Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ __call__() (magmap.gui.pixel_display.PixelDisplay method) __repr__() (magmap.cv.colocalizer.BlobMatch method) (magmap.settings.profiles.SettingsDict method) A A (magmap.settings.config.ItkSnapLabels attribute) ABA_ID (magmap.settings.config.ABAKeys attribute) ABAKeys (class in magmap.settings.config) ABS_X (magmap.cv.detector.Blobs.Cols attribute) ABS_Y (magmap.cv.detector.Blobs.Cols attribute) ABS_Z (magmap.cv.detector.Blobs.Cols attribute) AccessAtlasThread (class in magmap.brain_globe.bg_controller) ACRONYM (magmap.settings.config.ABAKeys attribute) ACTIVE (magmap.settings.profiles.RegKeys attribute) adaptive_closing (magmap.settings.config.SmoothingModes attribute) adaptive_erosion (magmap.settings.config.SmoothingModes attribute) adaptive_opening (magmap.settings.config.SmoothingModes attribute) add_artist() (magmap.gui.image_viewer.Blitter method) add_cols_df() (in module magmap.io.df_io) ADD_CSV_COLS (magmap.settings.config.DFTasks attribute) add_file_handler() (in module magmap.settings.logs) add_missing_keys() (in module magmap.io.libmag) add_profiles() (magmap.settings.profiles.SettingsDict method) add_scale_bar() (in module magmap.plot.plot_support) add_vspans() (in module magmap.plot.plot_support) additive_blend (magmap.gui.roi_editor.ROIEditor property) (magmap.plot.plot_support.ImageOverlayer attribute) (magmap.plot.plot_support.ImageSyncMixin property) affine_nd() (in module magmap.cv.cv_nd) aggr_smoothing_metrics() (in module magmap.atlas.atlas_refiner) alpha (magmap.gui.plot_editor.PlotEditor attribute) alpha_blend_intersection() (in module magmap.plot.plot_support) ALPHA_DEFAULT (magmap.gui.plot_editor.PlotEditor attribute) alpha_img3d (magmap.gui.plot_editor.PlotEditor attribute) alpha_reset() (magmap.gui.atlas_editor.AtlasEditor method) alpha_update() (magmap.gui.atlas_editor.AtlasEditor method) alpha_updater() (magmap.gui.plot_editor.PlotEditor method) ALPHAS_CHL (magmap.settings.config.PlotLabels attribute) angle_indices() (in module magmap.cv.cv_nd) animate_imgs() (in module magmap.io.export_stack) ANIMATED (magmap.settings.config.ProcessTypes attribute) ANNOT_COL (magmap.settings.config.PlotLabels attribute) annotate_labels() (magmap.plot.plot_support.ImageOverlayer method) AnnotateLabels (class in magmap.gui.atlas_threads) ANNOTATION (magmap.settings.config.RegSuffixes attribute) app_dir (in module magmap.settings.config) APP_NAME (in module magmap.settings.config) append_cols() (in module magmap.io.df_io) APPEND_CSVS_COLS (magmap.settings.config.DFTasks attribute) ARGS_MAGMAP (in module magmap.io.load_env) args_to_dict() (in module magmap.io.cli) args_with_dict() (in module magmap.io.cli) artists (magmap.gui.image_viewer.Blitter property) aspect (magmap.plot.plot_support.ImageOverlayer attribute) assign_metadata() (in module magmap.io.importer) atlas (magmap.atlas.register.RegImgs attribute) ATLAS (magmap.settings.config.RegSuffixes attribute) ATLAS_ED (magmap.gui.vis_handler.ViewerTabs attribute) atlas_edge (magmap.cv.segmenter.SubSegmenter attribute) atlas_img_np (magmap.stats.vols.MeasureLabel attribute) atlas_mask (magmap.atlas.register.RegImgs attribute) AtlasEditor (class in magmap.gui.atlas_editor) AtlasLabels (class in magmap.settings.config) AtlasMetrics (class in magmap.settings.config) AtlasProfile (class in magmap.settings.atlas_prof) ax (magmap.plot.plot_support.ImageOverlayer attribute) axes_exit() (magmap.plot.plot_support.ImageSyncMixin method) B B (magmap.settings.config.ItkSnapLabels attribute) BACKGROUND (magmap.settings.config.PlotLabels attribute) backup_file() (in module magmap.io.libmag) BAR_PLOT (magmap.settings.config.Plot2DTypes attribute) BAR_PLOT_VOLS_STATS (magmap.settings.config.Plot2DTypes attribute) BAR_PLOT_VOLS_STATS_EFFECTS (magmap.settings.config.Plot2DTypes attribute) BASENAME (magmap.cv.detector.Blobs.Keys attribute) bg_mm (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) (magmap.brain_globe.bg_controller.SetupAtlasesThread attribute) BINARY (magmap.settings.config.AtlasLabels attribute) Blitter (class in magmap.gui.image_viewer) blitter (magmap.gui.plot_editor.PlotEditor attribute) blob (magmap.gui.verifier_editor.VerifierEditor.BlobView attribute) BLOB1 (magmap.cv.colocalizer.BlobMatch.Cols attribute) BLOB1_ID (magmap.cv.colocalizer.BlobMatch.Cols attribute) BLOB2 (magmap.cv.colocalizer.BlobMatch.Cols attribute) BLOB2_ID (magmap.cv.colocalizer.BlobMatch.Cols attribute) BLOB_COLORS (magmap.gui.roi_editor.DraggableCircle attribute) blob_for_db() (magmap.cv.detector.Blobs class method) BLOB_MATCHES (magmap.settings.config.LoadData attribute) BLOB_PREPROCESSING (magmap.settings.roi_prof.ROIProfile attribute) BlobMatch (class in magmap.cv.colocalizer) BlobMatch.Cols (class in magmap.cv.colocalizer) Blobs (class in magmap.cv.detector) blobs (in module magmap.settings.config) (magmap.cv.classifier.ClassifyImage attribute) (magmap.cv.colocalizer.StackColocalizer attribute) (magmap.cv.detector.Blobs property) BLOBS (magmap.cv.detector.Blobs.Keys attribute) (magmap.settings.config.LoadData attribute) blobs (magmap.stats.clustering.ClusterByLabel attribute) (magmap.stats.vols.MeasureLabel attribute) Blobs.Cols (class in magmap.cv.detector) Blobs.Keys (class in magmap.cv.detector) blobs_in_channel() (magmap.cv.detector.Blobs class method) BLOBS_NP_VER (magmap.cv.detector.Blobs attribute) blobs_to_csv() (in module magmap.io.export_rois) blobs_to_prune (magmap.cv.stack_detect.StackPruner attribute) blobs_truth (magmap.io.sqlite.ClrDB attribute) BLOCK_SIZES (magmap.settings.roi_prof.ROIProfile attribute) Blocks (class in magmap.cv.stack_detect) borders (magmap.atlas.register.RegImgs attribute) BORDERS (magmap.settings.config.RegSuffixes attribute) borders_distance() (in module magmap.cv.cv_nd) BOTH (magmap.settings.config.HemSides attribute) BOTTOM (magmap.gui.roi_editor.ROIEditor.ZLevels attribute) bounds (magmap.gui.atlas_editor.InterpolatePlanes property) BRAIN_GLOBE (magmap.settings.config.LoadIO attribute) BrainGlobeCtrl (class in magmap.brain_globe.bg_controller) BrainGlobeMM (class in magmap.brain_globe.bg_model) build_ground_truth() (in module magmap.plot.plot_3d) build_heat_map() (in module magmap.cv.cv_nd) build_labels_diff_images() (in module magmap.atlas.reg_tasks) build_pool_init() (magmap.cv.chunking.SharedArrsContainer class method) build_stack() (magmap.io.export_stack.StackPlaneIO method) C calc_compactness() (in module magmap.cv.cv_nd) calc_intensity_bounds() (in module magmap.io.importer) calc_isotropic_factor() (in module magmap.cv.cv_nd) calc_overlap() (in module magmap.cv.detector) calc_scaling() (in module magmap.io.importer) calc_scaling_factor() (in module magmap.cv.detector) calc_sens_ppv() (in module magmap.stats.atlas_stats) carve() (in module magmap.cv.cv_nd) CAT_PLOT (magmap.settings.config.Plot2DTypes attribute) change_brightness_contrast() (magmap.gui.plot_editor.PlotEditor static method) channel (in module magmap.settings.config) CHANNEL (magmap.cv.detector.Blobs.Cols attribute) channel (magmap.cv.stack_detect.StackDetector attribute) CHANNEL (magmap.settings.config.AtlasMetrics attribute) CHANNEL_SEPARATOR (in module magmap.io.importer) channels (magmap.cv.colocalizer.StackColocalizer attribute) check_file_changed() (magmap.settings.profiles.SettingsDict method) check_mirrorred() (in module magmap.atlas.atlas_refiner) CHILDREN (magmap.settings.config.ABAKeys attribute) CIRCLES (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) classifier (in module magmap.settings.config) ClassifierData (class in magmap.settings.config) CLASSIFY (magmap.settings.config.ProcessTypes attribute) classify_blobs() (in module magmap.cv.classifier) classify_chunk() (magmap.cv.classifier.ClassifyImage class method) classify_patches() (in module magmap.cv.classifier) classify_whole_image() (magmap.cv.classifier.ClassifyImage class method) ClassifyImage (class in magmap.cv.classifier) clean_up_blobs() (in module magmap.io.sqlite) clear_scene() (magmap.gui.vis_3d.Vis3D method) closed() (magmap.gui.vis_handler.VisHandler method) closing (magmap.settings.config.SmoothingModes attribute) ClrDB (class in magmap.io.sqlite) CLUSTER_BLOBS (magmap.settings.config.RegisterTypes attribute) cluster_blobs() (in module magmap.stats.clustering) cluster_by_label() (magmap.stats.clustering.ClusterByLabel class method) cluster_dbscan_metrics() (in module magmap.stats.clustering) cluster_within_label() (magmap.stats.clustering.ClusterByLabel class method) ClusterByLabel (class in magmap.stats.clustering) CMAP_BUBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_CYBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_GRBK_NAME (magmap.settings.config.Cmaps attribute) cmap_labels (in module magmap.settings.config) (magmap.gui.plot_editor.PlotEditor attribute) CMAP_MGBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_RDBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_YLBK_NAME (magmap.settings.config.Cmaps attribute) Cmaps (class in magmap.settings.config) COEFVAR (magmap.settings.config.RegisterTypes attribute) coefvar_df() (in module magmap.io.df_io) COEFVAR_INTENS (magmap.stats.vols.MetricCombos attribute) COEFVAR_NUC (magmap.stats.vols.MetricCombos attribute) CoefVarIntens (magmap.stats.vols.LabelMetrics attribute) CoefVarNuc (magmap.stats.vols.LabelMetrics attribute) coloc (magmap.cv.stack_detect.StackDetector attribute) COLOC_MATCH (magmap.settings.config.ProcessTypes attribute) colocalize_blobs() (in module magmap.cv.colocalizer) colocalize_blobs_match() (in module