Index

A

affine_initializer_check() (in module unravel.register.affine_initializer_check) affine_initializer_wrapper() (in module unravel.register.affine_initializer) aggregate_files_from_sample_dirs() (in module unravel.utilities.aggregate_files_from_sample_dirs) apply_2D_mean_filter() (in module unravel.image_tools.spatial_averaging) apply_mask_to_ndarray() (in module unravel.voxel_stats.apply_mask)

apply_operation() (in module unravel.image_tools.math) apply_rgb_to_cell() (in module unravel.cluster_stats.legend) AttrDict (class in unravel.core.config) auto_zoom() (in module unravel.allen_institute.abca.merfish.utils) AverageTimePerIterationColumn (class in unravel.core.utils)

B

bias_correction() (in module unravel.register.reg)

build_neuron_subset() (in module unravel.allen_institute.abca.merfish.utils)

C

calculate_fragments() (in module unravel.voxel_stats.vstats) calculate_mean_intensity() (in module unravel.region_stats.rstats_mean_IF) (in module unravel.region_stats.rstats_mean_IF_in_segmented_voxels) calculate_mean_intensity_in_clusters() (in module unravel.cluster_stats.mean_IF) calculate_padded_dimensions() (in module unravel.warp.to_fixed) calculate_regional_densities() (in module unravel.region_stats.rstats) calculate_regional_volumes() (in module unravel.cluster_stats.sunburst) (in module unravel.region_stats.rstats) calculate_resampled_padded_dimensions() (in module unravel.warp.to_native) calculate_top_regions() (in module unravel.cluster_stats.table) can_collapse() (in module unravel.cluster_stats.table) ccf30_to_merfish() (in module unravel.warp.ccf30_to_merfish) cell_type_proportions() (in module unravel.allen_institute.mapmysections.cell_type_proportions) check_fdr_command() (in module unravel.voxel_stats.vstats) clean_tifs_dir() (in module unravel.utilities.clean_tif_dirs) cluster_bbox() (in module unravel.cluster_stats.validation) cluster_bbox_parallel() (in module unravel.cluster_stats.validation) cluster_index() (in module unravel.cluster_stats.fdr) cluster_summary() (in module unravel.cluster_stats.stats_table) cluster_validation_data_df() (in module unravel.cluster_stats.cstats) collapse_hierarchy() (in module unravel.cluster_stats.table) compress_or_decompress_zarr() (in module unravel.image_io.zarr_compress) compute_proportions() (in module unravel.allen_institute.mapmysections.segmentation_summary)

condition_selector() (in module unravel.cluster_stats.cstats) (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) Config (class in unravel.core.config) Configuration (class in unravel.core.config) convert_dtype() (in module unravel.image_io.io_nii) convert_img() (in module unravel.image_io.convert_img) copy_files() (in module unravel.core.utils) copy_nii_header() (in module unravel.warp.to_atlas) copy_specific_tifs() (in module unravel.segment.copy_tifs) copy_stats_files() (in module unravel.cluster_stats.org_data) count_cells() (in module unravel.cluster_stats.validation) count_cells_in_regions() (in module unravel.region_stats.rstats) count_files() (in module unravel.segment.ilastik_pixel_classification) cp() (in module unravel.cluster_stats.org_data) create_design_ttest2() (in module unravel.voxel_stats.vstats) create_outline() (in module unravel.allen_institute.genetic_tools_atlas.auto_crop) crop() (in module unravel.core.img_tools) crop_outer_space() (in module unravel.cluster_stats.validation) CustomHelpAction (class in unravel.core.help_formatter) CustomMofNCompleteColumn (class in unravel.core.utils) CustomTimeElapsedColumn (class in unravel.core.utils) CustomTimeRemainingColumn (class in unravel.core.utils)

D

define_zarr_to_nii_output() (in module unravel.image_io.zarr_to_nii) density_in_cluster() (in module unravel.cluster_stats.validation) density_in_cluster_parallel() (in module unravel.cluster_stats.validation)

detect_outliers() (in module unravel.voxel_stats.other.IF_outliers) difference_of_gaussians() (in module unravel.image_tools.DoG) dilate_mask() (in module unravel.voxel_stats.apply_mask)

E

edit_columns() (in module unravel.tabular.edit_columns) extend_one_side_3d_array() (in module unravel.image_tools.extend)

extract_resolution() (in module unravel.core.img_io) extract_unique_regions_from_file() (in module unravel.cluster_stats.legend)

