry linumpy.geometry.crop linumpy.geometry.galvo linumpy.geometry.interface linumpy.geometry.resample linumpy.geometry.resampling linumpy.gpu linumpy.gpu.array_ops linumpy.gpu.bias_field linumpy.gpu.bspline linumpy.gpu.corrections linumpy.gpu.fft_ops linumpy.gpu.image_quality linumpy.gpu.interpolation linumpy.gpu.morphology linumpy.gpu.n4 linumpy.gpu.registration linumpy.imaging linumpy.imaging.orientation linumpy.imaging.overlay linumpy.imaging.transform linumpy.imaging.visualization linumpy.intensity linumpy.intensity.artifact linumpy.intensity.attenuation linumpy.intensity.bias_field linumpy.intensity.convert linumpy.intensity.normalization linumpy.intensity.normalize linumpy.intensity.psf_model linumpy.intensity.vignette linumpy.io linumpy.io.slice_config linumpy.io.test_data linumpy.io.thorlabs linumpy.io.zarr linumpy.metrics linumpy.metrics.image_quality linumpy.microscope linumpy.microscope.oct linumpy.mosaic linumpy.mosaic.discovery linumpy.mosaic.grid linumpy.mosaic.interpolation linumpy.mosaic.motor linumpy.mosaic.overlap linumpy.mosaic.quick_stitch linumpy.mosaic.stacking linumpy.psf linumpy.psf.extract linumpy.psf.synthetic linumpy.reference linumpy.reference.allen linumpy.registration linumpy.registration.manual linumpy.registration.phase_correlation linumpy.registration.refinement linumpy.registration.sitk linumpy.registration.transforms linumpy.segmentation linumpy.segmentation.brain linumpy.stack_alignment linumpy.stack_alignment.filter linumpy.stack_alignment.io linumpy.stack_alignment.units

MosaicGrid (class in linumpy.mosaic.grid)

N

n4_correct() (in module linumpy.intensity.bias_field) n4_correct_gpu() (in module linumpy.gpu.n4) n4_correct_per_section() (in module linumpy.intensity.bias_field) ndim (linumpy.io.OmeZarrWriter property) (linumpy.io.zarr.OmeZarrWriter property) NEXT_REF_LABEL (in module linumpy.registration.manual) NO_REF_LABEL (in module linumpy.registration.manual) normalize() (in module linumpy.imaging.transform) (in module linumpy.intensity.normalize)

normalize_image() (in module linumpy.metrics.image_quality) normalize_image_gpu() (in module linumpy.gpu.image_quality) normalize_minmax() (in module linumpy.gpu.array_ops) normalize_percentile() (in module linumpy.gpu.array_ops) normalize_slice_id() (in module linumpy.io.slice_config) normalize_volume() (in module linumpy.intensity.normalization) numpy_to_sitk_image() (in module linumpy.reference.allen)

O

OCT (class in linumpy.microscope.oct) oct_signal_faber2004_model() (in module linumpy.intensity.attenuation) OmeZarrWriter (class in linumpy.io) (class in linumpy.io.zarr) on_change_offset_a() (linumpy.registration.manual.ManualImageCorrection method) on_change_offset_b() (linumpy.registration.manual.ManualImageCorrection method) on_change_ref_z() (linumpy.registration.manual.ManualImageCorrection method) on_change_scaling() (linumpy.registration.manual.ManualImageCorrection method)

on_change_theta() (linumpy.registration.manual.ManualImageCorrection method) on_change_x() (linumpy.registration.manual.ManualImageCorrection method) on_change_y() (linumpy.registration.manual.ManualImageCorrection method) on_change_z() (linumpy.registration.manual.ManualImageCorrection method) optimize_affine() (linumpy.mosaic.grid.MosaicGrid method) optimize_overlap() (linumpy.mosaic.grid.MosaicGrid method) orient_volume_psoct() (linumpy.io.thorlabs.ThorOCT static method) output_dir (linumpy.metrics.PipelineMetrics attribute) overlap_fraction (linumpy.mosaic.grid.MosaicGrid attribute)

P

pair_wise_phase_correlation() (in module linumpy.registration.phase_correlation) parse_orientation_code() (in module linumpy.imaging.orientation) parse_processes_arg() (in module linumpy.cli.args) path (linumpy.io.thorlabs.ThorOCT attribute) phase_correlation() (in module linumpy.gpu.fft_ops) PipelineMetrics (class in linumpy.metrics)

pool_pairs_and_fit_global_affine() (in module linumpy.mosaic.motor) position (linumpy.microscope.oct.OCT property) position_available (linumpy.microscope.oct.OCT property) PreprocessingConfig (class in linumpy.io.thorlabs) PREV_REF_LABEL (in module linumpy.registration.manual) print_gpu_info() (in module linumpy.gpu) print_gpu_status() (in module linumpy.gpu)

Q

quadratic_interface() (in module linumpy.geometry.interface)

quick_stitch() (in module linumpy.mosaic.quick_stitch)

