README.md
pyproject.toml
./_other/_legacy/CCF30_to_gubra.py
./_other/_legacy/gubra_to_CCF30.py
./_other/_legacy/gubra_to_CCF50.py
./_other/_testing/_test.py
./_other/_testing/_test2.py
./_other/_testing/_test3.py
./_other/drafts/360_animation.py
./_other/drafts/ANOVA_draft.py
./_other/drafts/cluster_ttests.py
./_other/drafts/collapse_atlas.py
./_other/drafts/cstats_adding_stats_options.py
./_other/drafts/csv_to_nii.py
./_other/drafts/ez_thr.py
./_other/drafts/filter_objects_by_size.py
./_other/drafts/fsleyes.py
./_other/drafts/h5_to_tifs_batch.py
./_other/drafts/img_stats_draft.py
./_other/drafts/load_czi_subset.py
./_other/drafts/native_cluster_crop.py
./_other/drafts/native_cluster_crop_legacy.py
./_other/drafts/native_clusters_crop.py
./_other/drafts/native_clusters_mean_IF_in_seg.py
./_other/drafts/nii_to_csv.py
./_other/drafts/prep_ilastik_h5.py
./_other/drafts/rstats_mean_IF_summary_v2.py
./_other/drafts/setup.py
./_other/drafts/sexes_to_cluster_densities_csv.py
./_other/drafts/volcano.py
./_other/drafts/_ABCA/CCF30_to_MERFISH30.py
./_other/drafts/_ABCA/RNAseq_dot_plot.py
./_other/drafts/_ABCA/RNAseq_dot_plot_based_on_merfish_dot_plot.py
./_other/drafts/_ABCA/RNAseq_expression_in_cell_types.py
./_other/drafts/_ABCA/RNAseq_expression_in_mice.py
./_other/drafts/_ABCA/RNAseq_expression_in_mice_heatmap.py
./_other/drafts/_ABCA/RNAseq_expression_in_mice_neurons_astro_ug.py
./_other/drafts/_ABCA/RNAseq_expression_in_mouse_MSNs.py
./_other/drafts/_ABCA/RNAseq_expression_in_mouse_cells_test.py
./_other/drafts/_ABCA/RNAseq_expression_in_neurons_astro_ug.py
./_other/drafts/_ABCA/correlation_comparison.py
./_other/drafts/_ABCA/correlation_parallel.py
./_other/drafts/_ABCA/correlation_parallel_to_nii.py
./_other/drafts/_ABCA/correlation_permutation.py
./_other/drafts/_ABCA/correlation_plot.py
./_other/drafts/_ABCA/merfish_dot_plot.py
./_other/drafts/_ABCA/merfish_dot_plot_legend.py
./_other/drafts/_ABCA/merfish_filter_expression.py
./_other/drafts/_ABCA/merfish_heatmap.py
./_other/drafts/_ABCA/merfish_imputed_genes.py
./_other/drafts/_ABCA/merfish_resample.py
./_other/drafts/_ABCA/_other/mixedlm.py
./_other/drafts/_ABCA/_other/mixedlm_LSFM_csv.py
./_other/drafts/_ABCA/_other/mixedlm_MERFISH_csv.py
./_other/drafts/_ABCA/_other/mixedlm_combine_csv.py
./_other/drafts/_ABCA/_other/mixedlm_global_relationship.py
./_other/drafts/_abc_atlas_tutorials/Allen_RNAseq_expression_in_mice_tutorial.py
./_other/drafts/_nii/variance.py
./_other/drafts/_project_specific/_angiography/pngs_to_mip_tif.py
./_other/drafts/_project_specific/_ketamine/merfish_cell_types_across_slices.py
./_other/drafts/_project_specific/_ketamine/merfish_expression_across_img_slices.py
./_other/drafts/_project_specific/_oliver/parquet_groupby.py
./_other/drafts/_project_specific/_oliver/parquet_to_nii.py
./_other/drafts/_project_specific/_oliver/parquet_unique_intensities.py
./_other/drafts/_project_specific/_oliver/parquet_unique_values.py
./_other/drafts/_project_specific/_oliver/voxel_info.py
./_other/drafts/mouse_connectivity/image_download_draft_in_progress.py
./_other/drafts/mouse_connectivity/projection_densities.py
./_other/example_scripts/example_script_for_processing_samples.py