F

fdr() (in module unravel.cluster_stats.fdr) fdr_range() (in module unravel.cluster_stats.fdr_range) fill_na_with_last_known() (in module unravel.cluster_stats.table) filter_brain_section() (in module unravel.allen_institute.abca.merfish.utils) filter_dataframe() (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) filter_help_output() (unravel.core.help_formatter.RichArgumentParser method) filter_neurons() (in module unravel.allen_institute.abca.merfish.utils) filter_non_neuronal_cells() (in module unravel.allen_institute.abca.sunburst.sunburst) filter_region_ids() (in module unravel.region_stats.rstats_mean_IF_summary)

filter_region_summary() (in module unravel.utilities.region_info) filter_table() (in module unravel.tabular.filter_rows) filter_values() (in module unravel.tabular.unique_values) find_and_copy_files() (in module unravel.utilities.aggregate_files_recursively) find_bounding_box() (in module unravel.core.img_tools) find_incongruent_clusters() (in module unravel.cluster_stats.find_incongruent_clusters) find_matching_directory() (in module unravel.cluster_stats.org_data) find_max_intensity() (in module unravel.image_tools.max) format_argparse_help() (in module unravel.core.help_formatter) format_docstring_for_terminal() (in module unravel.core.help_formatter) format_usage() (unravel.core.help_formatter.RichArgumentParser method) forward_warp() (in module unravel.warp.to_fixed)

G

generate_summary_table() (in module unravel.cluster_stats.prism) generate_sunburst() (in module unravel.cluster_stats.index) generate_wireframe() (in module unravel.image_tools.atlas.wireframe) genes_in_imputed_merfish_data() (in module unravel.allen_institute.abca.merfish.utils) genes_in_merfish_data() (in module unravel.allen_institute.abca.merfish.utils) get_all_region_ids() (in module unravel.region_stats.rstats_mean_IF_summary) get_atlas_region_at_coords() (in module unravel.region_stats.rstats) get_dims_from_tifs() (in module unravel.image_io.metadata) get_extension() (in module unravel.core.utils) get_fill_color() (in module unravel.cluster_stats.table)

get_groups_info() (in module unravel.voxel_stats.vstats) get_max_region_id_from_csvs() (in module unravel.region_stats.rstats_mean_IF_summary) get_pad_percent() (in module unravel.core.utils) get_region_details() (in module unravel.region_stats.rstats_mean_IF_summary) (in module unravel.region_stats.rstats_summary) get_samples() (in module unravel.core.utils) get_seg_voxel_counts() (in module unravel.allen_institute.mapmysections.segmentation_summary) get_stem() (in module unravel.core.utils) get_top_regions_and_percent_vols() (in module unravel.cluster_stats.table) group_hemisphere_data() (in module unravel.cluster_stats.group_bilateral_data)

H

hedges_g() (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute)

hemi_to_LR_avg() (in module unravel.voxel_stats.hemi_to_LR_avg)

I

img_to_points() (in module unravel.image_io.img_to_points)

initialize_progress_bar() (in module unravel.core.utils)

J

join_cell_metadata() (in module unravel.allen_institute.abca.merfish.merfish_slice) join_cluster_colors() (in module unravel.allen_institute.abca.merfish.utils) join_cluster_details() (in module unravel.allen_institute.abca.merfish.utils)

join_expression_to_section() (in module unravel.allen_institute.abca.merfish.utils) join_parcellation_annotation() (in module unravel.allen_institute.abca.merfish.utils) join_parcellation_color() (in module unravel.allen_institute.abca.merfish.utils) join_reconstructed_coords() (in module unravel.allen_institute.abca.merfish.utils)

L

label_IDs() (in module unravel.core.img_tools) legend_prep() (in module unravel.allen_institute.abca.merfish.merfish_slice) load_3D_img() (in module unravel.core.img_io) load_3D_tif() (in module unravel.core.img_io) load_and_prepare_points() (in module unravel.image_io.points_to_img) load_cell_metadata() (in module unravel.allen_institute.abca.merfish.utils) load_config() (in module unravel.core.utils) load_czi() (in module unravel.core.img_io) load_data() (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.region_stats.rstats_mean_IF_summary) load_expression_data() (in module unravel.allen_institute.abca.merfish.utils) load_h5() (in module unravel.core.img_io) (in module unravel.image_io.h5_to_tifs)

load_image_metadata_from_txt() (in module unravel.core.img_io) load_mask() (in module unravel.voxel_stats.apply_mask) load_nii() (in module unravel.core.img_io) load_nii_subset() (in module unravel.core.img_io) load_region_boundaries() (in module unravel.allen_institute.abca.merfish.utils) load_tabular_file() (in module unravel.tabular.utils) load_text_from_file() (in module unravel.core.utils) load_tif() (in module unravel.image_tools.DoG) (in module unravel.image_tools.rb) load_tifs() (in module unravel.core.img_io) load_zarr() (in module unravel.core.img_io) log_command() (in module unravel.core.utils)