magmap.cv.colocalizer) colocalize_block() (magmap.cv.colocalizer.StackColocalizer class method) colocalize_stack() (magmap.cv.colocalizer.StackColocalizer class method) COLOCS (magmap.cv.detector.Blobs.Keys attribute) color_picker_changed() (magmap.gui.atlas_editor.AtlasEditor method) cols (magmap.cv.detector.Blobs property) COLS (magmap.cv.detector.Blobs.Keys attribute) combine_arrs() (in module magmap.io.libmag) COMBINE_COLS (magmap.settings.config.RegisterTypes attribute) combine_cols() (in module magmap.io.df_io) combine_paths() (in module magmap.io.libmag) COMBINED (magmap.settings.config.RegNames attribute) compact_float() (in module magmap.io.libmag) COMPACTION (magmap.settings.config.SmoothingMetrics attribute) COMPACTNESS (magmap.settings.config.SmoothingMetrics attribute) Compactness (magmap.stats.vols.LabelMetrics attribute) compactness_3d() (in module magmap.cv.cv_nd) compactness_count() (in module magmap.cv.cv_nd) COMPACTNESS_CV (magmap.settings.config.SmoothingMetrics attribute) COMPACTNESS_ORIG (magmap.settings.config.SmoothingMetrics attribute) COMPACTNESS_SD (magmap.settings.config.SmoothingMetrics attribute) compress_file() (in module magmap.io.subproc_io) cond_to_cols_df() (in module magmap.io.df_io) CONDITION (magmap.settings.config.AtlasMetrics attribute) (magmap.settings.config.PlotLabels attribute) CONFIRMED (magmap.cv.detector.Blobs.Cols attribute) conn (magmap.io.sqlite.ClrDB attribute) connect() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) convert_bin_magnitude() (in module magmap.io.libmag) convert_img() (in module magmap.io.sitk_io) convert_img_labels() (magmap.plot.colormaps.DiscreteColormap method) convert_imgs() (magmap.io.export_stack.StackPlaneIO class method) convert_indices_to_int() (in module magmap.io.libmag) CONVERT_ITKSNAP_LABELS (magmap.settings.config.RegisterTypes attribute) convert_itksnap_to_df() (in module magmap.atlas.ontology) convert_shared_arr() (magmap.cv.chunking.SharedArrsContainer class method) coords_for_indexing() (in module magmap.io.libmag) copy_backup() (in module magmap.io.libmag) create_aba_reverse_lookup() (magmap.atlas.ontology.LabelsRef method) create_lookup_pd() (magmap.atlas.ontology.LabelsRef method) create_ref_lookup() (magmap.atlas.ontology.LabelsRef method) create_reverse_lookup() (magmap.atlas.ontology.LabelsRef method) create_symlink() (in module magmap.io.libmag) crop_mid_str() (in module magmap.io.libmag) crop_to_labels() (in module magmap.cv.cv_nd) crop_to_orig() (in module magmap.atlas.atlas_refiner) cur (magmap.io.sqlite.ClrDB attribute) curate_img() (in module magmap.atlas.register) CUT (magmap.gui.roi_editor.DraggableCircle attribute) D DARK (magmap.settings.config.Themes attribute) data_frames_to_csv() (in module magmap.io.df_io) DataClass (class in magmap.settings.config) DataClassProtocol (class in magmap.settings.config) DBSCAN_EPS (magmap.settings.profiles.RegKeys attribute) DBSCAN_MINPTS (magmap.settings.profiles.RegKeys attribute) decompress_file() (in module magmap.io.subproc_io) deconstruct_img_name() (in module magmap.io.importer) deconvolve() (in module magmap.plot.plot_3d) DECORATE_PLOT (magmap.settings.config.Plot2DTypes attribute) decorate_plot() (in module magmap.plot.plot_2d) DEFAULT (magmap.settings.config.Themes attribute) DEFAULT_IMG_STACK_NAME (in module magmap.io.importer) DEFAULT_NAME (magmap.settings.profiles.SettingsDict attribute) DEFAULT_SAVEFIG (in module magmap.settings.config) delete_blobs() (in module magmap.io.sqlite) DENOISE (magmap.settings.config.PreProcessKeys attribute) denoise_max_shape (magmap.cv.stack_detect.Blocks attribute) (magmap.cv.stack_detect.StackDetector attribute) denoise_roi() (in module magmap.plot.plot_3d) DENSITY (magmap.settings.config.RegSuffixes attribute) Density (magmap.stats.vols.LabelMetrics attribute) DensityIntens (magmap.stats.vols.LabelMetrics attribute) DETECT (magmap.settings.config.ProcessTypes attribute) detect_blobs() (in module magmap.cv.detector) detect_blobs_blocks() (in module magmap.cv.stack_detect) detect_blobs_stack() (in module magmap.cv.stack_detect) detect_blobs_sub_rois() (magmap.cv.stack_detect.StackDetector class method) DETECT_COLOC (magmap.settings.config.ProcessTypes attribute) detect_sub_roi() (magmap.cv.stack_detect.StackDetector class method) detect_sub_roi_from_data() (magmap.cv.stack_detect.StackDetector class method) DETECTION (magmap.cv.stack_detect.StackTimes attribute) df (magmap.stats.vols.MeasureLabel attribute) (magmap.stats.vols.MeasureLabelOverlap attribute) df_add() (in module magmap.io.df_io) df_div() (in module magmap.io.df_io) df_subtract() (in module magmap.io.df_io) DFTasks (class in magmap.settings.config) dict_to_data_frame() (in module magmap.io.df_io) disconnect() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) discrete_colormap() (in module magmap.plot.colormaps) DiscreteColormap (class in magmap.plot.colormaps) DiscreteModes (class in magmap.plot.colormaps) DISPLACEMENT (magmap.settings.config.SmoothingMetrics attribute) DIST (magmap.cv.colocalizer.BlobMatch.Cols attribute) Dist (magmap.stats.vols.LabelMetrics attribute) dist_to_orig (magmap.stats.vols.MeasureLabel attribute) DIVIDE_COLS (magmap.settings.config.DFTasks attribute) DNS_REVERSE (in module magmap.settings.config) DOCS_URL (magmap.settings.config.DocsURLs attribute) DOCS_URL_SETTINGS (magmap.settings.config.DocsURLs attribute) DOCS_URL_VIEWER (magmap.settings.config.DocsURLs attribute) DocsURLs (class in magmap.settings.config) Downsampler (class in magmap.atlas.transformer) DPI (magmap.settings.config.PlotLabels attribute) DraggableCircle (class in magmap.gui.roi_editor) draw_crosslines() (magmap.gui.plot_editor.PlotEditor method) DROP_DUPS (magmap.settings.config.PlotLabels attribute) DSC_ATLAS_LABELS (magmap.settings.config.AtlasMetrics attribute) DSC_ATLAS_LABELS_HEM (magmap.settings.config.AtlasMetrics attribute) DSC_ATLAS_SAMPLE (magmap.settings.config.AtlasMetrics attribute) DSC_ATLAS_SAMPLE_CUR (magmap.settings.config.AtlasMetrics attribute) DSC_LABELS_ORIG_NEW_COMBINED (magmap.settings.config.AtlasMetrics attribute) DSC_LABELS_ORIG_NEW_INDIV (magmap.settings.config.AtlasMetrics attribute) DSC_SAMPLE_LABELS (magmap.settings.config.AtlasMetrics attribute) DTYPE (magmap.settings.config.MetaKeys attribute) dtype_within_range() (in module magmap.io.libmag) E EDGE_AWARE_REANNOTATION (magmap.settings.profiles.RegKeys attribute) edge_aware_segmentation() (in module magmap.atlas.edge_seg) edge_distances() (in module magmap.atlas.edge_seg) EdgeDistMean (magmap.stats.vols.LabelMetrics attribute) EdgeDistSum (magmap.stats.vols.LabelMetrics attribute) EdgeSize (magmap.stats.vols.LabelMetrics attribute) EDIT (magmap.settings.config.TruthDBModes attribute) edit_mode (magmap.gui.plot_editor.PlotEditor property) edited (magmap.plot.plot_support.ImageSyncMixin attribute) enable_btn() (magmap.plot.plot_support.ImageSyncMixin static method) EntropyIntensity (magmap.stats.vols.LabelMetrics attribute) enum_dict_aslist() (in module magmap.io.libmag) enum_names_aslist() (in module magmap.io.libmag) ENV_NAME (in module magmap.io.load_env) erode_label() (magmap.cv.segmenter.LabelToMarkerErosion class method) erode_labels() (in module magmap.atlas.edge_seg) ERR_COL (magmap.settings.config.PlotLabels attribute) ERR_COL_ABS (magmap.settings.config.PlotLabels attribute) eventFilter() (magmap.gui.event_handlers.FileOpenHandler method) exclude_border (magmap.cv.stack_detect.Blocks attribute) (magmap.cv.stack_detect.StackDetector attribute) exp (magmap.atlas.register.RegImgs attribute) exp_mask (magmap.atlas.register.RegImgs attribute) exp_orig (magmap.atlas.register.RegImgs attribute) EXPORT_BLOBS (magmap.settings.config.ProcessTypes attribute) EXPORT_COMMON_LABELS (magmap.settings.config.RegisterTypes attribute) export_common_labels() (in module magmap.io.export_regions) EXPORT_METRICS_COMPACTNESS (magmap.settings.config.RegisterTypes attribute) EXPORT_PLANES (magmap.settings.config.ProcessTypes attribute) export_planes() (in module magmap.io.export_stack) EXPORT_PLANES_CHANNELS (magmap.settings.config.ProcessTypes attribute) EXPORT_RAW (magmap.settings.config.ProcessTypes attribute) export_region_ids() (in module magmap.io.export_regions) export_region_network() (in module magmap.io.export_regions) EXPORT_REGIONS (magmap.settings.config.RegisterTypes attribute) EXPORT_ROIS (magmap.settings.config.ProcessTypes attribute) export_rois() (in module magmap.io.export_rois) EXPORT_TIF (magmap.settings.config.ProcessTypes attribute) EXPS_BY_REGION (magmap.settings.config.DFTasks attribute) exps_by_regions() (in module magmap.io.df_io) extend_edge() (in module magmap.atlas.atlas_refiner) exterior_nd() (in module magmap.cv.cv_nd) EXTRACT (magmap.settings.config.ProcessTypes attribute) EXTRACT_FROM_CSV (magmap.settings.config.DFTasks attribute) extract_patches() (in module magmap.cv.classifier) extract_planes() (in module magmap.plot.plot_support) extract_region() (in module magmap.cv.cv_nd) EXTS_3D (in module magmap.io.sitk_io) F FDR (magmap.stats.mlearn.GridSearchStats attribute) fig (magmap.gui.image_viewer.Blitter attribute) (magmap.plot.plot_support.ImageSyncMixin attribute) fig_save_dir (magmap.settings.prefs_prof.PrefsProfile attribute) filename_to_base() (in module magmap.io.importer) filenames (in module magmap.settings.config) FileOpenHandler (class in magmap.gui.event_handlers) filter_adaptive_size() (in module magmap.cv.cv_nd) filter_dfs_on_vals() (in module magmap.io.df_io) FILTER_SIZE (magmap.settings.config.SmoothingMetrics attribute) find_atlas_labels() (in module magmap.io.sitk_io) find_closest_blobs_cdist() (in