./_other/example_scripts/example_script_for_processing_samples_w_comments.py
./_other/uncommon_scripts/brain_mask_outline.py
./tests/allen_institute/abca/merfish/test_utils.py
./unravel/__init__.py
./unravel/unravel_commands.py
./unravel/allen_institute/abca/cache.py
./unravel/allen_institute/abca/merfish/gene_catalog.py
./unravel/allen_institute/abca/merfish/merfish.py
./unravel/allen_institute/abca/merfish/merfish_cells_to_nii.py
./unravel/allen_institute/abca/merfish/merfish_expression_to_nii.py
./unravel/allen_institute/abca/merfish/merfish_filter.py
./unravel/allen_institute/abca/merfish/merfish_filter_by_mask.py
./unravel/allen_institute/abca/merfish/merfish_join_gene.py
./unravel/allen_institute/abca/merfish/merfish_slice.py
./unravel/allen_institute/abca/merfish/utils.py
./unravel/allen_institute/abca/scRNA_seq/expression.py
./unravel/allen_institute/abca/scRNA_seq/filter.py
./unravel/allen_institute/abca/scRNA_seq/join_gene.py
./unravel/allen_institute/abca/sunburst/mean_expression_color_scale.py
./unravel/allen_institute/abca/sunburst/percent_expression_color_scale.py
./unravel/allen_institute/abca/sunburst/sunburst.py
./unravel/allen_institute/abca/sunburst/sunburst_expression.py
./unravel/allen_institute/abca/sunburst/sunburst_filter_by_expression.py
./unravel/allen_institute/abca/sunburst/sunburst_filter_by_proportion.py
./unravel/allen_institute/genetic_tools_atlas/auto_crop.py
./unravel/allen_institute/genetic_tools_atlas/bbox_crop.py
./unravel/allen_institute/genetic_tools_atlas/download.py
./unravel/allen_institute/genetic_tools_atlas/org_samples.py
./unravel/allen_institute/genetic_tools_atlas/simplify_metadata.py
./unravel/allen_institute/mapmysections/cell_type_proportions.py
./unravel/allen_institute/mapmysections/cell_type_proportions_concat.py
./unravel/allen_institute/mapmysections/csv_concat_with_source.py
./unravel/allen_institute/mapmysections/segmentation_summary.py
./unravel/allen_institute/mapmysections/soma_ratio.py
./unravel/cluster_stats/__init__.py
./unravel/cluster_stats/brain_model.py
./unravel/cluster_stats/clusters.py
./unravel/cluster_stats/crop.py
./unravel/cluster_stats/cstats.py
./unravel/cluster_stats/drop_clusters.py
./unravel/cluster_stats/fdr.py
./unravel/cluster_stats/fdr_range.py
./unravel/cluster_stats/find_incongruent_clusters.py
./unravel/cluster_stats/fstat_sig_vx_mask.py
./unravel/cluster_stats/group_bilateral_data.py
./unravel/cluster_stats/index.py
./unravel/cluster_stats/legend.py
./unravel/cluster_stats/mean_IF.py
./unravel/cluster_stats/mean_IF_summary.py
./unravel/cluster_stats/org_data.py
./unravel/cluster_stats/prism.py
./unravel/cluster_stats/recursively_mirror_rev_cluster_indices.py
./unravel/cluster_stats/stats_table.py
./unravel/cluster_stats/summary.py
./unravel/cluster_stats/summary_config.py
./unravel/cluster_stats/sunburst.py
./unravel/cluster_stats/table.py
./unravel/cluster_stats/validation.py
./unravel/cluster_stats/effect_sizes/__init__.py
./unravel/cluster_stats/effect_sizes/effect_sizes.py
./unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.py
./unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.py
./unravel/core/__init__.py
./unravel/core/config.py
./unravel/core/help_formatter.py