M

main() (in module unravel.allen_institute.abca.merfish.merfish_cells_to_nii) (in module unravel.allen_institute.abca.merfish.merfish_slice) (in module unravel.allen_institute.abca.sunburst.mean_expression_color_scale) (in module unravel.allen_institute.abca.sunburst.percent_expression_color_scale) (in module unravel.allen_institute.abca.sunburst.sunburst) (in module unravel.allen_institute.abca.sunburst.sunburst_expression) (in module unravel.allen_institute.abca.sunburst.sunburst_filter_by_expression) (in module unravel.allen_institute.abca.sunburst.sunburst_filter_by_proportion) (in module unravel.allen_institute.genetic_tools_atlas.auto_crop) (in module unravel.allen_institute.genetic_tools_atlas.bbox_crop) (in module unravel.allen_institute.genetic_tools_atlas.org_samples) (in module unravel.allen_institute.genetic_tools_atlas.simplify_metadata) (in module unravel.allen_institute.mapmysections.cell_type_proportions) (in module unravel.allen_institute.mapmysections.cell_type_proportions_concat) (in module unravel.allen_institute.mapmysections.csv_concat_with_source) (in module unravel.allen_institute.mapmysections.segmentation_summary) (in module unravel.cluster_stats.brain_model) (in module unravel.cluster_stats.clusters) (in module unravel.cluster_stats.crop) (in module unravel.cluster_stats.cstats) (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) (in module unravel.cluster_stats.fdr) (in module unravel.cluster_stats.fdr_range) (in module unravel.cluster_stats.find_incongruent_clusters) (in module unravel.cluster_stats.fstat_sig_vx_mask) (in module unravel.cluster_stats.group_bilateral_data) (in module unravel.cluster_stats.index) (in module unravel.cluster_stats.legend) (in module unravel.cluster_stats.mean_IF) (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.cluster_stats.org_data) (in module unravel.cluster_stats.prism) (in module unravel.cluster_stats.recursively_mirror_rev_cluster_indices) (in module unravel.cluster_stats.stats_table) (in module unravel.cluster_stats.summary) (in module unravel.cluster_stats.summary_config) (in module unravel.cluster_stats.sunburst) (in module unravel.cluster_stats.table) (in module unravel.cluster_stats.validation) (in module unravel.image_io.convert_img) (in module unravel.image_io.h5_to_tifs) (in module unravel.image_io.img_to_npy) (in module unravel.image_io.img_to_points) (in module unravel.image_io.io_nii) (in module unravel.image_io.metadata) (in module unravel.image_io.nii_hd) (in module unravel.image_io.nii_info) (in module unravel.image_io.nii_to_tifs) (in module unravel.image_io.nii_to_zarr) (in module unravel.image_io.points_to_img) (in module unravel.image_io.reorient_nii) (in module unravel.image_io.tif_to_tifs) (in module unravel.image_io.zarr_compress) (in module unravel.image_io.zarr_to_nii) (in module unravel.image_tools.atlas.relabel_nii) (in module unravel.image_tools.atlas.wireframe) (in module unravel.image_tools.avg) (in module unravel.image_tools.bbox) (in module unravel.image_tools.DoG) (in module unravel.image_tools.extend) (in module unravel.image_tools.math) (in module unravel.image_tools.max) (in module unravel.image_tools.modify_labels) (in module unravel.image_tools.pad) (in module unravel.image_tools.rb) (in module unravel.image_tools.resample) (in module unravel.image_tools.resample_points) (in module unravel.image_tools.spatial_averaging) (in module unravel.image_tools.transpose_axes) (in module unravel.image_tools.unique_intensities) (in module unravel.region_stats.rstats) (in module unravel.region_stats.rstats_mean_IF) (in module unravel.region_stats.rstats_mean_IF_in_segmented_voxels) (in module unravel.region_stats.rstats_mean_IF_summary) (in module unravel.region_stats.rstats_summary) (in module unravel.register.affine_initializer) (in module unravel.register.affine_initializer_check) (in module unravel.register.reg) (in module unravel.register.reg_check) (in module unravel.register.reg_check_brain_mask) (in module unravel.register.reg_check_fsleyes) (in module unravel.register.reg_prep) (in module unravel.segment.brain_mask) (in module unravel.segment.copy_tifs) (in module unravel.segment.ilastik_pixel_classification) (in module unravel.segment.labels_to_masks) (in module unravel.tabular.columns) (in module unravel.tabular.edit_columns) (in module unravel.tabular.filter_rows) (in module unravel.tabular.key_value_to_table) (in module unravel.tabular.unique_values) (in module unravel.unravel_commands) (in module unravel.utilities.aggregate_files_from_sample_dirs) (in module unravel.utilities.aggregate_files_recursively) (in module unravel.utilities.clean_tif_dirs) (in module unravel.utilities.get_samples) (in module unravel.utilities.points_compressor) (in module unravel.utilities.prepend_conditions) (in module unravel.utilities.process_samples) (in module unravel.utilities.region_info) (in module unravel.utilities.rename) (in module unravel.utilities.toggle_samples) (in module unravel.voxel_stats.apply_mask) (in module unravel.voxel_stats.hemi_to_LR_avg) (in module unravel.voxel_stats.mirror) (in module unravel.voxel_stats.other.IF_outliers) (in module unravel.voxel_stats.other.r_to_p) (in module unravel.voxel_stats.vstats) (in module unravel.voxel_stats.vstats_check_fsleyes) (in module unravel.voxel_stats.vstats_prep) (in module unravel.voxel_stats.whole_to_LR_avg) (in module unravel.voxel_stats.z_score) (in module unravel.voxel_stats.z_score_cwd) (in module unravel.warp.ccf30_to_merfish) (in module unravel.warp.points_to_atlas) (in module unravel.warp.to_atlas) (in module unravel.warp.to_fixed) (in module unravel.warp.to_native) (in module unravel.warp.warp) match_files() (in module unravel.core.utils) mean_intensity_in_brain() (in module unravel.voxel_stats.apply_mask) mean_intensity_within_mask() (in module unravel.voxel_stats.other.IF_outliers) mean_std_count() (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) merfish_cells_to_img() (in module unravel.allen_institute.abca.merfish.merfish_cells_to_nii) metadata() (in module unravel.core.img_io) metadata_from_h5() (in module unravel.image_io.h5_to_tifs) mirror() (in module unravel.voxel_stats.mirror)