module magmap.cv.verifier) find_label_edge() (magmap.stats.vols.LabelToEdge class method) find_labels_lost() (in module magmap.atlas.atlas_refiner) find_scaling() (in module magmap.io.np_io) find_sizes() (in module magmap.io.importer) find_symmetric_axis() (in module magmap.atlas.atlas_refiner) fit_frame_to_image() (in module magmap.plot.plot_support) FIXED_MASK (magmap.settings.config.RegSuffixes attribute) flatten() (in module magmap.io.libmag) FLIP (magmap.settings.config.Transforms attribute) FLIP_HORIZ (magmap.settings.config.Transforms attribute) FLIP_VERT (magmap.settings.config.Transforms attribute) flush() (magmap.settings.logs.LogWriter method) FN (magmap.stats.mlearn.GridSearchStats attribute) fn_feedback (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_opened_atlas (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_progress (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_set_atlases_table (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_update_blob (magmap.gui.verifier_editor.VerifierEditor attribute) fn_update_coords (magmap.gui.plot_editor.PlotEditor attribute) footprint (magmap.stats.vols.LabelToEdge attribute) format_blobs() (magmap.cv.detector.Blobs method) format_bytes() (in module magmap.io.libmag) format_import_err() (in module magmap.settings.config) format_num() (in module magmap.io.libmag) FORMATS_3D (in module magmap.settings.config) FP (magmap.stats.mlearn.GridSearchStats attribute) FROM_LABEL (magmap.atlas.ontology.LabelColumns attribute) FULL_ANNOTATION (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) func_to_paired_cols() (in module magmap.io.df_io) G G (magmap.settings.config.ItkSnapLabels attribute) gaussian (magmap.settings.config.SmoothingModes attribute) get_aspect_ratio() (in module magmap.plot.plot_support) get_atlas() (magmap.brain_globe.bg_model.BrainGlobeMM method) get_avail_atlases() (magmap.brain_globe.bg_model.BrainGlobeMM method) get_bbox_region() (in module magmap.cv.cv_nd) get_blob_abs_coords() (magmap.cv.detector.Blobs class method) get_blob_col() (magmap.cv.detector.Blobs class method) get_blob_confirmed() (magmap.cv.detector.Blobs class method) get_blob_truth() (magmap.cv.detector.Blobs class method) get_blobs() (magmap.cv.colocalizer.BlobMatch method) get_blobs_all() (magmap.cv.colocalizer.BlobMatch method) get_blobs_channel() (magmap.cv.detector.Blobs class method) get_blobs_in_roi() (in module magmap.cv.detector) get_blobs_interior() (in module magmap.cv.detector) get_borders_colormap() (in module magmap.plot.colormaps) get_children_from_id() (in module magmap.atlas.ontology) get_children_from_id_df() (in module magmap.atlas.ontology) get_cmap() (in module magmap.plot.colormaps) get_dict_keys_from_val() (in module magmap.io.libmag) get_displayed_img() (magmap.gui.plot_editor.PlotEditor method) get_downsample_max_sizes() (in module magmap.plot.plot_support) get_dtype_info() (in module magmap.io.libmag) get_enum() (in module magmap.io.libmag) get_exp_name() (in module magmap.io.sqlite) get_filename_without_ext() (in module magmap.io.libmag) get_files() (magmap.settings.atlas_prof.AtlasProfile static method) (magmap.settings.grid_search_prof.GridSearchProfile static method) (magmap.settings.profiles.SettingsDict static method) (magmap.settings.roi_prof.ROIProfile static method) get_git_commit() (in module magmap.io.libmag) get_if_within() (in module magmap.io.libmag) get_img_display_settings() (magmap.plot.plot_support.ImageSyncMixin method) get_int() (in module magmap.io.libmag) get_isotropic_vis() (in module magmap.plot.plot_3d) get_label() (in module magmap.atlas.ontology) get_label_at_level() (in module magmap.atlas.ontology) get_label_bbox() (in module magmap.cv.cv_nd) get_label_ids_from_position() (in module magmap.atlas.ontology) get_label_item() (in module magmap.atlas.ontology) get_label_name() (in module magmap.atlas.ontology) get_label_props() (in module magmap.cv.cv_nd) get_label_side() (in module magmap.atlas.ontology) get_labels_discrete_colormap() (in module magmap.plot.colormaps) get_local_atlases() (magmap.brain_globe.bg_model.BrainGlobeMM method) get_mean_coords() (magmap.cv.colocalizer.BlobMatch method) get_metric_weight_col() (in module magmap.stats.vols) get_mp_pool() (in module magmap.cv.chunking) get_msg() (magmap.gui.pixel_display.PixelDisplay method) get_node() (magmap.atlas.ontology.LabelsRef method) get_num_channels() (in module magmap.io.np_io) get_order() (magmap.atlas.register.RegImgs static method) get_pkg_egg() (in module magmap.io.packaging) get_pkg_path() (in module magmap.io.packaging) get_plane_axis() (in module magmap.plot.plot_support) get_plot_ax_img() (magmap.gui.plot_editor.PlotEditor static method) get_profile() (magmap.settings.profiles.SettingsDict method) get_ref_lookup_as_df() (magmap.atlas.ontology.LabelsRef method) get_region_middle() (in module magmap.atlas.ontology) get_roi_offset() (in module magmap.io.sqlite) get_roi_path() (in module magmap.io.naming) get_roi_profile() (in module magmap.settings.config) get_roi_size() (in module magmap.io.sqlite) get_rois() (magmap.io.sqlite.ClrDB method) get_save_path() (magmap.gui.atlas_editor.AtlasEditor method) (magmap.gui.roi_editor.ROIEditor method) get_scaled_regionprops() (in module magmap.atlas.register) get_selem() (in module magmap.cv.cv_nd) get_single_label() (in module magmap.stats.vols) get_split_stack_total_shape() (in module magmap.cv.chunking) get_thresholded_regionprops() (in module magmap.cv.cv_nd) get_transposed_image_path() (in module magmap.atlas.transformer) get_version() (in module magmap.io.libmag) GRID (magmap.plot.colormaps.DiscreteModes attribute) grid_search() (in module magmap.stats.mlearn) grid_search_profile (in module magmap.settings.config) GridSearchProfile (class in magmap.settings.grid_search_prof) GridSearchStats (class in magmap.stats.mlearn) GROUP (magmap.settings.config.RegisterTypes attribute) GROUP_COL (magmap.settings.config.PlotLabels attribute) H heat_map (magmap.stats.vols.MeasureLabel attribute) (magmap.stats.vols.MeasureLabelOverlap attribute) HemSides (class in magmap.settings.config) hide_axes() (in module magmap.plot.plot_support) HighIntensity (magmap.stats.vols.LabelMetrics attribute) HLINE (magmap.settings.config.PlotLabels attribute) HOMOGENEITY (magmap.stats.vols.MetricCombos attribute) hyperparams (magmap.settings.grid_search_prof.GridSearchProfile attribute) I ICON_PATH (in module magmap.settings.config) ID (magmap.settings.config.AtlasLabels attribute) (magmap.settings.config.ItkSnapLabels attribute) ID_COL (magmap.settings.config.PlotLabels attribute) ignore_invis (magmap.plot.plot_support.ImageOverlayer attribute) IMAGE (magmap.gui.vis_handler.StaleFlags attribute) Image5d (class in magmap.io.np_io) image5d (magmap.cv.classifier.ClassifyImage attribute) (magmap.gui.roi_editor.ROIEditor attribute) image5d_io (in module magmap.settings.config) ImageOverlayer (class in magmap.plot.plot_support) ImageOverlayer.RotTransform (class in magmap.plot.plot_support) ImageSyncMixin (class in magmap.plot.plot_support) img (magmap.atlas.transformer.Downsampler attribute) (magmap.cv.stack_detect.StackDetector attribute) (magmap.gui.plot_editor.PlotAxImg attribute) img3d (magmap.gui.plot_editor.PlotEditor attribute) img3d_labels (magmap.gui.plot_editor.PlotEditor attribute) img5d (in module magmap.settings.config) (magmap.plot.plot_support.ImageSyncMixin attribute) IMG_ATLAS (magmap.settings.config.RegNames attribute) IMG_ATLAS_EDGE (magmap.settings.config.RegNames attribute) IMG_ATLAS_LOG (magmap.settings.config.RegNames attribute) IMG_ATLAS_MASK (magmap.settings.config.RegNames attribute) IMG_ATLAS_PRECUR (magmap.settings.config.RegNames attribute) IMG_BORDERS (magmap.settings.config.RegNames attribute) IMG_EXP (magmap.settings.config.RegNames attribute) IMG_EXP_MASK (magmap.settings.config.RegNames attribute) IMG_GROUPED (magmap.settings.config.RegNames attribute) IMG_HEAT_COLOC (magmap.settings.config.RegNames attribute) IMG_HEAT_MAP (magmap.settings.config.RegNames attribute) IMG_LABELS (magmap.settings.config.RegNames attribute) IMG_LABELS_DIFF (magmap.settings.config.RegNames attribute) IMG_LABELS_DIST (magmap.settings.config.RegNames attribute) IMG_LABELS_EDGE (magmap.settings.config.RegNames attribute) IMG_LABELS_EDGE_LEVEL (magmap.settings.config.RegNames attribute) IMG_LABELS_INTERIOR (magmap.settings.config.RegNames attribute) IMG_LABELS_LEVEL (magmap.settings.config.RegNames attribute) IMG_LABELS_MARKERS (magmap.settings.config.RegNames attribute) IMG_LABELS_PRECUR (magmap.settings.config.RegNames attribute) IMG_LABELS_SUBSEG (magmap.settings.config.RegNames attribute) IMG_LABELS_TRANS (magmap.settings.config.RegNames attribute) IMG_LABELS_TRUNC (magmap.settings.config.RegNames attribute) IMG_LABELS_TRUNC_PRECUR (magmap.settings.config.RegNames attribute) img_open_path (magmap.settings.prefs_prof.PrefsProfile attribute) img_to_blobs_path() (in module magmap.io.np_io) imgs (magmap.io.export_stack.StackPlaneIO attribute) IMPORT_ATLAS (magmap.settings.config.RegisterTypes attribute) import_atlas() (in module magmap.atlas.atlas_refiner) import_dir (magmap.settings.prefs_prof.PrefsProfile attribute) import_img() (magmap.io.export_stack.StackPlaneIO class method) import_multiplane_images() (in module magmap.io.importer) IMPORT_ONLY (magmap.settings.config.ProcessTypes attribute) import_planes_to_stack() (in module magmap.io.importer) imshow_multichannel() (magmap.plot.plot_support.ImageOverlayer method) in_paint() (in module magmap.cv.cv_nd) include (magmap.settings.config.ClassifierData attribute) init() (magmap.gui.vis_handler.VisHandler