Index

A

a_ids (neu_eval.assign.Completeness attribute) (neu_eval.overlap.Contingency attribute) a_to_b (neu_eval.assign.Match attribute) a_totals() (neu_eval.overlap.Contingency method) absolute() (in module neu_vol.mapped) accepted() (in module neu_proc.ops.dilate) add() (neu_draw.scene.Scene method) add_block() (neu_morpho.measure.sweep.SweepTotals method) add_layer() (neu_glance.serving.Server method) add_mesh() (neu_draw.scene.Scene method) add_nodes() (neu_morpho.measure.sweep.SweepTotals method) add_points() (neu_draw.scene.Scene method) add_skeleton() (neu_draw.scene.Scene method) address() (in module neu_vol.dvid) adjudicated (neu_eval.compare.Report attribute) adjudicated_summary (neu_eval.compare.Report attribute) agglomerate_table() (in module neu_vol.webknossos) align_box() (in module neu_lib.grid) align_grid() (in module neu_vol.ops.align) aligned() (neu_lib.grid.BBox method) aligned_to() (neu_draw.scene.Placed method) (neu_draw.scene.Scene method) all_body_annotations() (in module neu_mark.notebook) allowlist (neu_morpho.pipeline.Plan attribute) allowlist_path (neu_morpho.pipeline.Plan property) alpha (neu_draw.scene.LinesDrawable attribute) (neu_draw.scene.MeshDrawable attribute) (neu_draw.scene.PointsDrawable attribute) anchor_of() (in module neu_draw.scene) anchor_point() (in module neu_draw.layout) ANCHORS (in module neu_draw.layout) (in module neu_draw.scene) angles() (in module neu_draw.orbit) AnimateProblem animation (neu_draw.toolbar.Toolbar attribute) annotate() (neu_glance.serving.Server method) ANNOTATE_LAYER (in module neu_glance.serving) annotation_csv() (in module neu_eval.tables) annotation_extent() (in module neu_glance.state) annotation_ids() (in module neu_mark.annsource) annotation_layer() (in module neu_glance.sources) annotation_source() (in module neu_mark.ops) annotation_source_extent() (in module neu_glance.sources) annotation_source_voxel_size() (in module neu_glance.sources) ANNOTATION_TOOLS (in module neu_glance.serving) ANNOTATION_TYPE (in module neu_glance.sources) ANNOTATION_TYPES (in module neu_glance.layers)

api() (in module neu_vol.webknossos) apply() (in module neu_eval.adjudicate) (in module neu_glance.config) (neu_lib.piece.Piece method) (neu_mark.rules.RuleSet method) apply_compartment_block() (neu_morpho.metrics_db.MetricsDB method) apply_counts_block() (neu_morpho.metrics_db.MetricsDB method) apply_index_block() (neu_morpho.metrics_db.MetricsDB method) apply_mask_values() (in module neu_vol.ops.maskvalue) apply_relabel() (in module neu_vol.ops.relabel) apply_rules() (in module neu_mark.explore) apply_skel_batch() (neu_morpho.metrics_db.MetricsDB method) arrange() (neu_draw.scene.Scene method) arrange_offsets() (in module neu_draw.layout) array (neu_glance.served_layer.ServedLayer attribute) (neu_lib.piece.Piece attribute) (neu_lib.vec.Vec3 property) array_module() (in module neu_proc.ops.backend) ArrayBackend (class in neu_vol.backends.base) as_dict() (neu_eval.assign.Completeness method) (neu_eval.voxel.Rand method) (neu_eval.voxel.Voi method) as_directory() (in module neu_vol.location) as_hex_color() (in module neu_glance.shaders) as_mapping() (neu_mark.rules.RuleSet method) as_table() (in module neu_mark.segprops) assemble_body() (in module neu_morpho.mesh) assign_colors() (in module neu_draw.colors) at (neu_eval.assign.Completeness attribute) (neu_glance.movie.animate.Tween attribute) at() (neu_glance.movie.animate.Timeline method) AT_TYPE (in module neu_mark.annotations) (in module neu_mark.segprops) (in module neu_vol.sharded) attach() (in module neu_draw.toolbar) attach_points() (in module neu_morpho.measure.paths) auto_factor() (in module neu_vol.pyramid) available_rois() (in module neu_vol.dvid) AXES (in module neu_draw.layout) (in module neu_glance.movie.animate) (in module neu_mark.tables) axes_string() (in module neu_vol.backends.hdf5) axes_visible (neu_draw.scene.Scene attribute) Axis (in module neu_draw.orbit) axis_index() (in module neu_draw.layout) axis_quaternion() (in module neu_draw.orbit) (in module neu_glance.movie.animate)