module unravel.allen_institute.abca.merfish.merfish_cells_to_nii unravel.allen_institute.abca.merfish.merfish_slice unravel.allen_institute.abca.merfish.utils unravel.allen_institute.abca.sunburst.mean_expression_color_scale unravel.allen_institute.abca.sunburst.percent_expression_color_scale unravel.allen_institute.abca.sunburst.sunburst unravel.allen_institute.abca.sunburst.sunburst_expression unravel.allen_institute.abca.sunburst.sunburst_filter_by_expression unravel.allen_institute.abca.sunburst.sunburst_filter_by_proportion unravel.allen_institute.genetic_tools_atlas.auto_crop unravel.allen_institute.genetic_tools_atlas.bbox_crop unravel.allen_institute.genetic_tools_atlas.org_samples unravel.allen_institute.genetic_tools_atlas.simplify_metadata unravel.allen_institute.mapmysections.cell_type_proportions unravel.allen_institute.mapmysections.cell_type_proportions_concat unravel.allen_institute.mapmysections.csv_concat_with_source unravel.allen_institute.mapmysections.segmentation_summary unravel.cluster_stats.brain_model unravel.cluster_stats.clusters unravel.cluster_stats.crop unravel.cluster_stats.cstats unravel.cluster_stats.effect_sizes.effect_sizes unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative unravel.cluster_stats.fdr unravel.cluster_stats.fdr_range unravel.cluster_stats.find_incongruent_clusters unravel.cluster_stats.fstat_sig_vx_mask unravel.cluster_stats.group_bilateral_data unravel.cluster_stats.index unravel.cluster_stats.legend unravel.cluster_stats.mean_IF unravel.cluster_stats.mean_IF_summary unravel.cluster_stats.org_data unravel.cluster_stats.prism unravel.cluster_stats.recursively_mirror_rev_cluster_indices unravel.cluster_stats.stats_table unravel.cluster_stats.summary unravel.cluster_stats.summary_config unravel.cluster_stats.sunburst unravel.cluster_stats.table unravel.cluster_stats.validation unravel.core.config unravel.core.help_formatter unravel.core.img_io unravel.core.img_tools unravel.core.utils unravel.image_io.convert_img unravel.image_io.h5_to_tifs unravel.image_io.img_to_npy unravel.image_io.img_to_points unravel.image_io.io_nii unravel.image_io.metadata unravel.image_io.nii_hd unravel.image_io.nii_info unravel.image_io.nii_to_tifs unravel.image_io.nii_to_zarr unravel.image_io.points_to_img unravel.image_io.reorient_nii unravel.image_io.tif_to_tifs unravel.image_io.zarr_compress unravel.image_io.zarr_to_nii unravel.image_tools.atlas.relabel_nii unravel.image_tools.atlas.wireframe unravel.image_tools.avg unravel.image_tools.bbox unravel.image_tools.DoG unravel.image_tools.extend unravel.image_tools.math unravel.image_tools.max unravel.image_tools.modify_labels unravel.image_tools.pad unravel.image_tools.rb unravel.image_tools.resample unravel.image_tools.resample_points unravel.image_tools.spatial_averaging unravel.image_tools.transpose_axes unravel.image_tools.unique_intensities unravel.region_stats.rstats unravel.region_stats.rstats_mean_IF unravel.region_stats.rstats_mean_IF_in_segmented_voxels unravel.region_stats.rstats_mean_IF_summary unravel.region_stats.rstats_summary unravel.register.affine_initializer unravel.register.affine_initializer_check unravel.register.reg unravel.register.reg_check unravel.register.reg_check_brain_mask unravel.register.reg_check_fsleyes unravel.register.reg_prep unravel.segment.brain_mask unravel.segment.copy_tifs unravel.segment.ilastik_pixel_classification unravel.segment.labels_to_masks unravel.tabular.columns unravel.tabular.edit_columns unravel.tabular.filter_rows unravel.tabular.key_value_to_table unravel.tabular.unique_values unravel.tabular.utils unravel.unravel_commands unravel.utilities.aggregate_files_from_sample_dirs unravel.utilities.aggregate_files_recursively unravel.utilities.clean_tif_dirs unravel.utilities.get_samples unravel.utilities.points_compressor unravel.utilities.prepend_conditions unravel.utilities.process_samples unravel.utilities.region_info unravel.utilities.rename unravel.utilities.toggle_samples unravel.voxel_stats.apply_mask unravel.voxel_stats.hemi_to_LR_avg unravel.voxel_stats.mirror unravel.voxel_stats.other.IF_outliers unravel.voxel_stats.other.r_to_p unravel.voxel_stats.vstats unravel.voxel_stats.vstats_check_fsleyes unravel.voxel_stats.vstats_prep unravel.voxel_stats.whole_to_LR_avg unravel.voxel_stats.z_score unravel.voxel_stats.z_score_cwd unravel.warp.ccf30_to_merfish unravel.warp.points_to_atlas unravel.warp.to_atlas unravel.warp.to_fixed unravel.warp.to_native unravel.warp.warp