method) init_shared_container() (in module magmap.cv.chunking) input_img (magmap.gui.plot_editor.PlotAxImg attribute) insert_about() (in module magmap.io.sqlite) insert_before_ext() (in module magmap.io.libmag) insert_blob_matches() (magmap.io.sqlite.ClrDB method) insert_blobs() (in module magmap.io.sqlite) insert_experiment() (in module magmap.io.sqlite) insert_matches() (in module magmap.cv.colocalizer) insert_roi() (in module magmap.io.sqlite) Intensity (magmap.stats.vols.LabelMetrics attribute) interp_order (magmap.io.export_stack.StackPlaneIO attribute) interpolate() (magmap.gui.atlas_editor.AtlasEditor method) (magmap.gui.atlas_editor.InterpolatePlanes method) interpolate_contours() (in module magmap.cv.cv_nd) interpolate_label_between_planes() (in module magmap.cv.cv_nd) InterpolatePlanes (class in magmap.gui.atlas_editor) INTERPOLATION (magmap.settings.config.Transforms attribute) is_binary() (in module magmap.io.libmag) is_conda_activated() (in module magmap.io.load_env) is_fork() (in module magmap.cv.chunking) is_identical_settings() (magmap.settings.profiles.SettingsDict static method) is_int() (in module magmap.io.libmag) is_javabridge_loaded() (in module magmap.io.importer) is_nan() (in module magmap.io.libmag) is_number() (in module magmap.io.libmag) is_seq() (in module magmap.io.libmag) is_venv_activated() (in module magmap.io.load_env) itk_to_sitk_img() (in module magmap.io.sitk_io) ItkSnapLabels (class in magmap.settings.config) J join_dfs() (in module magmap.io.df_io) K knn_dist() (in module magmap.stats.clustering) KNN_N (magmap.settings.profiles.RegKeys attribute) L LABEL_LOSS (magmap.settings.config.SmoothingMetrics attribute) label_metrics() (magmap.stats.vols.MeasureLabel class method) label_motion_thresh (magmap.gui.plot_editor.PlotEditor attribute) label_smoothing_metric() (in module magmap.atlas.atlas_refiner) LabelColumns (class in magmap.atlas.ontology) LabelMetrics (class in magmap.stats.vols) labels (magmap.atlas.register.RegImgs attribute) labels_annots (magmap.plot.plot_support.ImageOverlayer attribute) LABELS_DIFF (magmap.settings.config.RegisterTypes attribute) LABELS_DIFF_STATS (magmap.settings.config.RegisterTypes attribute) LABELS_DIST (magmap.settings.config.RegisterTypes attribute) labels_distance() (in module magmap.stats.vols) labels_edge (magmap.stats.vols.MeasureLabel attribute) labels_img (in module magmap.settings.config) (magmap.cv.segmenter.LabelToMarkerErosion attribute) (magmap.stats.vols.LabelToEdge attribute) labels_img_np (magmap.cv.segmenter.SubSegmenter attribute) (magmap.stats.vols.MeasureLabel attribute) labels_img_orig (in module magmap.settings.config) labels_img_sitk (in module magmap.settings.config) labels_imgs (magmap.stats.vols.MeasureLabelOverlap attribute) labels_interior (magmap.stats.vols.MeasureLabel attribute) labels_level (in module magmap.settings.config) (magmap.gui.plot_editor.PlotEditor attribute) labels_markers (magmap.atlas.register.RegImgs attribute) labels_metadata (in module magmap.settings.config) labels_ref (in module magmap.settings.config) labels_scaling (in module magmap.settings.config) labels_to_markers_blob() (in module magmap.cv.segmenter) labels_to_markers_erosion() (in module magmap.cv.segmenter) labels_to_parent() (in module magmap.atlas.ontology) LabelsMeta (class in magmap.atlas.labels_meta) LabelsRef (class in magmap.atlas.ontology) LabelToEdge (class in magmap.stats.vols) LabelToMarkerErosion (class in magmap.cv.segmenter) laplacian_of_gaussian_img() (in module magmap.cv.cv_nd) last_coord (magmap.cv.stack_detect.StackDetector attribute) last_lines() (in module magmap.io.libmag) LAT_UNLBL_PLANES (magmap.settings.config.AtlasMetrics attribute) LAT_UNLBL_VOL (magmap.settings.config.AtlasMetrics attribute) launch_magmap() (in module magmap.io.load_env) launch_subprocess() (in module magmap.io.load_env) LAYOUT (magmap.settings.config.PlotLabels attribute) LEFT (magmap.settings.config.HemSides attribute) LEGEND_NAMES (magmap.settings.config.PlotLabels attribute) LEVEL (magmap.settings.config.ABAKeys attribute) (magmap.settings.config.AtlasLabels attribute) (magmap.settings.config.AtlasMetrics attribute) (magmap.settings.config.Verbosity attribute) LINE_PLOT (magmap.settings.config.Plot2DTypes attribute) LOAD (magmap.settings.config.ProcessTypes attribute) load() (magmap.atlas.labels_meta.LabelsMeta method) (magmap.atlas.ontology.LabelsRef method) load_blobs() (magmap.cv.detector.Blobs method) load_db() (magmap.io.sqlite.ClrDB method) load_labels (in module magmap.settings.config) load_labels_ref() (magmap.atlas.ontology.LabelsRef method) load_metadata() (in module magmap.io.importer) load_numpy_to_sitk() (in module magmap.io.sitk_io) load_registered_img() (in module magmap.io.sitk_io) load_registered_imgs() (in module magmap.io.sitk_io) load_roi_files() (in module magmap.io.export_rois) load_truth_blobs() (magmap.io.sqlite.ClrDB method) load_truth_db() (in module magmap.io.sqlite) load_yaml() (in module magmap.io.yaml_io) LoadData (class in magmap.settings.config) LoadIO (class in magmap.settings.config) log_once() (in module magmap.io.libmag) log_path (in module magmap.settings.config) LOG_PATH (magmap.settings.config.Verbosity attribute) log_uncaught_exception() (in module magmap.io.load_env) logger (in module magmap.settings.config) LogWriter (class in magmap.settings.logs) LowIntensity (magmap.stats.vols.LabelMetrics attribute) M magmap module magmap.atlas module magmap.atlas.atlas_refiner module magmap.atlas.edge_seg module magmap.atlas.labels_meta module magmap.atlas.ontology module magmap.atlas.reg_tasks module magmap.atlas.register module magmap.atlas.transformer module magmap.brain_globe module magmap.brain_globe.bg_controller module magmap.brain_globe.bg_model module magmap.cloud module magmap.cloud.notify module magmap.cv module magmap.cv.chunking module magmap.cv.classifier module magmap.cv.colocalizer module magmap.cv.cv_nd module magmap.cv.detector module magmap.cv.segmenter module magmap.cv.stack_detect module magmap.cv.verifier module magmap.gui module magmap.gui.atlas_editor module magmap.gui.atlas_threads module magmap.gui.event_handlers module magmap.gui.image_viewer module magmap.gui.pixel_display module magmap.gui.plot_editor module magmap.gui.roi_editor module magmap.gui.verifier_editor module magmap.gui.vis_3d module magmap.gui.vis_handler module magmap.io module magmap.io.cli module magmap.io.df_io module magmap.io.export_regions module magmap.io.export_rois module magmap.io.export_stack module magmap.io.importer module magmap.io.libmag module magmap.io.load_env module magmap.io.naming module magmap.io.np_io module magmap.io.packaging module magmap.io.sitk_io module magmap.io.sqlite module magmap.io.subproc_io module magmap.io.yaml_io module magmap.plot module magmap.plot.colormaps module magmap.plot.plot_2d module magmap.plot.plot_3d module magmap.plot.plot_support module magmap.settings module magmap.settings.atlas_prof module magmap.settings.config module magmap.settings.grid_search_prof module magmap.settings.logs module magmap.settings.prefs_prof module magmap.settings.profiles module magmap.settings.roi_prof module magmap.stats module magmap.stats.atlas_stats module magmap.stats.clustering module magmap.stats.mlearn module magmap.stats.vols module magmap.tests module magmap.tests.test_chunking module magmap.tests.test_classifier module magmap.tests.test_cv_nd module magmap.tests.test_detector module magmap.tests.test_img_equality module magmap.tests.test_libmag module magmap.tests.test_np_io module magmap.tests.unit_testing module magnification (in module magmap.settings.config) MAGNIFICATION (magmap.settings.config.MetaKeys attribute) main() (in module magmap.atlas.register) (in module magmap.cloud.notify) (in module magmap.io.cli) (in module magmap.io.df_io) (in module magmap.io.load_env) (in module magmap.io.sqlite) (in module magmap.plot.plot_2d) (in module stitch.tile_config) make_acronym() (in module magmap.io.libmag) make_binary_cmap() (in module magmap.plot.colormaps) make_cmap() (magmap.plot.colormaps.DiscreteColormap method) make_dark_linear_cmap() (in module magmap.plot.colormaps) make_density_image() (in module magmap.io.export_regions) MAKE_DENSITY_IMAGES (magmap.settings.config.RegisterTypes attribute) make_density_images_mp() (in module magmap.io.export_regions) MAKE_EDGE_IMAGES (magmap.settings.config.RegisterTypes attribute) make_edge_images() (in module magmap.atlas.edge_seg) MAKE_EDGE_IMAGES_EXP (magmap.settings.config.RegisterTypes attribute) make_filenames() (in module magmap.io.importer) make_hyperparm_arr() (in module magmap.settings.grid_search_prof) make_isotropic() (in module magmap.cv.cv_nd) make_label_ids_set() (in module magmap.atlas.register) make_labels_edge() (magmap.stats.vols.LabelToEdge class method) make_labels_fg() (in module magmap.atlas.atlas_refiner) MAKE_LABELS_LEVEL (magmap.settings.config.RegisterTypes attribute) make_labels_level() (in module magmap.atlas.ontology) make_labels_level_img() (in module magmap.io.export_regions) make_modifier_plane() (in module magmap.atlas.transformer) make_modifier_resized() (in module magmap.atlas.transformer) make_modifier_scale() (in module magmap.atlas.transformer) make_out_path() (in module magmap.io.libmag) make_random_blobs() (magmap.tests.test_detector.TestDetector method) make_roi_paths() (in module magmap.io.export_rois) make_sub_segmented_labels() (in module magmap.atlas.edge_seg) make_subimage_name() (in module magmap.io.naming) MAKE_SUBSEGS (magmap.settings.config.RegisterTypes