./unravel/core/img_io.py
./unravel/core/img_tools.py
./unravel/core/utils.py
./unravel/docs/conf.py
./unravel/image_io/__init__.py
./unravel/image_io/convert_img.py
./unravel/image_io/h5_to_tifs.py
./unravel/image_io/img_to_npy.py
./unravel/image_io/img_to_points.py
./unravel/image_io/io_nii.py
./unravel/image_io/metadata.py
./unravel/image_io/nii_hd.py
./unravel/image_io/nii_info.py
./unravel/image_io/nii_to_tifs.py
./unravel/image_io/nii_to_zarr.py
./unravel/image_io/points_to_img.py
./unravel/image_io/reorient_nii.py
./unravel/image_io/tif_to_tifs.py
./unravel/image_io/zarr_compress.py
./unravel/image_io/zarr_to_nii.py
./unravel/image_tools/DoG.py
./unravel/image_tools/__init__.py
./unravel/image_tools/avg.py
./unravel/image_tools/bbox.py
./unravel/image_tools/extend.py
./unravel/image_tools/filter_objects_by_size.py
./unravel/image_tools/math.py
./unravel/image_tools/max.py
./unravel/image_tools/modify_labels.py
./unravel/image_tools/pad.py
./unravel/image_tools/rb.py
./unravel/image_tools/resample.py
./unravel/image_tools/resample_points.py
./unravel/image_tools/spatial_averaging.py
./unravel/image_tools/transpose_axes.py
./unravel/image_tools/unique_intensities.py
./unravel/image_tools/atlas/__init__.py
./unravel/image_tools/atlas/relabel_nii.py
./unravel/image_tools/atlas/wireframe.py
./unravel/region_stats/__init__.py
./unravel/region_stats/rstats.py
./unravel/region_stats/rstats_mean_IF.py
./unravel/region_stats/rstats_mean_IF_in_segmented_voxels.py
./unravel/region_stats/rstats_mean_IF_summary.py
./unravel/region_stats/rstats_summary.py
./unravel/register/__init__.py
./unravel/register/affine_initializer.py
./unravel/register/affine_initializer_check.py
./unravel/register/reg.py
./unravel/register/reg_check.py
./unravel/register/reg_check_brain_mask.py
./unravel/register/reg_check_fsleyes.py
./unravel/register/reg_prep.py
./unravel/segment/__init__.py
./unravel/segment/brain_mask.py
./unravel/segment/copy_tifs.py
./unravel/segment/ilastik_pixel_classification.py
./unravel/segment/labels_to_masks.py
./unravel/tabular/columns.py
./unravel/tabular/edit_columns.py
./unravel/tabular/filter_rows.py
./unravel/tabular/key_value_to_table.py
./unravel/tabular/unique_values.py
./unravel/tabular/utils.py
./unravel/utilities/__init__.py
./unravel/utilities/aggregate_files_from_sample_dirs.py
./unravel/utilities/aggregate_files_recursively.py
./unravel/utilities/clean_tif_dirs.py
./unravel/utilities/get_samples.py
./unravel/utilities/points_compressor.py
./unravel/utilities/prepend_conditions.py
./unravel/utilities/process_samples.py
./unravel/utilities/region_info.py
./unravel/utilities/rename.py
./unravel/utilities/toggle_samples.py
./unravel/voxel_stats/__init__.py
./unravel/voxel_stats/apply_mask.py
./unravel/voxel_stats/hemi_to_LR_avg.py
./unravel/voxel_stats/mirror.py
./unravel/voxel_stats/vstats.py
./unravel/voxel_stats/vstats_check_fsleyes.py
./unravel/voxel_stats/vstats_prep.py
./unravel/voxel_stats/whole_to_LR_avg.py
./unravel/voxel_stats/z_score.py
./unravel/voxel_stats/z_score_cwd.py
./unravel/voxel_stats/other/IF_outliers.py
./unravel/voxel_stats/other/r_to_p.py
./unravel/warp/__init__.py
./unravel/warp/ccf30_to_merfish.py
./unravel/warp/points_to_atlas.py