N

nii_axis_codes() (in module unravel.image_io.nii_info) nii_path_or_nii() (in module unravel.core.img_io) nii_to_ndarray() (in module unravel.core.img_io) (in module unravel.image_io.nii_to_zarr)

nii_to_tifs() (in module unravel.image_io.nii_to_tifs) nii_voxel_size() (in module unravel.core.img_io)

O

org_samples() (in module unravel.allen_institute.genetic_tools_atlas.org_samples)

organize_validation_data() (in module unravel.cluster_stats.org_data)

P

pack_points() (in module unravel.utilities.points_compressor) pad() (in module unravel.core.img_tools) parse_args() (in module unravel.allen_institute.abca.merfish.merfish_cells_to_nii) (in module unravel.allen_institute.abca.merfish.merfish_slice) (in module unravel.allen_institute.abca.sunburst.mean_expression_color_scale) (in module unravel.allen_institute.abca.sunburst.percent_expression_color_scale) (in module unravel.allen_institute.abca.sunburst.sunburst) (in module unravel.allen_institute.abca.sunburst.sunburst_expression) (in module unravel.allen_institute.abca.sunburst.sunburst_filter_by_expression) (in module unravel.allen_institute.abca.sunburst.sunburst_filter_by_proportion) (in module unravel.allen_institute.genetic_tools_atlas.auto_crop) (in module unravel.allen_institute.genetic_tools_atlas.bbox_crop) (in module unravel.allen_institute.genetic_tools_atlas.org_samples) (in module unravel.allen_institute.genetic_tools_atlas.simplify_metadata) (in module unravel.allen_institute.mapmysections.cell_type_proportions) (in module unravel.allen_institute.mapmysections.cell_type_proportions_concat) (in module unravel.allen_institute.mapmysections.csv_concat_with_source) (in module unravel.allen_institute.mapmysections.segmentation_summary) (in module unravel.cluster_stats.brain_model) (in module unravel.cluster_stats.clusters) (in module unravel.cluster_stats.crop) (in module unravel.cluster_stats.cstats) (in module unravel.cluster_stats.effect_sizes.effect_sizes) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute) (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) (in module unravel.cluster_stats.fdr) (in module unravel.cluster_stats.fdr_range) (in module unravel.cluster_stats.find_incongruent_clusters) (in module unravel.cluster_stats.fstat_sig_vx_mask) (in module unravel.cluster_stats.group_bilateral_data) (in module unravel.cluster_stats.index) (in module unravel.cluster_stats.legend) (in module unravel.cluster_stats.mean_IF) (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.cluster_stats.org_data) (in module unravel.cluster_stats.prism) (in module unravel.cluster_stats.recursively_mirror_rev_cluster_indices) (in module unravel.cluster_stats.stats_table) (in module unravel.cluster_stats.summary) (in module unravel.cluster_stats.summary_config) (in module unravel.cluster_stats.sunburst) (in module unravel.cluster_stats.table) (in module unravel.cluster_stats.validation) (in module unravel.image_io.convert_img) (in module unravel.image_io.h5_to_tifs) (in module unravel.image_io.img_to_npy) (in module unravel.image_io.img_to_points) (in module unravel.image_io.io_nii) (in module unravel.image_io.metadata) (in module unravel.image_io.nii_hd) (in module unravel.image_io.nii_info) (in module unravel.image_io.nii_to_tifs) (in module unravel.image_io.nii_to_zarr) (in module unravel.image_io.points_to_img) (in module unravel.image_io.reorient_nii) (in module unravel.image_io.tif_to_tifs) (in module unravel.image_io.zarr_compress) (in module unravel.image_io.zarr_to_nii) (in module unravel.image_tools.atlas.relabel_nii) (in module unravel.image_tools.atlas.wireframe) (in module unravel.image_tools.avg) (in module unravel.image_tools.bbox) (in module unravel.image_tools.DoG) (in module unravel.image_tools.extend) (in module unravel.image_tools.math) (in module unravel.image_tools.max) (in module unravel.image_tools.modify_labels) (in module unravel.image_tools.pad) (in module unravel.image_tools.rb) (in module unravel.image_tools.resample) (in module unravel.image_tools.resample_points) (in module unravel.image_tools.spatial_averaging) (in module unravel.image_tools.transpose_axes) (in module unravel.image_tools.unique_intensities) (in module unravel.region_stats.rstats) (in module unravel.region_stats.rstats_mean_IF) (in module unravel.region_stats.rstats_mean_IF_in_segmented_voxels) (in module unravel.region_stats.rstats_mean_IF_summary) (in module unravel.region_stats.rstats_summary) (in module unravel.register.affine_initializer) (in module unravel.register.affine_initializer_check) (in module unravel.register.reg) (in module unravel.register.reg_check) (in module unravel.register.reg_check_brain_mask) (in module unravel.register.reg_check_fsleyes) (in module unravel.register.reg_prep) (in module unravel.segment.brain_mask) (in module unravel.segment.copy_tifs) (in module unravel.segment.ilastik_pixel_classification) (in module unravel.segment.labels_to_masks) (in module unravel.tabular.columns) (in module unravel.tabular.edit_columns) (in module unravel.tabular.filter_rows) (in module unravel.tabular.key_value_to_table) (in module unravel.tabular.unique_values) (in module unravel.unravel_commands) (in module unravel.utilities.aggregate_files_from_sample_dirs) (in module unravel.utilities.aggregate_files_recursively) (in module unravel.utilities.clean_tif_dirs) (in module unravel.utilities.get_samples) (in module unravel.utilities.points_compressor) (in module unravel.utilities.prepend_conditions) (in module unravel.utilities.process_samples) (in module unravel.utilities.region_info) (in module unravel.utilities.rename) (in module unravel.utilities.toggle_samples) (in module unravel.voxel_stats.apply_mask) (in module unravel.voxel_stats.hemi_to_LR_avg) (in module unravel.voxel_stats.mirror) (in module unravel.voxel_stats.other.IF_outliers) (in module unravel.voxel_stats.other.r_to_p) (in module unravel.voxel_stats.vstats) (in module unravel.voxel_stats.vstats_check_fsleyes) (in module unravel.voxel_stats.vstats_prep) (in module unravel.voxel_stats.whole_to_LR_avg) (in module unravel.voxel_stats.z_score) (in module unravel.voxel_stats.z_score_cwd) (in module unravel.warp.ccf30_to_merfish) (in module unravel.warp.points_to_atlas) (in module unravel.warp.to_atlas) (in module unravel.warp.to_fixed) (in module unravel.warp.to_native) (in module unravel.warp.warp)