attribute) map_meas_to_labels() (in module magmap.stats.vols) map_metric_to_labels_img() (in module magmap.io.export_regions) MARGIN (magmap.settings.config.PlotLabels attribute) MARKER (magmap.settings.config.PlotLabels attribute) MARKER_EROSION (magmap.settings.profiles.RegKeys attribute) MARKER_EROSION_MIN (magmap.settings.profiles.RegKeys attribute) MARKER_EROSION_USE_MIN (magmap.settings.profiles.RegKeys attribute) mask_atlas() (in module magmap.cv.segmenter) match_atlas_labels() (in module magmap.atlas.atlas_refiner) match_blobs_roi() (in module magmap.cv.verifier) match_elements() (in module magmap.io.sqlite) match_ext() (in module magmap.io.libmag) MATCH_ID (magmap.cv.colocalizer.BlobMatch.Cols attribute) match_tol (magmap.cv.colocalizer.StackColocalizer attribute) match_world_info() (in module magmap.io.sitk_io) matplotlib_style (in module magmap.settings.config) max_pixels (magmap.cv.stack_detect.Blocks attribute) max_plane() (in module magmap.plot.plot_support) MAYAVI (magmap.gui.vis_handler.ViewerTabs attribute) MeanIntensity (magmap.stats.vols.LabelMetrics attribute) MeanNuclei (magmap.stats.vols.LabelMetrics attribute) meas_detection_accuracy() (in module magmap.cv.verifier) meas_dice() (in module magmap.stats.atlas_stats) MEAS_IMPROVEMENT (magmap.settings.config.RegisterTypes attribute) meas_improvement() (in module magmap.stats.atlas_stats) meas_landmark_dist() (in module magmap.stats.atlas_stats) meas_plot_coefvar() (in module magmap.stats.atlas_stats) meas_plot_zscores() (in module magmap.stats.atlas_stats) meas_pruning_ratio() (in module magmap.cv.detector) meas_region() (in module magmap.cv.cv_nd) meas_wt() (magmap.cv.segmenter.LabelToMarkerErosion class method) measure_atlas_refinement() (in module magmap.atlas.atlas_refiner) measure_counts() (magmap.stats.vols.MeasureLabel class method) measure_edge_dist() (magmap.stats.vols.MeasureLabel class method) measure_labels_metrics() (in module magmap.stats.vols) measure_labels_overlap() (in module magmap.stats.vols) measure_overlap() (in module magmap.atlas.atlas_refiner) (magmap.stats.vols.MeasureLabelOverlap class method) measure_overlap_combined_labels() (in module magmap.atlas.atlas_refiner) measure_overlap_labels() (in module magmap.atlas.atlas_refiner) measure_point_cloud() (magmap.stats.vols.MeasureLabel class method) measure_shapes() (magmap.stats.vols.MeasureLabel class method) measure_variation() (magmap.stats.vols.MeasureLabel class method) MeasureLabel (class in magmap.stats.vols) MeasureLabelOverlap (class in magmap.stats.vols) MedIntensity (magmap.stats.vols.LabelMetrics attribute) MELT_COLS (magmap.settings.config.RegisterTypes attribute) melt_cols() (in module magmap.io.df_io) merge_atlas_segmentations() (in module magmap.atlas.edge_seg) MERGE_ATLAS_SEGS (magmap.settings.config.RegisterTypes attribute) MERGE_ATLAS_SEGS_EXP (magmap.settings.config.RegisterTypes attribute) merge_blobs() (in module magmap.cv.chunking) MERGE_CSVS (magmap.settings.config.DFTasks attribute) merge_csvs() (in module magmap.io.df_io) MERGE_CSVS_COLS (magmap.settings.config.DFTasks attribute) MERGE_EXCELS (magmap.settings.config.DFTasks attribute) merge_excels() (in module magmap.io.df_io) MERGE_IMAGES (magmap.settings.config.RegisterTypes attribute) merge_images() (in module magmap.io.sitk_io) MERGE_IMAGES_CHANNELS (magmap.settings.config.RegisterTypes attribute) merge_split_stack() (in module magmap.cv.chunking) merge_split_stack2() (in module magmap.cv.chunking) merge_truth_dbs() (in module magmap.io.sqlite) MESH (magmap.settings.config.ItkSnapLabels attribute) meta_dict (in module magmap.settings.config) metadata_paths (in module magmap.settings.config) metadatas (in module magmap.settings.config) MetaKeys (class in magmap.settings.config) MetricCombos (class in magmap.stats.vols) MetricGroups (class in magmap.settings.config) METRICS_CLUSTER (magmap.settings.profiles.RegKeys attribute) MIDDLE (magmap.gui.roi_editor.ROIEditor.ZLevels attribute) mirror_planes() (in module magmap.atlas.atlas_refiner) MODE (magmap.settings.config.TruthDB attribute) model (magmap.settings.config.ClassifierData attribute) modified_cmap() (magmap.plot.colormaps.DiscreteColormap method) modify_settings() (magmap.settings.profiles.SettingsDict method) module magmap magmap.atlas magmap.atlas.atlas_refiner magmap.atlas.edge_seg magmap.atlas.labels_meta magmap.atlas.ontology magmap.atlas.reg_tasks magmap.atlas.register magmap.atlas.transformer magmap.brain_globe magmap.brain_globe.bg_controller magmap.brain_globe.bg_model magmap.cloud magmap.cloud.notify magmap.cv magmap.cv.chunking magmap.cv.classifier magmap.cv.colocalizer magmap.cv.cv_nd magmap.cv.detector magmap.cv.segmenter magmap.cv.stack_detect magmap.cv.verifier magmap.gui magmap.gui.atlas_editor magmap.gui.atlas_threads magmap.gui.event_handlers magmap.gui.image_viewer magmap.gui.pixel_display magmap.gui.plot_editor magmap.gui.roi_editor magmap.gui.verifier_editor magmap.gui.vis_3d magmap.gui.vis_handler magmap.io magmap.io.cli magmap.io.df_io magmap.io.export_regions magmap.io.export_rois magmap.io.export_stack magmap.io.importer magmap.io.libmag magmap.io.load_env magmap.io.naming magmap.io.np_io magmap.io.packaging magmap.io.sitk_io magmap.io.sqlite magmap.io.subproc_io magmap.io.yaml_io magmap.plot magmap.plot.colormaps magmap.plot.plot_2d magmap.plot.plot_3d magmap.plot.plot_support magmap.settings magmap.settings.atlas_prof magmap.settings.config magmap.settings.grid_search_prof magmap.settings.logs magmap.settings.prefs_prof magmap.settings.profiles magmap.settings.roi_prof magmap.stats magmap.stats.atlas_stats magmap.stats.clustering magmap.stats.mlearn magmap.stats.vols magmap.tests magmap.tests.test_chunking magmap.tests.test_classifier magmap.tests.test_cv_nd magmap.tests.test_detector magmap.tests.test_img_equality magmap.tests.test_libmag magmap.tests.test_np_io magmap.tests.unit_testing run stitch.tile_config MOVING_MASK (magmap.settings.config.RegSuffixes attribute) multiply_blob_abs_coords() (magmap.cv.detector.Blobs class method) multiply_blob_rel_coords() (magmap.cv.detector.Blobs class method) MULTIPLY_COLS (magmap.settings.config.DFTasks attribute) N NAME (magmap.settings.config.ABAKeys attribute) (magmap.settings.config.ItkSnapLabels attribute) NAME_KEY (magmap.settings.profiles.SettingsDict attribute) NAN_COLOR (magmap.settings.config.PlotLabels attribute) nav_motion_thresh (magmap.gui.plot_editor.PlotEditor attribute) NEW_ATLAS (magmap.settings.config.RegisterTypes attribute) NO_CIRCLES (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) NORMALIZE (magmap.settings.config.DFTasks attribute) normalize() (in module magmap.io.libmag) normalize_df() (in module magmap.io.df_io) NP (magmap.settings.config.LoadIO attribute) npstr_to_array() (in module magmap.io.libmag) NucClusLarg (magmap.stats.vols.LabelMetrics attribute) NucClusNoise (magmap.stats.vols.LabelMetrics attribute) NucCluster (magmap.stats.vols.LabelMetrics attribute) NucDSC (magmap.stats.vols.LabelMetrics attribute) Nuclei (magmap.stats.vols.LabelMetrics attribute) NucOut (magmap.stats.vols.LabelMetrics attribute) O object__import_feedback_changed() (magmap.gui.vis_handler.VisHandler method) object__profiles_reset_prefs_changed() (magmap.gui.vis_handler.VisHandler method) object__roi_feedback_changed() (magmap.gui.vis_handler.VisHandler method) object_mpl_fig_active_changed() (magmap.gui.vis_handler.VisHandler method) object_select_controls_tab_changed() (magmap.gui.vis_handler.VisHandler method) OFFSET (magmap.settings.config.AtlasMetrics attribute) on_axes_exit() (magmap.gui.plot_editor.PlotEditor method) on_close() (magmap.plot.plot_support.ImageSyncMixin method) on_draw() (magmap.gui.image_viewer.Blitter method) on_key_press() (magmap.gui.atlas_editor.AtlasEditor method) (magmap.gui.plot_editor.PlotEditor method) on_motion() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) on_pick() (magmap.gui.roi_editor.DraggableCircle method) on_press() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) on_release() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) open_atlas() (magmap.brain_globe.bg_controller.BrainGlobeCtrl method) opening (magmap.settings.config.SmoothingModes attribute) ORIG_COLORS (magmap.settings.config.AtlasLabels attribute) origin (magmap.plot.plot_support.ImageOverlayer attribute) overlap (magmap.cv.stack_detect.Blocks attribute) overlap_base (magmap.cv.stack_detect.Blocks attribute) overlap_padding (magmap.cv.stack_detect.Blocks attribute) overlay_images() (magmap.plot.plot_support.ImageOverlayer method) overlay_registered_imgs() (in module magmap.atlas.register) overlayer (magmap.gui.plot_editor.PlotEditor attribute) OVERLAYS (magmap.settings.config.RegisterTypes attribute) P pad_img() (in module magmap.plot.plot_3d) pad_seq() (in module magmap.io.libmag) PADDING (magmap.settings.config.PlotLabels attribute) PARAM (magmap.stats.mlearn.GridSearchStats attribute) PARENT (magmap.settings.config.AtlasMetrics attribute) PARENT_ID (magmap.settings.config.ABAKeys attribute) parse_deconstructed_name() (in module magmap.io.importer) parse_grid_stats() (in module magmap.stats.mlearn) parse_ome() (in module magmap.io.importer) parse_ome_raw() (in module magmap.io.importer) PATH (magmap.settings.config.TruthDB attribute) PATH_LABELS_META (magmap.atlas.labels_meta.LabelsMeta attribute) PATH_PREFIX (magmap.settings.atlas_prof.AtlasProfile attribute) (magmap.settings.grid_search_prof.GridSearchProfile attribute) (magmap.settings.roi_prof.ROIProfile attribute) PATH_PROFILES (magmap.settings.profiles.SettingsDict attribute) PATH_REF (magmap.settings.config.AtlasLabels