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Installation
LSFM/STPT Guide
MapMySections Guide
unravel package
GitHub
Section Navigation
unravel.unravel_commands module
unravel.register package
unravel.register.reg_prep module
unravel.register.reg module
unravel.register.affine_initializer module
unravel.register.affine_initializer_check module
unravel.register.reg_check module
unravel.register.reg_check_fsleyes module
unravel.register.reg_check_brain_mask module
unravel.warp package
unravel.warp.to_atlas module
unravel.warp.to_fixed module
unravel.warp.to_native module
unravel.warp.warp module
unravel.warp.points_to_atlas module
unravel.warp.ccf30_to_merfish module
unravel.segment package
unravel.segment.brain_mask module
unravel.segment.copy_tifs module
unravel.segment.ilastik_pixel_classification module
unravel.segment.labels_to_masks module
unravel.voxel_stats package
unravel.voxel_stats.apply_mask module
unravel.voxel_stats.vstats_prep module
unravel.voxel_stats.z_score module
unravel.voxel_stats.z_score_cwd module
unravel.voxel_stats.whole_to_LR_avg module
unravel.voxel_stats.hemi_to_LR_avg module
unravel.voxel_stats.vstats module
unravel.voxel_stats.mirror module
unravel.voxel_stats.vstats_check_fsleyes module
unravel.voxel_stats.other package
unravel.voxel_stats.other.IF_outliers module
unravel.voxel_stats.other.r_to_p module
unravel.cluster_stats package
unravel.cluster_stats.fdr_range module
unravel.cluster_stats.fdr module
unravel.cluster_stats.fstat_sig_vx_mask module
unravel.cluster_stats.recursively_mirror_rev_cluster_indices module
unravel.cluster_stats.validation module
unravel.cluster_stats.summary_config module
unravel.cluster_stats.summary module
unravel.cluster_stats.brain_model module
unravel.cluster_stats.find_incongruent_clusters module
unravel.cluster_stats.group_bilateral_data module
unravel.cluster_stats.mean_IF module
unravel.cluster_stats.legend module
unravel.cluster_stats.org_data module
unravel.cluster_stats.prism module
unravel.cluster_stats.cstats module
unravel.cluster_stats.stats_table module
unravel.cluster_stats.sunburst module
unravel.cluster_stats.table module
unravel.cluster_stats.crop module
unravel.cluster_stats.index module
unravel.cluster_stats.mean_IF_summary module
unravel.cluster_stats.clusters module
unravel.cluster_stats.effect_sizes package
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.region_stats package
unravel.region_stats.rstats module
unravel.region_stats.rstats_summary 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.core package
unravel.core.help_formatter module
unravel.core.config module
unravel.core.img_io module
unravel.core.img_tools module
unravel.core.utils module
unravel.image_io package
unravel.image_io.h5_to_tifs module
unravel.image_io.img_to_npy module
unravel.image_io.convert_img module
unravel.image_io.metadata module
unravel.image_io.nii_hd module
unravel.image_io.nii_info module
unravel.image_io.io_nii module
unravel.image_io.nii_to_tifs module
unravel.image_io.nii_to_zarr module
unravel.image_io.reorient_nii module
unravel.image_io.tif_to_tifs module
unravel.image_io.zarr_to_nii module
unravel.image_io.zarr_compress module
unravel.image_io.points_to_img module
unravel.image_io.img_to_points module
unravel.image_tools package
unravel.image_tools.math module
unravel.image_tools.avg module
unravel.image_tools.bbox module
unravel.image_tools.extend module
unravel.image_tools.max module
unravel.image_tools.pad module
unravel.image_tools.resample module
unravel.image_tools.spatial_averaging module
unravel.image_tools.DoG module
unravel.image_tools.rb module
unravel.image_tools.transpose_axes module
unravel.image_tools.unique_intensities module
unravel.image_tools.resample_points module
unravel.image_tools.modify_labels module
unravel.image_tools.atlas package
unravel.image_tools.atlas.relabel_nii module
unravel.image_tools.atlas.wireframe module
unravel.utilities package
unravel.utilities.get_samples module
unravel.utilities.region_info module
unravel.utilities.aggregate_files_from_sample_dirs module
unravel.utilities.aggregate_files_recursively module
unravel.utilities.clean_tif_dirs module
unravel.utilities.prepend_conditions module
unravel.utilities.process_samples module
unravel.utilities.rename module
unravel.utilities.toggle_samples module
unravel.utilities.points_compressor module
unravel.segment package
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.allen_institute package
unravel.allen_institute.abca package
unravel.allen_institute.abca.cache module
unravel.allen_institute.abca.merfish package
unravel.allen_institute.abca.merfish.utils module
unravel.allen_institute.abca.merfish.merfish module
unravel.allen_institute.abca.merfish.merfish_slice module
unravel.allen_institute.abca.merfish.merfish_filter module
unravel.allen_institute.abca.merfish.merfish_filter_by_mask module
unravel.allen_institute.abca.merfish.merfish_cells_to_nii module
unravel.allen_institute.abca.merfish.merfish_expression_to_nii module
unravel.allen_institute.abca.merfish.merfish_join_gene module
unravel.allen_institute.abca.sunburst package
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.abca.sunburst.mean_expression_color_scale module
unravel.allen_institute.abca.sunburst.percent_expression_color_scale module
unravel.allen_institute.abca.scRNA_seq package
unravel.allen_institute.abca.scRNA_seq.filter module
unravel.allen_institute.abca.scRNA_seq.expression module
unravel.allen_institute.abca.scRNA_seq.join_gene module
unravel.allen_institute.genetic_tools_atlas package
unravel.allen_institute.genetic_tools_atlas.download module
unravel.allen_institute.genetic_tools_atlas.simplify_metadata module
unravel.allen_institute.genetic_tools_atlas.org_samples module
unravel.allen_institute.genetic_tools_atlas.auto_crop module
unravel.allen_institute.genetic_tools_atlas.bbox_crop module
unravel.allen_institute.mapmysections package
unravel.allen_institute.mapmysections.cell_type_proportions_concat module
unravel.allen_institute.mapmysections.cell_type_proportions module
unravel.allen_institute.mapmysections.csv_concat_with_source module
unravel.allen_institute.mapmysections.segmentation_summary module
unravel.allen_institute.mapmysections.soma_ratio module
unravel package
unravel.allen_institute package
unravel.allen_institute.mapmysections package
unravel.allen_institute.mapmysections.soma_ratio module
unravel.allen_institute.mapmysections.soma_ratio module
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