parse_color_argument() (in module unravel.region_stats.rstats_summary) perform_t_tests() (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.region_stats.rstats_mean_IF_summary) perform_tukey_test() (in module unravel.cluster_stats.cstats) pixel_classification() (in module unravel.core.img_tools) plot_data() (in module unravel.cluster_stats.mean_IF_summary) (in module unravel.region_stats.rstats_mean_IF_summary) plot_slice_color() (in module unravel.allen_institute.abca.merfish.utils) plot_slice_gene() (in module unravel.allen_institute.abca.merfish.utils) points_compressor() (in module unravel.utilities.points_compressor) points_to_img() (in module unravel.image_io.points_to_img) prepare_cells_table() (in module unravel.allen_institute.abca.merfish.utils) prepend_conditions() (in module unravel.utilities.prepend_conditions) print_func_name_args_times() (in module unravel.core.utils) print_help() (unravel.core.help_formatter.RichArgumentParser method) print_metadata() (in module unravel.image_io.metadata) print_values() (in module unravel.tabular.unique_values) process_and_plot_data() (in module unravel.region_stats.rstats_summary) process_and_write_line() (in module unravel.allen_institute.mapmysections.segmentation_summary) process_fdr_and_clusters() (in module unravel.cluster_stats.fdr) process_file() (in module unravel.cluster_stats.recursively_mirror_rev_cluster_indices) process_intensity() (in module unravel.image_tools.atlas.wireframe) process_samples() (in module unravel.utilities.process_samples) process_slice() (in module unravel.core.img_tools)