attribute) perimeter_nd() (in module magmap.cv.cv_nd) picked (magmap.gui.roi_editor.DraggableCircle attribute) PIVOT_CONDS (magmap.settings.config.RegisterTypes attribute) pivot_with_conditions() (in module magmap.io.df_io) PixelDisplay (class in magmap.gui.pixel_display) PLANE (in module magmap.settings.config) plane (magmap.gui.plot_editor.PlotEditor attribute) planes (magmap.gui.atlas_editor.AtlasEditor attribute) Plot2DTypes (class in magmap.settings.config) plot_2d_shadows() (magmap.gui.vis_3d.Vis3D method) plot_2d_stack() (magmap.gui.roi_editor.ROIEditor method) plot_3d_points() (magmap.gui.vis_3d.Vis3D method) plot_3d_surface() (magmap.gui.vis_3d.Vis3D method) plot_ax_imgs (magmap.gui.plot_editor.PlotEditor property) plot_bars() (in module magmap.plot.plot_2d) plot_catplot() (in module magmap.plot.plot_2d) PLOT_CLUSTER_BLOBS (magmap.settings.config.RegisterTypes attribute) plot_clusters_by_label() (in module magmap.stats.atlas_stats) plot_ed (magmap.gui.verifier_editor.VerifierEditor.BlobView attribute) plot_eds (magmap.plot.plot_support.ImageSyncMixin attribute) plot_histogram() (in module magmap.plot.plot_2d) plot_image() (in module magmap.plot.plot_2d) PLOT_INTENS_NUC (magmap.settings.config.RegisterTypes attribute) plot_intensity_nuclei() (in module magmap.stats.atlas_stats) PLOT_KNNS (magmap.settings.config.RegisterTypes attribute) plot_knns() (in module magmap.stats.clustering) plot_labels (in module magmap.settings.config) PLOT_LATERAL_UNLABELED (magmap.settings.config.RegisterTypes attribute) plot_lines() (in module magmap.plot.plot_2d) plot_overlays() (in module magmap.plot.plot_2d) plot_overlays_reg() (in module magmap.plot.plot_2d) plot_probability() (in module magmap.plot.plot_2d) PLOT_REGION_DEV (magmap.settings.config.RegisterTypes attribute) plot_region_development() (in module magmap.stats.atlas_stats) plot_roc() (in module magmap.plot.plot_2d) plot_roi() (magmap.gui.roi_editor.ROIEditor method) plot_scatter() (in module magmap.plot.plot_2d) PLOT_SMOOTHING_METRICS (magmap.settings.config.RegisterTypes attribute) plot_swarm() (in module magmap.plot.plot_2d) plot_unlabeled_hemisphere() (in module magmap.stats.atlas_stats) PlotAxImg (class in magmap.gui.plot_editor) PlotEditor (class in magmap.gui.plot_editor) PlotLabels (class in magmap.settings.config) POINT_CLOUD (magmap.settings.config.MetricGroups attribute) POS (magmap.stats.mlearn.GridSearchStats attribute) POS_THRESH (in module magmap.settings.config) post() (in module magmap.cloud.notify) post_plot() (in module magmap.plot.plot_2d) PPV (magmap.stats.mlearn.GridSearchStats attribute) prefix (in module magmap.settings.config) prefix_out (in module magmap.settings.config) prefixes (in module magmap.settings.config) prefixes_out (in module magmap.settings.config) prefs (in module magmap.settings.config) PREFS_PATH (in module magmap.settings.config) PrefsProfile (class in magmap.settings.prefs_prof) prepare_roi() (in module magmap.plot.plot_3d) prepare_subimg() (in module magmap.plot.plot_3d) PREPROCESS (magmap.settings.config.ProcessTypes attribute) preprocess_img() (in module magmap.atlas.transformer) PreProcessKeys (class in magmap.settings.config) print_compact() (in module magmap.io.libmag) print_data_frame() (in module magmap.io.df_io) printcb() (in module magmap.io.libmag) printv() (in module magmap.io.libmag) proc_type (in module magmap.settings.config) process_cli_args() (in module magmap.io.cli) process_file() (in module magmap.io.cli) process_plane() (magmap.io.export_stack.StackPlaneIO class method) process_proc_tasks() (in module magmap.io.cli) process_tasks() (in module magmap.io.cli) ProcessTypes (class in magmap.settings.config) profiles (magmap.settings.grid_search_prof.GridSearchProfile attribute) progress (magmap.brain_globe.bg_controller.AccessAtlasThread attribute) (magmap.brain_globe.bg_controller.SetupAtlasesThread attribute) prune_blobs_mp() (magmap.cv.stack_detect.StackPruner class method) prune_overlap() (magmap.cv.stack_detect.StackPruner class method) prune_overlap_by_index() (magmap.cv.stack_detect.StackPruner class method) PRUNING (magmap.cv.stack_detect.StackTimes attribute) R R (magmap.settings.config.ItkSnapLabels attribute) radial_dist() (in module magmap.cv.cv_nd) radial_dist_diff() (in module magmap.cv.cv_nd) RADIUS (magmap.cv.detector.Blobs.Cols attribute) RANDOMN (magmap.plot.colormaps.DiscreteModes attribute) rc_params (in module magmap.settings.config) read_file() (in module magmap.io.importer) read_img() (in module magmap.io.sitk_io) read_np_archive() (in module magmap.io.np_io) read_sitk() (in module magmap.io.sitk_io) read_sitk_files() (in module magmap.io.sitk_io) read_tif() (in module magmap.io.np_io) refresh_images() (magmap.gui.atlas_editor.AtlasEditor method) refresh_img3d_labels() (magmap.gui.plot_editor.PlotEditor method) refresh_profile() (magmap.settings.profiles.SettingsDict method) reg_out_path() (in module magmap.io.sitk_io) reg_planes_to_img() (in module magmap.io.export_stack) reg_suffixes (in module magmap.settings.config) RegDensityMean (magmap.stats.vols.LabelMetrics attribute) RegImgs (class in magmap.atlas.register) REGION (magmap.cv.detector.Blobs.Cols attribute) (magmap.settings.config.AtlasMetrics attribute) Region (magmap.stats.vols.LabelMetrics attribute) REGION_ABBR (magmap.settings.config.AtlasMetrics attribute) REGION_NAME (magmap.settings.config.AtlasMetrics attribute) region_props() (magmap.stats.vols.MeasureLabel class method) register() (in module magmap.atlas.register) register_duo() (in module magmap.atlas.register) register_group() (in module magmap.atlas.register) register_repeat() (in module magmap.atlas.register) REGISTER_REV (magmap.settings.config.RegisterTypes attribute) register_rev() (in module magmap.atlas.register) RegisterTypes (class in magmap.settings.config) RegKeys (class in magmap.settings.profiles) RegNames (class in magmap.settings.config) RegNucMean (magmap.stats.vols.LabelMetrics attribute) RegParamMap (class in magmap.settings.atlas_prof) RegSuffixes (class in magmap.settings.config) RegVolMean (magmap.stats.vols.LabelMetrics attribute) rel_to_abs_ages() (in module magmap.atlas.ontology) REMAP (magmap.settings.config.PreProcessKeys attribute) remap_intensity() (in module magmap.plot.plot_3d) RemapLevelThread (class in magmap.gui.atlas_threads) remove_abs_blob_coords() (magmap.cv.detector.Blobs method) remove_atlas() (magmap.brain_globe.bg_controller.BrainGlobeCtrl method) remove_bg_from_dil_fg() (in module magmap.cv.cv_nd) remove_close_blobs() (in module magmap.cv.detector) remove_close_blobs_within_array() (in module magmap.cv.detector) remove_close_blobs_within_sorted_array() (in module magmap.cv.detector) remove_duplicate_blobs() (in module magmap.cv.detector) remove_file() (in module magmap.io.libmag) remove_labels() (magmap.plot.plot_support.ImageOverlayer method) remove_local_atlas() (magmap.brain_globe.bg_model.BrainGlobeMM method) remove_self() (magmap.gui.roi_editor.DraggableCircle method) REPEAT_CIRCLES (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) replace_labels() (in module magmap.atlas.ontology) replace_rel_with_abs_blob_coords() (magmap.cv.detector.Blobs class method) replace_seq() (in module magmap.io.libmag) replace_sitk_with_numpy() (in module magmap.io.sitk_io) REPLACE_VALS (magmap.settings.config.DFTasks attribute) replace_vals() (in module magmap.io.df_io) replace_vol() (in module magmap.plot.plot_3d) RESCALE (magmap.settings.config.Transforms attribute) rescale_resize() (in module magmap.cv.cv_nd) rescale_sub_roi() (magmap.atlas.transformer.Downsampler class method) RESOLUTIONS (magmap.cv.detector.Blobs.Keys attribute) (magmap.settings.config.MetaKeys attribute) rgb (in module magmap.settings.config) (magmap.gui.plot_editor.PlotAxImg attribute) (magmap.io.np_io.Image5d attribute) (magmap.plot.plot_support.ImageOverlayer attribute) RIGHT (magmap.settings.config.HemSides attribute) ROC_CURVE (magmap.settings.config.Plot2DTypes attribute) ROI (magmap.gui.vis_handler.StaleFlags attribute) roi_center_to_offset() (in module magmap.plot.plot_3d) roi_circles (magmap.settings.prefs_prof.PrefsProfile attribute) ROI_COLS (magmap.gui.roi_editor.ROIEditor attribute) ROI_ED (magmap.gui.vis_handler.ViewerTabs attribute) ROI_ID (magmap.cv.colocalizer.BlobMatch.Cols attribute) ROI_OFFSET (magmap.cv.detector.Blobs.Keys attribute) roi_plane (magmap.settings.prefs_prof.PrefsProfile attribute) ROI_SIZE (magmap.cv.detector.Blobs.Keys attribute) roi_styles (magmap.settings.prefs_prof.PrefsProfile attribute) roi_to_image5d() (in module magmap.io.importer) ROIEditor (class in magmap.gui.roi_editor) ROIEditor.CircleStyles (class in magmap.gui.roi_editor) ROIEditor.ZLevels (class in magmap.gui.roi_editor) ROIProfile (class in magmap.settings.roi_prof) roll_elements() (in module magmap.io.libmag) ROTATE (magmap.settings.config.PreProcessKeys attribute) (magmap.settings.config.Transforms attribute) rotate90() (in module magmap.cv.cv_nd) ROTATE_DEG (magmap.settings.config.Transforms attribute) rotate_img() (in module magmap.atlas.transformer) rotate_nd() (in module magmap.cv.cv_nd) ROTATION (magmap.settings.config.PlotLabels attribute) run module run() (magmap.brain_globe.bg_controller.AccessAtlasThread method) (magmap.brain_globe.bg_controller.SetupAtlasesThread method) (magmap.gui.atlas_threads.AnnotateLabels method) (magmap.gui.atlas_threads.RemapLevelThread method) S SA_VOL (magmap.settings.config.SmoothingMetrics attribute) SA_VOL_FRAC (magmap.settings.config.SmoothingMetrics attribute) SA_VOL_ORIG (magmap.settings.config.SmoothingMetrics