./unravel/warp/to_atlas.py
./unravel/warp/to_fixed.py
./unravel/warp/to_native.py
./unravel/warp/warp.py
_other/_legacy/CCF30_to_gubra.py
_other/_legacy/gubra_to_CCF30.py
_other/_legacy/gubra_to_CCF50.py
_other/_testing/_test.py
_other/_testing/_test2.py
_other/_testing/_test3.py
_other/drafts/360_animation.py
_other/drafts/ANOVA_draft.py
_other/drafts/cluster_ttests.py
_other/drafts/collapse_atlas.py
_other/drafts/cstats_adding_stats_options.py
_other/drafts/csv_to_nii.py
_other/drafts/ez_thr.py
_other/drafts/filter_objects_by_size.py
_other/drafts/fsleyes.py
_other/drafts/h5_to_tifs_batch.py
_other/drafts/img_stats_draft.py
_other/drafts/load_czi_subset.py
_other/drafts/native_cluster_crop.py
_other/drafts/native_cluster_crop_legacy.py
_other/drafts/native_clusters_crop.py
_other/drafts/native_clusters_mean_IF_in_seg.py
_other/drafts/nii_to_csv.py
_other/drafts/prep_ilastik_h5.py
_other/drafts/rstats_mean_IF_summary_v2.py
_other/drafts/setup.py
_other/drafts/sexes_to_cluster_densities_csv.py
_other/drafts/volcano.py
_other/drafts/_ABCA/CCF30_to_MERFISH30.py
_other/drafts/_ABCA/RNAseq_dot_plot.py
_other/drafts/_ABCA/RNAseq_dot_plot_based_on_merfish_dot_plot.py
_other/drafts/_ABCA/RNAseq_expression_in_cell_types.py
_other/drafts/_ABCA/RNAseq_expression_in_mice.py
_other/drafts/_ABCA/RNAseq_expression_in_mice_heatmap.py
_other/drafts/_ABCA/RNAseq_expression_in_mice_neurons_astro_ug.py
_other/drafts/_ABCA/RNAseq_expression_in_mouse_MSNs.py
_other/drafts/_ABCA/RNAseq_expression_in_mouse_cells_test.py
_other/drafts/_ABCA/RNAseq_expression_in_neurons_astro_ug.py
_other/drafts/_ABCA/correlation_comparison.py
_other/drafts/_ABCA/correlation_parallel.py
_other/drafts/_ABCA/correlation_parallel_to_nii.py
_other/drafts/_ABCA/correlation_permutation.py
_other/drafts/_ABCA/correlation_plot.py
_other/drafts/_ABCA/merfish_dot_plot.py
_other/drafts/_ABCA/merfish_dot_plot_legend.py
_other/drafts/_ABCA/merfish_filter_expression.py
_other/drafts/_ABCA/merfish_heatmap.py
_other/drafts/_ABCA/merfish_imputed_genes.py
_other/drafts/_ABCA/merfish_resample.py
_other/drafts/_ABCA/_other/mixedlm.py
_other/drafts/_ABCA/_other/mixedlm_LSFM_csv.py
_other/drafts/_ABCA/_other/mixedlm_MERFISH_csv.py
_other/drafts/_ABCA/_other/mixedlm_combine_csv.py
_other/drafts/_ABCA/_other/mixedlm_global_relationship.py
_other/drafts/_abc_atlas_tutorials/Allen_RNAseq_expression_in_mice_tutorial.py
_other/drafts/_nii/variance.py
_other/drafts/_project_specific/_angiography/pngs_to_mip_tif.py
_other/drafts/_project_specific/_ketamine/merfish_cell_types_across_slices.py
_other/drafts/_project_specific/_ketamine/merfish_expression_across_img_slices.py
_other/drafts/_project_specific/_oliver/parquet_groupby.py
_other/drafts/_project_specific/_oliver/parquet_to_nii.py
_other/drafts/_project_specific/_oliver/parquet_unique_intensities.py
_other/drafts/_project_specific/_oliver/parquet_unique_values.py
_other/drafts/_project_specific/_oliver/voxel_info.py
_other/drafts/mouse_connectivity/image_download_draft_in_progress.py
_other/drafts/mouse_connectivity/projection_densities.py
_other/example_scripts/example_script_for_processing_samples.py
_other/example_scripts/example_script_for_processing_samples_w_comments.py