R

radio_buttons (linumpy.registration.manual.ManualImageCorrection attribute) read() (in module linumpy.io.slice_config) read_header() (in module linumpy.io.slice_config) read_omezarr() (in module linumpy.io) (in module linumpy.io.zarr) read_scan_info() (linumpy.microscope.oct.OCT method) ref_z_mode (linumpy.registration.manual.ManualImageCorrection attribute) refine_z_blend_overlap() (in module linumpy.mosaic.stacking) register_2d_gpu() (in module linumpy.gpu.registration) register_2d_images_sitk() (in module linumpy.registration.sitk) register_3d_rigid_to_allen() (in module linumpy.reference.allen) register_refinement() (in module linumpy.registration.refinement) remove_bottom() (in module linumpy.segmentation.brain) remove_hf_intensity_artifact() (in module linumpy.intensity.artifact) remove_reflection() (in module linumpy.intensity.artifact)

remove_z0_outliers() (in module linumpy.geometry.interface) reorder_resolution() (in module linumpy.imaging.orientation) resample_itk() (in module linumpy.geometry.resample) resample_mosaic_grid() (in module linumpy.geometry.resampling) resample_volume() (in module linumpy.gpu.interpolation) resize() (in module linumpy.gpu.interpolation) resize_image() (linumpy.io.CustomScaler method) (linumpy.io.zarr.CustomScaler method) resolution (linumpy.io.thorlabs.ThorOCT attribute) (linumpy.microscope.oct.OCT property) resolution_is_mm() (in module linumpy.geometry.resampling) return_complex (linumpy.io.thorlabs.PreprocessingConfig attribute) root (linumpy.io.OmeZarrWriter attribute) (linumpy.io.zarr.OmeZarrWriter attribute) rz (linumpy.microscope.oct.OCT attribute)

S

s_current_x (linumpy.registration.manual.ManualImageCorrection attribute) s_current_y (linumpy.registration.manual.ManualImageCorrection attribute) s_current_z (linumpy.registration.manual.ManualImageCorrection attribute) s_offset_a (linumpy.registration.manual.ManualImageCorrection attribute) s_offset_b (linumpy.registration.manual.ManualImageCorrection attribute) s_theta (linumpy.registration.manual.ManualImageCorrection attribute) save() (linumpy.metrics.PipelineMetrics method) save_annotated_views() (in module linumpy.imaging.visualization) save_omezarr() (in module linumpy.io) (in module linumpy.io.zarr) save_orthogonal_views() (in module linumpy.imaging.visualization) save_quickstitch() (in module linumpy.mosaic.quick_stitch) save_results() (linumpy.registration.manual.ManualImageCorrection method) scalebar (linumpy.registration.manual.ManualImageCorrection attribute) second_polarization (linumpy.io.thorlabs.ThorOCT attribute) segment_oct_3d() (in module linumpy.segmentation.brain) select_best_gpu() (in module linumpy.gpu)

select_gpu() (in module linumpy.gpu) set_affine() (linumpy.mosaic.grid.MosaicGrid method) set_blending_method() (linumpy.mosaic.grid.MosaicGrid method) set_tile() (linumpy.mosaic.grid.MosaicGrid method) shape (linumpy.io.OmeZarrWriter attribute) (linumpy.io.zarr.OmeZarrWriter attribute) (linumpy.microscope.oct.OCT property) sharpen_residual() (in module linumpy.gpu.n4) shrink() (in module linumpy.geometry.resample) size_x (linumpy.io.thorlabs.ThorOCT attribute) size_y (linumpy.io.thorlabs.ThorOCT attribute) size_z (linumpy.io.thorlabs.ThorOCT attribute) split_aline() (in module linumpy.intensity.attenuation) stamp() (in module linumpy.io.slice_config) stamp_many() (in module linumpy.io.slice_config) start() (linumpy.registration.manual.ManualImageCorrection method) step_name (linumpy.metrics.PipelineMetrics attribute) synthesize_3d_psf() (in module linumpy.psf.synthetic)

T

T_r() (in module linumpy.intensity.psf_model) ThorOCT (class in linumpy.io.thorlabs) threshold_otsu() (in module linumpy.gpu.array_ops) tile_shape (linumpy.mosaic.grid.MosaicGrid attribute) tile_size_x (linumpy.mosaic.grid.MosaicGrid attribute) tile_size_y (linumpy.mosaic.grid.MosaicGrid attribute) timestamp (linumpy.metrics.PipelineMetrics attribute)

to_cpu() (in module linumpy.gpu) to_dict() (linumpy.metrics.PipelineMetrics method) to_gpu() (in module linumpy.gpu) transform_and_rescale_slice() (in module linumpy.registration.manual) transform_coordinates() (linumpy.registration.manual.ManualImageCorrection method) transform_image() (linumpy.gpu.registration.GPUAcceleratedRegistration method) TRUE_STRINGS (in module linumpy.io.slice_config)

U

upsample_bias_gpu() (in module linumpy.gpu.bias_field)

use_gpu (linumpy.gpu.registration.GPUAcceleratedRegistration attribute)

V

validate_n_levels() (in module linumpy.io) (in module linumpy.io.zarr) vignette_gauss() (in module linumpy.intensity.vignette)

vignette_gauss_lin() (in module linumpy.intensity.vignette) vignette_quad() (in module linumpy.intensity.vignette) volume_normalization() (in module linumpy.intensity.psf_model)

W

warnings (linumpy.metrics.PipelineMetrics attribute)

write() (in module linumpy.io.slice_config)

Z

zarray (linumpy.io.OmeZarrWriter attribute) (linumpy.io.zarr.OmeZarrWriter attribute)