B

b_ids (neu_eval.assign.Completeness attribute) (neu_eval.overlap.Contingency attribute) b_to_a (neu_eval.assign.Match attribute) b_totals() (neu_eval.overlap.Contingency method) backdrop (neu_draw.backends.legend.LegendOverlay attribute) background (neu_draw.scene.Scene attribute) bake() (neu_draw.scene.Scene method) baked() (neu_draw.scene.LinesDrawable method) (neu_draw.scene.MeshDrawable method) (neu_draw.scene.PointsDrawable method) ball() (in module neu_proc.ops.kernels) base (neu_glance.movie.animate.Timeline attribute) BASELINE (in module neu_draw.vectorfile) BBox (class in neu_lib.grid) bbox (neu_draw.scene.Placed property) (neu_draw.scene.Scene property) (neu_glance.served_layer.ServedLayer property) (neu_lib.mesh.Mesh property) (neu_lib.piece.Piece property) (neu_lib.skeleton.Skeleton property) BENIGN_PATTERNS (in module neu_vol.logs) best_match() (in module neu_eval.assign) bin_to_nodes() (in module neu_morpho.measure.sweep) blob_signal() (in module neu_morpho.measure.sweep) Block (class in blockrun.engine) block (neu_morpho.pipeline.Plan attribute) block_align() (in module neu_morpho.ops.export_roi_seg) block_chunk_shape_xyz() (in module neu_morpho.coords) block_map() (in module blockrun.engine) block_shape (neu_morpho.config.MeshConfig attribute) BLOCK_STAGES (neu_morpho.metrics_db.MetricsDB attribute) blockrun module blockrun.dask_config module blockrun.dask_runner module blockrun.engine module blockrun.manifest module blocks (neu_morpho.measure.sweep.SweepTotals attribute)

blocks_from_mask() (in module neu_morpho.measure.sweep) bodies_by_size() (neu_morpho.metrics_db.MetricsDB method) body_annotations() (in module neu_mark.notebook) body_dir() (in module neu_morpho.fragments) BODY_DTYPE (in module neu_mark.tables) body_ids() (in module neu_mark.notebook) BODY_INSTANCE (in module neu_mark.dvid) body_mesh() (in module neu_draw.sources) body_meshes() (in module neu_draw.sources) body_neuropil_fractions() (in module neu_mark.tables) body_roi_counts() (in module neu_mark.tables) body_skeleton() (in module neu_draw.sources) body_skeletons() (in module neu_draw.sources) BODY_TABLES (in module neu_mark.ops) body_voxels (neu_morpho.measure.sweep.SweepTotals attribute) bound() (neu_mark.rules.Rule method) boundary_band() (in module neu_eval.overlap) bounds() (neu_glance.serving.Server method) bounds_nm (neu_glance.served_layer.ServedLayer property) (neu_lib.piece.Piece property) box() (in module neu_proc.ops.kernels) box_predicate() (in module neu_lib.predicates) boxes() (neu_glance.serving.Server method) boxes_layer() (in module neu_glance.layers) bridge_gaps() (in module neu_morpho.measure.paths) BROWSERS (in module neu_glance.movie.rendering) bucket_name() (in module neu_morpho.fragments) build() (in module neu_draw.backends.pygfx) (in module neu_mark.annsource) (in module neu_mark.roi_layers) (in module neu_mark.segprops) build_annotation() (in module neu_glance.layers) build_dataset() (in module neu_vol.ngff) build_entries() (neu_draw.backends.legend.LegendOverlay method) build_info() (in module neu_mark.annotations) build_multiscales_attrs() (in module neu_vol.ngff) build_record() (in module neu_vol.ops.provenance) build_scene() (in module neu_draw.scene) build_state() (in module neu_glance.state) BUILTIN_COLORS (in module neu_glance.shaders) bundled_configs() (in module blockrun.dask_config) BY_ID_KEY (in module neu_mark.annsource) by_label() (neu_draw.scene.Scene method)