attribute) SAMPLE (magmap.settings.config.AtlasMetrics attribute) SATURATE (magmap.settings.config.PreProcessKeys attribute) saturate_roi() (in module magmap.plot.plot_3d) save() (magmap.atlas.labels_meta.LabelsMeta method) save_archive() (magmap.cv.detector.Blobs method) save_atlas() (magmap.gui.atlas_editor.AtlasEditor method) save_fig() (in module magmap.plot.plot_support) (magmap.plot.plot_support.ImageSyncMixin method) save_image_info() (in module magmap.io.importer) save_np_image() (in module magmap.io.importer) save_path (magmap.atlas.labels_meta.LabelsMeta property) save_settings() (magmap.settings.profiles.SettingsDict method) SAVE_STEPS (magmap.settings.profiles.RegKeys attribute) save_yaml() (in module magmap.io.yaml_io) savefig (in module magmap.settings.config) scale_axes() (in module magmap.plot.plot_support) SCALE_BAR (magmap.settings.config.PlotLabels attribute) scale_coords() (in module magmap.atlas.ontology) scale_slice() (in module magmap.io.libmag) scale_xticks() (in module magmap.plot.plot_support) SCATTER_PLOT (magmap.settings.config.Plot2DTypes attribute) scroll_overview() (magmap.gui.atlas_editor.AtlasEditor method) (magmap.gui.plot_editor.PlotEditor method) scroll_plane() (in module magmap.plot.plot_support) scroll_to_bottom() (magmap.gui.vis_handler.VisHandler static method) segment_from_labels() (in module magmap.cv.segmenter) segment_rw() (in module magmap.cv.segmenter) segment_ws() (in module magmap.cv.segmenter) select_about() (in module magmap.io.sqlite) select_blob() (magmap.io.sqlite.ClrDB method) select_blob_by_id() (magmap.io.sqlite.ClrDB method) select_blob_matches() (magmap.io.sqlite.ClrDB method) select_blob_matches_by_blob_id() (magmap.io.sqlite.ClrDB method) select_blobs_by_position() (magmap.io.sqlite.ClrDB method) select_blobs_by_roi() (magmap.io.sqlite.ClrDB method) select_blobs_confirmed() (in module magmap.io.sqlite) select_experiment() (magmap.io.sqlite.ClrDB method) select_matches() (in module magmap.cv.colocalizer) select_or_insert_experiment() (magmap.io.sqlite.ClrDB method) select_or_insert_roi() (in module magmap.io.sqlite) select_roi() (in module magmap.io.sqlite) select_rois() (in module magmap.io.sqlite) SENS (magmap.stats.mlearn.GridSearchStats attribute) series (in module magmap.settings.config) series_as_str() (in module magmap.io.libmag) series_list (in module magmap.settings.config) set_blob_abs_coords() (magmap.cv.detector.Blobs class method) set_blob_channel() (magmap.cv.detector.Blobs class method) set_blob_col() (magmap.cv.detector.Blobs class method) set_blob_confirmed() (magmap.cv.detector.Blobs class method) set_blob_truth() (magmap.cv.detector.Blobs class method) set_circle_visibility() (magmap.gui.roi_editor.ROIEditor method) set_data() (magmap.atlas.transformer.Downsampler class method) (magmap.io.export_stack.StackPlaneIO class method) (magmap.stats.vols.MeasureLabel class method) (magmap.stats.vols.MeasureLabelOverlap class method) set_images() (magmap.cv.segmenter.SubSegmenter class method) set_labels_img() (magmap.cv.segmenter.LabelToMarkerErosion class method) set_labels_level() (magmap.plot.plot_support.ImageSyncMixin method) set_mp_start_method() (in module magmap.cv.chunking) set_overview_title() (in module magmap.plot.plot_support) set_scinot() (in module magmap.plot.plot_support) set_show_crosslines() (magmap.plot.plot_support.ImageSyncMixin method) set_show_label() (magmap.gui.plot_editor.PlotEditor method) set_show_labels() (magmap.plot.plot_support.ImageSyncMixin method) SettingsDict (class in magmap.settings.profiles) setUp() (magmap.tests.unit_testing.TestImageStackProcessing method) setup_atlas_profiles() (in module magmap.io.cli) setup_blocks() (in module magmap.cv.stack_detect) setup_channels() (in module magmap.plot.plot_3d) setup_classification_roi() (in module magmap.cv.classifier) setup_cmaps() (in module magmap.plot.colormaps) setup_colormaps() (in module magmap.plot.colormaps) setup_dbs() (in module magmap.io.cli) setup_fig() (in module magmap.plot.plot_support) setup_grid_search_profiles() (in module magmap.io.cli) setup_image() (in module magmap.io.cli) setup_images() (in module magmap.io.np_io) setup_images_for_plane() (in module magmap.plot.plot_support) setup_import_dir() (in module magmap.io.importer) setup_import_metadata() (in module magmap.io.importer) setup_import_multipage() (in module magmap.io.importer) setup_labels() (in module magmap.io.cli) setup_labels_cmap() (in module magmap.plot.colormaps) setup_logger() (in module magmap.settings.logs) setup_match_blobs_roi() (in module magmap.cv.verifier) setup_roi_profiles() (in module magmap.io.cli) setup_shared_arrs() (magmap.cv.chunking.SharedArrsContainer class method) setup_stack() (in module magmap.io.export_stack) setup_style() (in module magmap.plot.plot_2d) setup_transform() (magmap.plot.plot_support.ImageOverlayer method) setup_vspans() (in module magmap.plot.plot_support) SetupAtlasesThread (class in magmap.brain_globe.bg_controller) SHAPE (magmap.settings.config.MetaKeys attribute) SHAPES (magmap.settings.config.MetricGroups attribute) shared_arrs (magmap.cv.chunking.SharedArrsContainer attribute) SharedArr (class in magmap.cv.chunking) SharedArrsContainer (class in magmap.cv.chunking) shift_blob_abs_coords() (magmap.cv.detector.Blobs class method) shift_blob_rel_coords() (magmap.cv.detector.Blobs class method) shift_blobs() (magmap.cv.detector.Blobs class method) show (in module magmap.settings.config) show() (in module magmap.plot.plot_support) show_atlas() (magmap.gui.atlas_editor.AtlasEditor method) show_blob_surroundings() (in module magmap.cv.detector) show_blobs() (magmap.gui.vis_3d.Vis3D method) show_blobs_per_channel() (magmap.cv.detector.Blobs class method) show_colocalized_blobs() (magmap.gui.roi_editor.ROIEditor method) show_fig() (magmap.gui.verifier_editor.VerifierEditor method) show_full_arrays() (in module magmap.io.libmag) show_labels() (magmap.gui.plot_editor.PlotEditor method) show_labels_annots() (magmap.plot.plot_support.ImageSyncMixin method) show_overview() (magmap.gui.plot_editor.PlotEditor method) show_roi() (magmap.gui.plot_editor.PlotEditor method) show_roi_outline() (magmap.gui.vis_3d.Vis3D method) show_subplot() (magmap.gui.roi_editor.ROIEditor method) show_surface_labels() (in module magmap.plot.plot_3d) show_views() (magmap.gui.verifier_editor.VerifierEditor method) shutdown() (in module magmap.io.cli) SIDE (magmap.settings.config.AtlasMetrics attribute) signal (magmap.brain_globe.bg_controller.AccessAtlasThread attribute) (magmap.brain_globe.bg_controller.SetupAtlasesThread attribute) (magmap.gui.atlas_threads.AnnotateLabels attribute) (magmap.gui.atlas_threads.RemapLevelThread attribute) signal_prog (magmap.gui.atlas_threads.AnnotateLabels attribute) (magmap.gui.atlas_threads.RemapLevelThread attribute) signed_distance_transform() (in module magmap.cv.cv_nd) SIMILARITY_METRIC (magmap.settings.config.AtlasMetrics attribute) SINGLE (magmap.settings.config.RegisterTypes attribute) SITK (magmap.settings.config.LoadIO attribute) sitk_to_itk_img() (in module magmap.io.sitk_io) SIZE (magmap.settings.config.AtlasMetrics attribute) (magmap.settings.config.PlotLabels attribute) SKELETON_EROSION (magmap.settings.profiles.RegKeys attribute) SM_QUALITY (magmap.settings.config.SmoothingMetrics attribute) smooth_labels() (in module magmap.atlas.atlas_refiner) SMOOTHING_METRICS_AGGR (magmap.settings.config.RegisterTypes attribute) smoothing_peak() (in module magmap.stats.atlas_stats) SMOOTHING_PEAKS (magmap.settings.config.RegisterTypes attribute) SmoothingMetrics (class in magmap.settings.config) SmoothingModes (class in magmap.settings.config) sort_blobs() (in module magmap.cv.detector) spacing (magmap.stats.vols.MeasureLabel attribute) spectral_unmixing (magmap.settings.roi_prof.ROIProfile attribute) splice_before() (in module magmap.io.libmag) splitext() (in module magmap.io.libmag) stack_split_remerge() (magmap.tests.test_chunking.TestChunking static method) stack_splitter() (in module magmap.cv.chunking) stack_to_img() (in module magmap.io.export_stack) StackColocalizer (class in magmap.cv.colocalizer) StackDetector (class in magmap.cv.stack_detect) StackPlaneIO (class in magmap.io.export_stack) StackPruner (class in magmap.cv.stack_detect) StackTimes (class in magmap.cv.stack_detect) StaleFlags (class in magmap.gui.vis_handler) start_db() (magmap.io.sqlite.ClrDB method) start_jvm() (in module magmap.io.importer) stitch.tile_config module stop_jvm() (in module magmap.io.importer) STR_FN (in module magmap.settings.config) str_to_disp() (in module magmap.io.libmag) sub_roi_slices (magmap.cv.stack_detect.Blocks attribute) sub_rois_offsets (magmap.cv.stack_detect.Blocks attribute) sub_segment() (magmap.cv.segmenter.SubSegmenter class method) sub_segment_labels() (in module magmap.cv.segmenter) subseg (magmap.stats.vols.MeasureLabel attribute) SubSegmenter (class in magmap.cv.segmenter) SUBTRACT_COLS (magmap.settings.config.DFTasks attribute) suffix (in module magmap.settings.config) SUFFIX_BLOB_CLUSTERS (in module magmap.settings.config) SUFFIX_BLOBS (in module magmap.settings.config) SUFFIX_IMAGE5D (in module magmap.settings.config) SUFFIX_META (in module magmap.settings.config) SUFFIX_SUBIMG (in module magmap.settings.config) SUM_COLS (magmap.settings.config.DFTasks attribute) surface_area_3d() (in module magmap.cv.cv_nd) SurfaceArea (magmap.stats.vols.LabelMetrics attribute) swap_elements() (in module magmap.io.libmag) SWARM_PLOT (magmap.settings.config.Plot2DTypes attribute) SYMMETRIC_COLORS (magmap.settings.config.AtlasLabels attribute) T