_other/uncommon_scripts/brain_mask_outline.py
heifetslab_unravel.egg-info/PKG-INFO
heifetslab_unravel.egg-info/SOURCES.txt
heifetslab_unravel.egg-info/dependency_links.txt
heifetslab_unravel.egg-info/entry_points.txt
heifetslab_unravel.egg-info/requires.txt
heifetslab_unravel.egg-info/top_level.txt
tests/allen_institute/abca/merfish/test_utils.py
unravel/__init__.py
unravel/unravel_commands.py
unravel/allen_institute/abca/cache.py
unravel/allen_institute/abca/merfish/gene_catalog.py
unravel/allen_institute/abca/merfish/merfish.py
unravel/allen_institute/abca/merfish/merfish_cells_to_nii.py
unravel/allen_institute/abca/merfish/merfish_expression_to_nii.py
unravel/allen_institute/abca/merfish/merfish_filter.py
unravel/allen_institute/abca/merfish/merfish_filter_by_mask.py
unravel/allen_institute/abca/merfish/merfish_join_gene.py
unravel/allen_institute/abca/merfish/merfish_slice.py
unravel/allen_institute/abca/merfish/utils.py
unravel/allen_institute/abca/scRNA_seq/expression.py
unravel/allen_institute/abca/scRNA_seq/filter.py
unravel/allen_institute/abca/scRNA_seq/join_gene.py
unravel/allen_institute/abca/sunburst/mean_expression_color_scale.py
unravel/allen_institute/abca/sunburst/percent_expression_color_scale.py
unravel/allen_institute/abca/sunburst/sunburst.py
unravel/allen_institute/abca/sunburst/sunburst_expression.py
unravel/allen_institute/abca/sunburst/sunburst_filter_by_expression.py
unravel/allen_institute/abca/sunburst/sunburst_filter_by_proportion.py
unravel/allen_institute/genetic_tools_atlas/auto_crop.py
unravel/allen_institute/genetic_tools_atlas/bbox_crop.py
unravel/allen_institute/genetic_tools_atlas/download.py
unravel/allen_institute/genetic_tools_atlas/org_samples.py
unravel/allen_institute/genetic_tools_atlas/simplify_metadata.py
unravel/allen_institute/mapmysections/cell_type_proportions.py
unravel/allen_institute/mapmysections/cell_type_proportions_concat.py
unravel/allen_institute/mapmysections/csv_concat_with_source.py
unravel/allen_institute/mapmysections/segmentation_summary.py
unravel/allen_institute/mapmysections/soma_ratio.py
unravel/cluster_stats/__init__.py
unravel/cluster_stats/brain_model.py
unravel/cluster_stats/clusters.py
unravel/cluster_stats/crop.py
unravel/cluster_stats/cstats.py
unravel/cluster_stats/drop_clusters.py
unravel/cluster_stats/fdr.py
unravel/cluster_stats/fdr_range.py
unravel/cluster_stats/find_incongruent_clusters.py
unravel/cluster_stats/fstat_sig_vx_mask.py
unravel/cluster_stats/group_bilateral_data.py
unravel/cluster_stats/index.py
unravel/cluster_stats/legend.py
unravel/cluster_stats/mean_IF.py
unravel/cluster_stats/mean_IF_summary.py
unravel/cluster_stats/org_data.py
unravel/cluster_stats/prism.py
unravel/cluster_stats/recursively_mirror_rev_cluster_indices.py
unravel/cluster_stats/stats_table.py
unravel/cluster_stats/summary.py
unravel/cluster_stats/summary_config.py
unravel/cluster_stats/sunburst.py
unravel/cluster_stats/table.py
unravel/cluster_stats/validation.py
unravel/cluster_stats/effect_sizes/__init__.py
unravel/cluster_stats/effect_sizes/effect_sizes.py
unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.py
unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.py