R

r_to_z() (in module unravel.voxel_stats.other.r_to_p) reg_prep() (in module unravel.register.reg_prep) relative_hedges_g() (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative) remove_zero_intensity_regions() (in module unravel.region_stats.rstats_mean_IF_summary) rename_files() (in module unravel.utilities.rename) rename_items() (in module unravel.utilities.prepend_conditions) render() (unravel.core.utils.AverageTimePerIterationColumn method) (unravel.core.utils.CustomMofNCompleteColumn method) (unravel.core.utils.CustomTimeElapsedColumn method) (unravel.core.utils.CustomTimeRemainingColumn method) reorient_axes() (in module unravel.core.img_tools) reorient_ndarray() (in module unravel.core.img_tools) reorient_ndarray2() (in module unravel.core.img_tools) reorient_nii() (in module unravel.image_io.reorient_nii)

resample() (in module unravel.core.img_tools) resample_and_convert_points() (in module unravel.image_tools.resample_points) reshape_key_value_blocks() (in module unravel.tabular.key_value_to_table) resolve_path() (in module unravel.core.img_io) retain_labels() (in module unravel.image_tools.modify_labels) return_3D_img() (in module unravel.core.img_io) reverse_clusters() (in module unravel.cluster_stats.fdr) reverse_reorient_axes() (in module unravel.core.img_tools) RichArgumentParser (class in unravel.core.help_formatter) rolling_ball_subtraction() (in module unravel.image_tools.rb) rolling_ball_subtraction_opencv_parallel() (in module unravel.core.img_tools) run_in_parallel() (in module unravel.image_io.zarr_compress) run_randomise_parallel() (in module unravel.voxel_stats.vstats) run_script() (in module unravel.cluster_stats.summary) run_with_timeout() (in module unravel.register.affine_initializer)

S

save_3D_img() (in module unravel.core.img_io) save_as_h5() (in module unravel.core.img_io) save_as_nii() (in module unravel.core.img_io) (in module unravel.image_io.zarr_to_nii) save_as_tifs() (in module unravel.core.img_io) (in module unravel.image_io.h5_to_tifs) save_as_zarr() (in module unravel.core.img_io) (in module unravel.image_io.nii_to_zarr) save_cropped_img() (in module unravel.cluster_stats.crop) save_labels_as_masks() (in module unravel.segment.ilastik_pixel_classification) (in module unravel.segment.labels_to_masks) save_metadata_to_file() (in module unravel.core.img_io) save_tabular_file() (in module unravel.tabular.utils) save_tif() (in module unravel.image_tools.DoG) (in module unravel.image_tools.rb)

scale_bool_to_full_res() (in module unravel.voxel_stats.apply_mask) scale_to_full_res() (in module unravel.warp.to_native) select_gene() (in module unravel.allen_institute.abca.merfish.utils) set_labels() (in module unravel.image_tools.modify_labels) slice_index_dict() (in module unravel.allen_institute.abca.merfish.utils) SM (class in unravel.core.help_formatter) smart_float_format() (in module unravel.cluster_stats.fdr_range) sort_samples() (in module unravel.cluster_stats.prism) sort_sunburst_hierarchy() (in module unravel.cluster_stats.table) spatial_average_2D() (in module unravel.image_tools.spatial_averaging) spatial_average_3D() (in module unravel.image_tools.spatial_averaging) split_clusters_based_on_effect() (in module unravel.cluster_stats.fdr) summarize_points() (in module unravel.utilities.points_compressor) summarize_significance() (in module unravel.region_stats.rstats_summary) sunburst() (in module unravel.cluster_stats.sunburst) SuppressMetavar (class in unravel.core.help_formatter)

T

threshold_image() (in module unravel.image_tools.math) threshold_points_by_region_id() (in module unravel.image_io.points_to_img) tissue_mask_to_atlas_space() (in module unravel.voxel_stats.z_score)

to_atlas() (in module unravel.warp.to_atlas) to_native() (in module unravel.warp.to_native) transform_nii_affine() (in module unravel.image_io.reorient_nii) transpose_img() (in module unravel.image_tools.transpose_axes)