test_angle_indices() (magmap.tests.test_cv_nd.TestCvNd method) test_blob_accessors() (magmap.tests.test_detector.TestDetector method) test_combine_paths() (magmap.tests.test_libmag.TestLibmag method) test_compression() (in module magmap.io.subproc_io) test_flatten() (magmap.tests.test_libmag.TestLibmag method) test_format_bytes() (magmap.tests.test_libmag.TestLibmag method) test_get_filename_without_ext() (magmap.tests.test_libmag.TestLibmag method) test_get_int() (magmap.tests.test_libmag.TestLibmag method) test_get_num_channels() (magmap.tests.test_np_io.TestLibmag method) test_insert_before_ext() (magmap.tests.test_libmag.TestLibmag method) test_is_int() (magmap.tests.test_libmag.TestLibmag method) test_is_number() (magmap.tests.test_libmag.TestLibmag method) test_load_image() (magmap.tests.unit_testing.TestImageStackProcessing method) test_make_abbreviation() (magmap.tests.test_libmag.TestLibmag method) test_match_ext() (magmap.tests.test_libmag.TestLibmag method) test_pad_seq() (magmap.tests.test_libmag.TestLibmag method) test_process_whole_image() (magmap.tests.unit_testing.TestImageStackProcessing method) test_reg_img() (magmap.tests.test_img_equality.TestImgEquality method) test_replace_seq() (magmap.tests.test_libmag.TestLibmag method) test_rescale_resize() (magmap.tests.test_cv_nd.TestCvNd method) test_series_as_str() (magmap.tests.test_libmag.TestLibmag method) test_setup_classification_roi() (magmap.tests.test_classifier.TestClassifier method) test_splice_before() (magmap.tests.test_libmag.TestLibmag method) test_splitext() (magmap.tests.test_libmag.TestLibmag method) test_stack_splitter() (magmap.tests.test_chunking.TestChunking method) test_str_to_disp() (magmap.tests.test_libmag.TestLibmag method) TestChunking (class in magmap.tests.test_chunking) TestClassifier (class in magmap.tests.test_classifier) TestCvNd (class in magmap.tests.test_cv_nd) TestDetector (class in magmap.tests.test_detector) TestImageStackProcessing (class in magmap.tests.unit_testing) TestImgEquality (class in magmap.tests.test_img_equality) TestLibmag (class in magmap.tests.test_libmag) (class in magmap.tests.test_np_io) TEXT_POS (magmap.settings.config.PlotLabels attribute) Themes (class in magmap.settings.config) threshold() (in module magmap.plot.plot_3d) TIFFFILE (magmap.settings.config.LoadIO attribute) TITLE (magmap.settings.config.PlotLabels attribute) TN (magmap.stats.mlearn.GridSearchStats attribute) TO_LABEL (magmap.atlas.ontology.LabelColumns attribute) to_seq() (in module magmap.io.libmag) toggle_btn() (magmap.plot.plot_support.ImageSyncMixin static method) toggle_edit_mode() (magmap.gui.atlas_editor.AtlasEditor method) tol (magmap.cv.stack_detect.Blocks attribute) TOP (magmap.gui.roi_editor.ROIEditor.ZLevels attribute) TOTAL (magmap.cv.stack_detect.StackTimes attribute) TP (magmap.stats.mlearn.GridSearchStats attribute) transform (magmap.plot.plot_support.ImageOverlayer.RotTransform attribute) TRANSFORM (magmap.settings.config.ProcessTypes attribute) Transforms (class in magmap.settings.config) TRANSLATE_CHILDREN (magmap.settings.config.AtlasLabels attribute) translate_coord() (magmap.gui.plot_editor.PlotEditor method) TRANSLATE_LABELS (magmap.settings.config.AtlasLabels attribute) transpose_1d() (in module magmap.io.libmag) transpose_1d_rev() (in module magmap.io.libmag) transpose_images() (in module magmap.plot.plot_support) transpose_img() (in module magmap.atlas.atlas_refiner) (in module magmap.atlas.transformer) truncate_decimal_digit() (in module magmap.io.libmag) truncate_labels() (in module magmap.atlas.atlas_refiner) TRUTH (magmap.cv.detector.Blobs.Cols attribute) truth_db_mode (in module magmap.settings.config) TruthDB (class in magmap.settings.config) TruthDBModes (class in magmap.settings.config) U unit_factor (in module magmap.settings.config) update() (magmap.gui.image_viewer.Blitter method) update_alpha_blend() (magmap.gui.plot_editor.PlotEditor method) update_atlas_table() (magmap.brain_globe.bg_controller.BrainGlobeCtrl method) update_blobs() (magmap.cv.colocalizer.BlobMatch method) update_btn() (magmap.gui.atlas_editor.InterpolatePlanes method) update_color_picker() (magmap.gui.atlas_editor.AtlasEditor method) update_coord() (magmap.gui.plot_editor.PlotEditor method) update_coords() (magmap.gui.atlas_editor.AtlasEditor method) update_fields() (magmap.atlas.register.RegImgs method) update_img_display() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.vis_3d.Vis3D method) update_imgs_display() (magmap.gui.roi_editor.ROIEditor method) (magmap.plot.plot_support.ImageSyncMixin method) update_log_level() (in module magmap.settings.logs) update_max_intens_proj() (magmap.gui.roi_editor.ROIEditor method) (magmap.plot.plot_support.ImageSyncMixin method) update_plane() (magmap.gui.atlas_editor.InterpolatePlanes method) update_plane_slider() (magmap.gui.plot_editor.PlotEditor method) update_plot_ax_img_display() (magmap.gui.plot_editor.PlotEditor static method) update_profiles() (in module magmap.io.cli) update_prog() (magmap.brain_globe.bg_controller.AccessAtlasThread method) (magmap.brain_globe.bg_controller.SetupAtlasesThread method) (magmap.gui.atlas_threads.AnnotateLabels method) (magmap.gui.atlas_threads.RemapLevelThread method) update_rois() (in module magmap.io.sqlite) upgrade_db() (in module magmap.io.sqlite) URI_SCHEME (in module magmap.settings.config) user_app_dirs (in module magmap.settings.config) V VarIntensDiff (magmap.stats.vols.LabelMetrics attribute) VarIntensIn (magmap.stats.vols.LabelMetrics attribute) VarIntensity (magmap.stats.vols.LabelMetrics attribute) VarIntensMatch (magmap.stats.vols.LabelMetrics attribute) VarIntensOut (magmap.stats.vols.LabelMetrics attribute) VarNucIn (magmap.stats.vols.LabelMetrics attribute) VarNuclei (magmap.stats.vols.LabelMetrics attribute) VarNucMatch (magmap.stats.vols.LabelMetrics attribute) VarNucOut (magmap.stats.vols.LabelMetrics attribute) VENV_DIR (in module magmap.io.load_env) VER (magmap.cv.detector.Blobs.Keys attribute) verbose (in module magmap.settings.config) Verbosity (class in magmap.settings.config) verbosity (in module magmap.settings.config) verification_stats() (in module magmap.io.sqlite) VERIFIED (magmap.settings.config.TruthDBModes attribute) VerifierEditor (class in magmap.gui.verifier_editor) VerifierEditor.BlobView (class in magmap.gui.verifier_editor) VERIFY (magmap.settings.config.TruthDBModes attribute) verify_rois() (in module magmap.cv.verifier) verify_stack() (in module magmap.cv.verifier) VIEW (magmap.settings.config.TruthDBModes attribute) view_subimg() (magmap.gui.atlas_editor.AtlasEditor method) (magmap.gui.plot_editor.PlotEditor method) ViewerTabs (class in magmap.gui.vis_handler) VIS (magmap.settings.config.ItkSnapLabels attribute) Vis3D (class in magmap.gui.vis_3d) VisHandler (class in magmap.gui.vis_handler) VOL (magmap.settings.config.SmoothingMetrics attribute) VOL_ATLAS (magmap.settings.config.AtlasMetrics attribute) VOL_COMPARE (magmap.settings.config.RegisterTypes attribute) VOL_LABELS (magmap.settings.config.AtlasMetrics attribute) VOL_ORIG (magmap.settings.config.SmoothingMetrics attribute) VOL_STATS (magmap.settings.config.RegisterTypes attribute) VolAlt (magmap.stats.vols.LabelMetrics attribute) VolAltPx (magmap.stats.vols.LabelMetrics attribute) VolDSC (magmap.stats.vols.LabelMetrics attribute) VolOut (magmap.stats.vols.LabelMetrics attribute) VolPx (magmap.stats.vols.LabelMetrics attribute) Volume (magmap.stats.vols.LabelMetrics attribute) volumes_by_id() (in module magmap.atlas.register) volumes_by_id_compare() (in module magmap.atlas.register) VSPAN_COL (magmap.settings.config.PlotLabels attribute) VSPAN_FORMAT (magmap.settings.config.PlotLabels attribute) W warn() (in module magmap.io.libmag) watershed_distance() (in module magmap.cv.segmenter) WATERSHED_MASK_FILTER (magmap.settings.profiles.RegKeys attribute) weight_mean() (in module magmap.io.df_io) weight_std() (in module magmap.io.df_io) write() (magmap.settings.logs.LogWriter method) write_img() (in module magmap.io.sitk_io) write_pts() (in module magmap.io.sitk_io) write_raw_file() (in module magmap.io.np_io) write_reg_images() (in module magmap.io.sitk_io) write_registered_image() (in module magmap.io.sitk_io) write_tif() (in module magmap.io.np_io) WT_COL (magmap.settings.config.PlotLabels attribute) wt_dists (magmap.cv.segmenter.LabelToMarkerErosion attribute) X X (magmap.cv.detector.Blobs.Cols attribute) X_COL (magmap.settings.config.PlotLabels attribute) X_LABEL (magmap.settings.config.PlotLabels attribute) X_LIM (magmap.settings.config.PlotLabels attribute) X_SCALE (magmap.settings.config.PlotLabels attribute) X_TICK_LABELS (magmap.settings.config.PlotLabels attribute) X_UNIT (magmap.settings.config.PlotLabels attribute) xlims (magmap.plot.plot_support.ImageOverlayer.RotTransform attribute) Y Y (magmap.cv.detector.Blobs.Cols attribute) Y_COL (magmap.settings.config.PlotLabels attribute) Y_LABEL (magmap.settings.config.PlotLabels attribute) Y_LIM (magmap.settings.config.PlotLabels attribute) Y_SCALE (magmap.settings.config.PlotLabels attribute) Y_TICK_LABELS (magmap.settings.config.PlotLabels attribute) Y_UNIT (magmap.settings.config.PlotLabels attribute) ylims (magmap.plot.plot_support.ImageOverlayer.RotTransform attribute) Z Z (magmap.cv.detector.Blobs.Cols attribute) zero_crossing() (in module magmap.cv.cv_nd) zoom (in module magmap.settings.config) ZOOM (magmap.settings.config.MetaKeys attribute) ZOOM_SHIFT (magmap.settings.config.PlotLabels attribute) zscore_df() (in module magmap.io.df_io) ZSCORES (magmap.settings.config.RegisterTypes attribute)