unravel/core/__init__.py
unravel/core/config.py
unravel/core/help_formatter.py
unravel/core/img_io.py
unravel/core/img_tools.py
unravel/core/utils.py
unravel/docs/conf.py
unravel/image_io/__init__.py
unravel/image_io/convert_img.py
unravel/image_io/h5_to_tifs.py
unravel/image_io/img_to_npy.py
unravel/image_io/img_to_points.py
unravel/image_io/io_nii.py
unravel/image_io/metadata.py
unravel/image_io/nii_hd.py
unravel/image_io/nii_info.py
unravel/image_io/nii_to_tifs.py
unravel/image_io/nii_to_zarr.py
unravel/image_io/points_to_img.py
unravel/image_io/reorient_nii.py
unravel/image_io/tif_to_tifs.py
unravel/image_io/zarr_compress.py
unravel/image_io/zarr_to_nii.py
unravel/image_tools/DoG.py
unravel/image_tools/__init__.py
unravel/image_tools/avg.py
unravel/image_tools/bbox.py
unravel/image_tools/extend.py
unravel/image_tools/filter_objects_by_size.py
unravel/image_tools/math.py
unravel/image_tools/max.py
unravel/image_tools/modify_labels.py
unravel/image_tools/pad.py
unravel/image_tools/rb.py
unravel/image_tools/resample.py
unravel/image_tools/resample_points.py
unravel/image_tools/spatial_averaging.py
unravel/image_tools/transpose_axes.py
unravel/image_tools/unique_intensities.py
unravel/image_tools/atlas/__init__.py
unravel/image_tools/atlas/relabel_nii.py
unravel/image_tools/atlas/wireframe.py
unravel/region_stats/__init__.py
unravel/region_stats/rstats.py
unravel/region_stats/rstats_mean_IF.py
unravel/region_stats/rstats_mean_IF_in_segmented_voxels.py
unravel/region_stats/rstats_mean_IF_summary.py
unravel/region_stats/rstats_summary.py
unravel/register/__init__.py
unravel/register/affine_initializer.py
unravel/register/affine_initializer_check.py
unravel/register/reg.py
unravel/register/reg_check.py
unravel/register/reg_check_brain_mask.py
unravel/register/reg_check_fsleyes.py
unravel/register/reg_prep.py
unravel/segment/__init__.py
unravel/segment/brain_mask.py
unravel/segment/copy_tifs.py
unravel/segment/ilastik_pixel_classification.py
unravel/segment/labels_to_masks.py
unravel/tabular/columns.py
unravel/tabular/edit_columns.py
unravel/tabular/filter_rows.py
unravel/tabular/key_value_to_table.py
unravel/tabular/unique_values.py
unravel/tabular/utils.py
unravel/utilities/__init__.py
unravel/utilities/aggregate_files_from_sample_dirs.py
unravel/utilities/aggregate_files_recursively.py
unravel/utilities/clean_tif_dirs.py
unravel/utilities/get_samples.py
unravel/utilities/points_compressor.py
unravel/utilities/prepend_conditions.py
unravel/utilities/process_samples.py
unravel/utilities/region_info.py
unravel/utilities/rename.py
unravel/utilities/toggle_samples.py
unravel/voxel_stats/__init__.py
unravel/voxel_stats/apply_mask.py
unravel/voxel_stats/hemi_to_LR_avg.py
unravel/voxel_stats/mirror.py
unravel/voxel_stats/vstats.py
unravel/voxel_stats/vstats_check_fsleyes.py
unravel/voxel_stats/vstats_prep.py
unravel/voxel_stats/whole_to_LR_avg.py
unravel/voxel_stats/z_score.py
unravel/voxel_stats/z_score_cwd.py
unravel/voxel_stats/other/IF_outliers.py
unravel/voxel_stats/other/r_to_p.py
unravel/warp/__init__.py
unravel/warp/ccf30_to_merfish.py
unravel/warp/points_to_atlas.py
unravel/warp/to_atlas.py
unravel/warp/to_fixed.py
unravel/warp/to_native.py
unravel/warp/warp.py