U

undo_fill_with_original() (in module unravel.cluster_stats.table) unpack_points() (in module unravel.utilities.points_compressor) unravel.allen_institute.abca.merfish.merfish_cells_to_nii module unravel.allen_institute.abca.merfish.merfish_slice module unravel.allen_institute.abca.merfish.utils module unravel.allen_institute.abca.sunburst.mean_expression_color_scale module unravel.allen_institute.abca.sunburst.percent_expression_color_scale module unravel.allen_institute.abca.sunburst.sunburst module unravel.allen_institute.abca.sunburst.sunburst_expression module unravel.allen_institute.abca.sunburst.sunburst_filter_by_expression module unravel.allen_institute.abca.sunburst.sunburst_filter_by_proportion module unravel.allen_institute.genetic_tools_atlas.auto_crop module unravel.allen_institute.genetic_tools_atlas.bbox_crop module unravel.allen_institute.genetic_tools_atlas.org_samples module unravel.allen_institute.genetic_tools_atlas.simplify_metadata module unravel.allen_institute.mapmysections.cell_type_proportions module unravel.allen_institute.mapmysections.cell_type_proportions_concat module unravel.allen_institute.mapmysections.csv_concat_with_source module unravel.allen_institute.mapmysections.segmentation_summary module unravel.cluster_stats.brain_model module unravel.cluster_stats.clusters module unravel.cluster_stats.crop module unravel.cluster_stats.cstats module unravel.cluster_stats.effect_sizes.effect_sizes module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative module unravel.cluster_stats.fdr module unravel.cluster_stats.fdr_range module unravel.cluster_stats.find_incongruent_clusters module unravel.cluster_stats.fstat_sig_vx_mask module unravel.cluster_stats.group_bilateral_data module unravel.cluster_stats.index module unravel.cluster_stats.legend module unravel.cluster_stats.mean_IF module unravel.cluster_stats.mean_IF_summary module unravel.cluster_stats.org_data module unravel.cluster_stats.prism module unravel.cluster_stats.recursively_mirror_rev_cluster_indices module unravel.cluster_stats.stats_table module unravel.cluster_stats.summary module unravel.cluster_stats.summary_config module unravel.cluster_stats.sunburst module unravel.cluster_stats.table module unravel.cluster_stats.validation module unravel.core.config module unravel.core.help_formatter module unravel.core.img_io module unravel.core.img_tools module unravel.core.utils module unravel.image_io.convert_img module unravel.image_io.h5_to_tifs module unravel.image_io.img_to_npy module unravel.image_io.img_to_points module unravel.image_io.io_nii module unravel.image_io.metadata module unravel.image_io.nii_hd module unravel.image_io.nii_info module unravel.image_io.nii_to_tifs module unravel.image_io.nii_to_zarr module unravel.image_io.points_to_img module unravel.image_io.reorient_nii module unravel.image_io.tif_to_tifs module unravel.image_io.zarr_compress module unravel.image_io.zarr_to_nii module unravel.image_tools.atlas.relabel_nii module unravel.image_tools.atlas.wireframe module

unravel.image_tools.avg module unravel.image_tools.bbox module unravel.image_tools.DoG module unravel.image_tools.extend module unravel.image_tools.math module unravel.image_tools.max module unravel.image_tools.modify_labels module unravel.image_tools.pad module unravel.image_tools.rb module unravel.image_tools.resample module unravel.image_tools.resample_points module unravel.image_tools.spatial_averaging module unravel.image_tools.transpose_axes module unravel.image_tools.unique_intensities module unravel.region_stats.rstats module unravel.region_stats.rstats_mean_IF module unravel.region_stats.rstats_mean_IF_in_segmented_voxels module unravel.region_stats.rstats_mean_IF_summary module unravel.region_stats.rstats_summary module unravel.register.affine_initializer module unravel.register.affine_initializer_check module unravel.register.reg module unravel.register.reg_check module unravel.register.reg_check_brain_mask module unravel.register.reg_check_fsleyes module unravel.register.reg_prep module unravel.segment.brain_mask module unravel.segment.copy_tifs module unravel.segment.ilastik_pixel_classification module unravel.segment.labels_to_masks module unravel.tabular.columns module unravel.tabular.edit_columns module unravel.tabular.filter_rows module unravel.tabular.key_value_to_table module unravel.tabular.unique_values module unravel.tabular.utils module unravel.unravel_commands module unravel.utilities.aggregate_files_from_sample_dirs module unravel.utilities.aggregate_files_recursively module unravel.utilities.clean_tif_dirs module unravel.utilities.get_samples module unravel.utilities.points_compressor module unravel.utilities.prepend_conditions module unravel.utilities.process_samples module unravel.utilities.region_info module unravel.utilities.rename module unravel.utilities.toggle_samples module unravel.voxel_stats.apply_mask module unravel.voxel_stats.hemi_to_LR_avg module unravel.voxel_stats.mirror module unravel.voxel_stats.other.IF_outliers module unravel.voxel_stats.other.r_to_p module unravel.voxel_stats.vstats module unravel.voxel_stats.vstats_check_fsleyes module unravel.voxel_stats.vstats_prep module unravel.voxel_stats.whole_to_LR_avg module unravel.voxel_stats.z_score module unravel.voxel_stats.z_score_cwd module unravel.warp.ccf30_to_merfish module unravel.warp.points_to_atlas module unravel.warp.to_atlas module unravel.warp.to_fixed module unravel.warp.to_native module unravel.warp.warp module

V

valid_clusters_t_test() (in module unravel.cluster_stats.cstats) verbose (unravel.core.config.Configuration attribute)

verbose_end_msg() (in module unravel.core.utils) verbose_start_msg() (in module unravel.core.utils)

W

warp() (in module unravel.warp.warp) whole_to_LR_avg() (in module unravel.voxel_stats.whole_to_LR_avg)

write_to_csv() (in module unravel.cluster_stats.mean_IF) (in module unravel.region_stats.rstats_mean_IF) (in module unravel.region_stats.rstats_mean_IF_in_segmented_voxels)

Z

z_score() (in module unravel.voxel_stats.z_score) z_score_img() (in module unravel.voxel_stats.z_score_cwd) z_score_mask() (in module unravel.voxel_stats.z_score)

z_to_p() (in module unravel.voxel_stats.other.r_to_p) zarr_level_to_tifs() (in module unravel.core.img_io) zarr_to_ndarray() (in module unravel.image_io.zarr_to_nii)