├── .github └── workflows │ └── deploy_docs.yml ├── .gitignore ├── LICENSE ├── README.md ├── _other ├── _legacy │ ├── CCF30_to_gubra.py │ ├── gubra_to_CCF30.py │ └── gubra_to_CCF50.py ├── _testing │ ├── _test.ini │ ├── _test.py │ ├── _test2.py │ └── _test3.py ├── drafts │ ├── 360_animation.py │ ├── ANOVA_draft.py │ ├── _ABCA │ │ ├── CCF30_to_MERFISH30.py │ │ ├── RNAseq_dot_plot.py │ │ ├── RNAseq_dot_plot_based_on_merfish_dot_plot.py │ │ ├── RNAseq_expression_in_cell_types.py │ │ ├── RNAseq_expression_in_mice.py │ │ ├── RNAseq_expression_in_mice_heatmap.py │ │ ├── RNAseq_expression_in_mice_neurons_astro_ug.py │ │ ├── RNAseq_expression_in_mouse_MSNs.py │ │ ├── RNAseq_expression_in_mouse_cells_test.py │ │ ├── RNAseq_expression_in_neurons_astro_ug.py │ │ ├── _other │ │ │ ├── mixedlm.py │ │ │ ├── mixedlm_LSFM_csv.py │ │ │ ├── mixedlm_MERFISH_csv.py │ │ │ ├── mixedlm_combine_csv.py │ │ │ └── mixedlm_global_relationship.py │ │ ├── correlation_comparison.py │ │ ├── correlation_parallel.py │ │ ├── correlation_parallel_to_nii.py │ │ ├── correlation_permutation.py │ │ ├── correlation_plot.py │ │ ├── merfish_dot_plot.py │ │ ├── merfish_dot_plot_legend.py │ │ ├── merfish_filter_expression.py │ │ ├── merfish_heatmap.py │ │ ├── merfish_imputed_genes.py │ │ └── merfish_resample.py │ ├── _abc_atlas_tutorials │ │ └── Allen_RNAseq_expression_in_mice_tutorial.py │ ├── _nii │ │ └── variance.py │ ├── _project_specific │ │ ├── _angiography │ │ │ └── pngs_to_mip_tif.py │ │ ├── _ketamine │ │ │ ├── merfish_cell_types_across_slices.py │ │ │ └── merfish_expression_across_img_slices.py │ │ └── _oliver │ │ │ ├── parquet_groupby.py │ │ │ ├── parquet_to_nii.py │ │ │ ├── parquet_unique_intensities.py │ │ │ ├── parquet_unique_values.py │ │ │ └── voxel_info.py │ ├── cluster_ttests.py │ ├── collapse_atlas.py │ ├── cstats_adding_stats_options.py │ ├── csv_to_nii.py │ ├── ez_thr.py │ ├── filter_objects_by_size.py │ ├── fsleyes.py │ ├── h5_to_tifs_batch.py │ ├── img_stats_draft.py │ ├── load_czi_subset.py │ ├── mouse_connectivity │ │ ├── image_download_draft_in_progress.py │ │ └── projection_densities.py │ ├── native_cluster_crop.py │ ├── native_cluster_crop_legacy.py │ ├── native_clusters_crop.py │ ├── native_clusters_mean_IF_in_seg.py │ ├── nii_to_csv.py │ ├── prep_ilastik_h5.py │ ├── rstats_mean_IF_summary_v2.py │ ├── setup.py │ ├── sexes_to_cluster_densities_csv.py │ └── volcano.py ├── example_scripts │ ├── example_script_for_processing_samples.py │ └── example_script_for_processing_samples_w_comments.py ├── fsleyes_luts │ ├── WHS_SD_rat_atlas_v4.lut │ ├── ccfv3_2017.lut │ ├── ccfv3_2020.lut │ └── instructions_for_setting_up_LUTs_for_FSLeyes.txt ├── images │ └── UNRAVEL_logo.png └── uncommon_scripts │ └── brain_mask_outline.py ├── pyproject.toml ├── tests └── allen_institute │ └── abca │ └── merfish │ └── test_utils.py └── unravel ├── __init__.py ├── allen_institute ├── abca │ ├── cache.py │ ├── merfish │ │ ├── gene_catalog.py │ │ ├── merfish.py │ │ ├── merfish_cells_to_nii.py │ │ ├── merfish_expression_to_nii.py │ │ ├── merfish_filter.py │ │ ├── merfish_filter_by_mask.py │ │ ├── merfish_join_gene.py │ │ ├── merfish_slice.py │ │ └── utils.py │ ├── scRNA_seq │ │ ├── expression.py │ │ ├── filter.py │ │ └── join_gene.py │ └── sunburst │ │ ├── mean_expression_color_scale.py │ │ ├── percent_expression_color_scale.py │ │ ├── sunburst.py │ │ ├── sunburst_expression.py │ │ ├── sunburst_filter_by_expression.py │ │ └── sunburst_filter_by_proportion.py ├── genetic_tools_atlas │ ├── SpecimenMetadata_subset.csv │ ├── auto_crop.py │ ├── bbox_crop.py │ ├── download.py │ ├── org_samples.py │ └── simplify_metadata.py └── mapmysections │ ├── cell_type_proportions.py │ ├── cell_type_proportions_concat.py │ ├── csv_concat_with_source.py │ ├── segmentation_summary.py │ └── soma_ratio.py ├── cluster_stats ├── __init__.py ├── brain_model.py ├── cluster_summary.ini ├── clusters.py ├── crop.py ├── cstats.py ├── drop_clusters.py ├── effect_sizes │ ├── __init__.py │ ├── effect_sizes.py │ ├── effect_sizes_by_sex__absolute.py │ └── effect_sizes_by_sex__relative.py ├── fdr.py ├── fdr_range.py ├── find_incongruent_clusters.py ├── fstat_sig_vx_mask.py ├── group_bilateral_data.py ├── index.py ├── legend.py ├── mean_IF.py ├── mean_IF_summary.py ├── org_data.py ├── prism.py ├── recursively_mirror_rev_cluster_indices.py ├── stats_table.py ├── summary.py ├── summary_config.py ├── sunburst.py ├── table.py └── validation.py ├── core ├── __init__.py ├── config.py ├── csvs │ ├── ABCA │ │ ├── WHB_cluster_to_cluster_annotation_membership_color.csv │ │ ├── WHB_cluster_to_cluster_annotation_membership_pivoted.csv │ │ ├── WHB_sunburst_colors.csv │ │ ├── WMB_sunburst_colors.csv │ │ └── WMB_unique_cell_types.csv │ ├── CCFv3-2017__regionID_side_IDpath_region_abbr.csv │ ├── CCFv3-2017_info.csv │ ├── CCFv3-2017_regional_summary.csv │ ├── CCFv3-2020__regionID_side_IDpath_region_abbr.csv │ ├── CCFv3-2020_info.csv │ ├── CCFv3-2020_regional_summary.csv │ ├── WHS_SD_rat_atlas_v4.01 │ │ ├── WHS_SD_rat_atlas_v4.01_labels.csv │ │ ├── WHS_SD_rat_atlas_v4.01_labels_sunburst_IDPath_Abbrv.csv │ │ ├── WHS_SD_rat_atlas_v4.01_labels_sunburst_RGBs.csv │ │ ├── WHS_SD_rat_atlas_v4_info.csv │ │ └── WHS_SD_rat_atlas_v4_regional_summary.csv │ ├── sunburst_IDPath_Abbrv.csv │ └── sunburst_RGBs.csv ├── help_formatter.py ├── img_io.py ├── img_tools.py └── utils.py ├── docs ├── .gitignore ├── Makefile ├── _static │ ├── FSLeyes_Ai14_image_in_CCFv3_30um_space.jpg │ ├── FSLeyes_atlas_warped_to_tissue_from_reg.jpg │ ├── FSLeyes_autofl_image_from_reg.jpg │ ├── Heifets_lab_logo.png │ ├── Ilastik_brain_mask_example.jpg │ ├── Ilastik_c-Fos_example.jpg │ ├── MapMySections_example.jpg │ ├── MapMySections_flow_chart.png │ ├── UNRAVEL_logo.png │ ├── UNRAVEL_visualizer.png │ ├── batch_stitching_1.JPG │ ├── batch_stitching_2.JPG │ ├── brain_model_layout.jpg │ ├── brain_model_settings_1.jpg │ ├── brain_model_settings_2.jpg │ ├── custom.css │ ├── favicon.png │ ├── favicon_.png │ ├── psilocybin_up_sunburst.mp4 │ ├── psilocybin_up_valid_clusters.mp4 │ ├── stitching.JPG │ ├── sunburst_1_flourish.jpg │ ├── sunburst_2_plot_types.jpg │ ├── sunburst_3_adding_data.jpg │ ├── sunburst_4_RGB_values.jpg │ ├── sunburst_5_plot_w_labels.jpg │ └── sunburst_6_plot_wo_labels.jpg ├── conf.py ├── guide.md ├── guide_mms.md ├── index.rst ├── installation.md ├── make.bat └── unravel │ ├── allen_institute │ ├── abca │ │ ├── cache.rst │ │ ├── merfish │ │ │ ├── merfish.rst │ │ │ ├── merfish_cells_to_nii.rst │ │ │ ├── merfish_expression_to_nii.rst │ │ │ ├── merfish_filter.rst │ │ │ ├── merfish_filter_by_mask.rst │ │ │ ├── merfish_join_gene.rst │ │ │ ├── merfish_slice.rst │ │ │ ├── toc.rst │ │ │ └── utils.rst │ │ ├── scRNA_seq │ │ │ ├── expression.rst │ │ │ ├── filter.rst │ │ │ ├── join_gene.rst │ │ │ └── toc.rst │ │ ├── sunburst │ │ │ ├── mean_expression_color_scale.rst │ │ │ ├── percent_expression_color_scale.rst │ │ │ ├── sunburst.rst │ │ │ ├── sunburst_expression.rst │ │ │ ├── sunburst_filter_by_expression.rst │ │ │ ├── sunburst_filter_by_proportion.rst │ │ │ └── toc.rst │ │ └── toc.rst │ ├── genetic_tools_atlas │ │ ├── auto_crop.rst │ │ ├── bbox_crop.rst │ │ ├── download.rst │ │ ├── org_samples.rst │ │ ├── simplify_metadata.rst │ │ └── toc.rst │ ├── mapmysections │ │ ├── cell_type_proportions.rst │ │ ├── cell_type_proportions_concat.rst │ │ ├── csv_concat_with_source.rst │ │ ├── segmentation_summary.rst │ │ ├── soma_in_grey.rst │ │ └── toc.rst │ └── toc.rst │ ├── cluster_stats │ ├── brain_model.rst │ ├── clusters.rst │ ├── crop.rst │ ├── cstats.rst │ ├── effect_sizes │ │ ├── effect_sizes.rst │ │ ├── effect_sizes_by_sex__absolute.rst │ │ ├── effect_sizes_by_sex__relative.rst │ │ └── toc.rst │ ├── fdr.rst │ ├── fdr_range.rst │ ├── find_incongruent_clusters.rst │ ├── fstat_sig_vx_mask.rst │ ├── group_bilateral_data.rst │ ├── index.rst │ ├── legend.rst │ ├── mean_IF.rst │ ├── mean_IF_summary.rst │ ├── org_data.rst │ ├── prism.rst │ ├── recursively_mirror_rev_cluster_indices.rst │ ├── stats_table.rst │ ├── summary.rst │ ├── summary_config.rst │ ├── sunburst.rst │ ├── table.rst │ ├── toc.rst │ └── validation.rst │ ├── core │ ├── config.rst │ ├── help_formatter.rst │ ├── img_io.rst │ ├── img_tools.rst │ ├── toc.rst │ └── utils.rst │ ├── image_io │ ├── convert_img.rst │ ├── h5_to_tifs.rst │ ├── img_to_npy.rst │ ├── img_to_points.rst │ ├── io_nii.rst │ ├── metadata.rst │ ├── nii_hd.rst │ ├── nii_info.rst │ ├── nii_to_tifs.rst │ ├── nii_to_zarr.rst │ ├── points_to_img.rst │ ├── reorient_nii.rst │ ├── tif_to_tifs.rst │ ├── toc.rst │ ├── zarr_compress.rst │ └── zarr_to_nii.rst │ ├── image_tools │ ├── DoG.rst │ ├── atlas │ │ ├── relabel_nii.rst │ │ ├── toc.rst │ │ └── wireframe.rst │ ├── avg.rst │ ├── bbox.rst │ ├── extend.rst │ ├── filter_objects_by_size.rst │ ├── math.rst │ ├── max.rst │ ├── modify_labels.rst │ ├── pad.rst │ ├── rb.rst │ ├── resample.rst │ ├── resample_points.rst │ ├── spatial_averaging.rst │ ├── toc.rst │ ├── transpose_axes.rst │ └── unique_intensities.rst │ ├── region_stats │ ├── rstats.rst │ ├── rstats_mean_IF.rst │ ├── rstats_mean_IF_in_segmented_voxels.rst │ ├── rstats_mean_IF_summary.rst │ ├── rstats_summary.rst │ └── toc.rst │ ├── register │ ├── affine_initializer.rst │ ├── affine_initializer_check.rst │ ├── reg.rst │ ├── reg_check.rst │ ├── reg_check_brain_mask.rst │ ├── reg_check_fsleyes.rst │ ├── reg_prep.rst │ └── toc.rst │ ├── segment │ ├── brain_mask.rst │ ├── copy_tifs.rst │ ├── ilastik_pixel_classification.rst │ ├── labels_to_masks.rst │ └── toc.rst │ ├── tabular │ ├── columns.rst │ ├── edit_columns.rst │ ├── filter_rows.rst │ ├── key_value_to_table.rst │ ├── toc.rst │ ├── unique_values.rst │ └── utils.rst │ ├── toc.rst │ ├── unravel_commands.rst │ ├── utilities │ ├── aggregate_files_from_sample_dirs.rst │ ├── aggregate_files_recursively.rst │ ├── clean_tif_dirs.rst │ ├── get_samples.rst │ ├── points_compressor.rst │ ├── prepend_conditions.rst │ ├── process_samples.rst │ ├── region_info.rst │ ├── rename.rst │ ├── toc.rst │ └── toggle_samples.rst │ ├── voxel_stats │ ├── apply_mask.rst │ ├── hemi_to_LR_avg.rst │ ├── mirror.rst │ ├── other │ │ ├── IF_outliers.rst │ │ ├── r_to_p.rst │ │ └── toc.rst │ ├── toc.rst │ ├── vstats.rst │ ├── vstats_check_fsleyes.rst │ ├── vstats_prep.rst │ ├── whole_to_LR_avg.rst │ ├── z_score.rst │ └── z_score_cwd.rst │ └── warp │ ├── ccf30_to_merfish.rst │ ├── points_to_atlas.rst │ ├── to_atlas.rst │ ├── to_fixed.rst │ ├── to_native.rst │ ├── toc.rst │ └── warp.rst ├── env_var.sh ├── image_io ├── __init__.py ├── convert_img.py ├── h5_to_tifs.py ├── img_to_npy.py ├── img_to_points.py ├── io_nii.py ├── metadata.py ├── nii_hd.py ├── nii_info.py ├── nii_to_tifs.py ├── nii_to_zarr.py ├── points_to_img.py ├── reorient_nii.py ├── tif_to_tifs.py ├── zarr_compress.py └── zarr_to_nii.py ├── image_tools ├── DoG.py ├── __init__.py ├── atlas │ ├── __init__.py │ ├── relabel_nii.py │ └── wireframe.py ├── avg.py ├── bbox.py ├── extend.py ├── filter_objects_by_size.py ├── math.py ├── max.py ├── modify_labels.py ├── pad.py ├── rb.py ├── resample.py ├── resample_points.py ├── spatial_averaging.py ├── transpose_axes.py └── unique_intensities.py ├── region_stats ├── __init__.py ├── rstats.py ├── rstats_mean_IF.py ├── rstats_mean_IF_in_segmented_voxels.py ├── rstats_mean_IF_summary.py └── rstats_summary.py ├── register ├── __init__.py ├── affine_initializer.py ├── affine_initializer_check.py ├── reg.py ├── reg_check.py ├── reg_check_brain_mask.py ├── reg_check_fsleyes.py └── reg_prep.py ├── segment ├── __init__.py ├── brain_mask.py ├── copy_tifs.py ├── ilastik_pixel_classification.py └── labels_to_masks.py ├── tabular ├── columns.py ├── edit_columns.py ├── filter_rows.py ├── key_value_to_table.py ├── unique_values.py └── utils.py ├── unravel_commands.py ├── utilities ├── __init__.py ├── aggregate_files_from_sample_dirs.py ├── aggregate_files_recursively.py ├── clean_tif_dirs.py ├── get_samples.py ├── points_compressor.py ├── 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