C

cable_length_nm() (in module neu_morpho.measure.metrics) cable_shares() (in module neu_morpho.measure.sweep) Cache (class in neu_draw.cache) CALLER_KEYS (in module neu_glance.config) Camera (class in neu_draw.scene) camera (neu_draw.backends.legend.LegendOverlay attribute) (neu_draw.backends.pygfx.View attribute) (neu_draw.scene.Scene attribute) (neu_draw.viewstate.ViewState attribute) CAMERA_KEYS (in module neu_glance.movie.animate) CAMERA_Z (in module neu_draw.backends.legend) canvas (neu_draw.backends.pygfx.View attribute) cap (neu_draw.vectorfile.Segments attribute) case_collisions() (in module neu_mark.segprops) center (neu_lib.grid.BBox property) center() (neu_draw.backends.pygfx.View method) centered() (neu_draw.scene.Placed method) (neu_draw.scene.Scene method) channel_axis (neu_glance.served_layer.ServedLayer attribute) (neu_lib.piece.Piece property) channels (neu_lib.piece.Piece property) check() (neu_glance.movie.animate.Timeline method) (neu_morpho.ops.manifest.FailureBreaker method) check_against_node() (in module neu_mark.roi_layers) check_fits() (in module neu_vol.ops.pack) check_grid() (in module neu_morpho.ops.manifest) check_hdf5_target() (in module neu_vol.ops.pack) check_instance_type() (in module neu_vol.dvid) check_manifest_matches_output() (in module neu_morpho.ops.manifest) check_mapping() (in module neu_vol.webknossos) check_quantization() (in module neu_morpho.precomputed) check_selection() (in module neu_morpho.ops.manifest) check_spec() (in module neu_mark.roi_survey) check_verdicts() (in module neu_eval.adjudicate) check_vocabulary() (in module neu_mark.segprops) check_work_dir_is_local() (neu_morpho.config.OutputConfig method) child() (neu_draw.vectorfile.Group method) children (neu_draw.vectorfile.Group attribute) CHROME_OFF (in module neu_glance.movie.rendering) CHUNK (in module neu_mark.roi_layers) chunk (neu_vol.profiles.StorageProfile attribute) chunked_dir (neu_morpho.config.OutputConfig attribute) chunks (neu_vol.backends.base.ArrayBackend property) (neu_vol.backends.cloudvolume.CloudVolumeBackend property) (neu_vol.backends.dvid.DVIDBackend property) (neu_vol.backends.hdf5.HDF5Backend property) (neu_vol.backends.imagestack.ImageStackBackend property) (neu_vol.backends.mapped.MappedBackend property) (neu_vol.backends.tensorstore.TensorStoreBackend property) (neu_vol.backends.view.CropBackend property) (neu_vol.backends.view.MaskBackend property) (neu_vol.backends.view.RemapBackend property) (neu_vol.backends.webknossos.WebknossosBackend property) clamp_box() (in module neu_lib.grid) clamped() (neu_lib.grid.BBox method) cleans (neu_mark.roi_layers.Layer property) clear() (in module neu_vol.sharded) clear_backend_cache() (in module neu_vol.backends.base) clear_cache() (in module neu_vol.mapped) (in module neu_vol.webknossos) clear_highlights() (neu_draw.backends.legend.LegendOverlay method) clear_node_cache() (in module neu_vol.dvid) Click (class in neu_glance.serving) clip_to_shape() (in module neu_morpho.roi) close() (blockrun.manifest.Manifest method) (neu_draw.backends.pygfx.View method) (neu_morpho.metrics_db.MetricsDB method) (neu_vol.backends.hdf5.HDF5Backend method)

close_blocks (neu_mark.roi_layers.Layer attribute) CloudVolumeBackend (class in neu_vol.backends.cloudvolume) color (neu_draw.scene.LinesDrawable attribute) (neu_draw.scene.MeshDrawable attribute) (neu_draw.scene.PointsDrawable attribute) (neu_glance.served_layer.ServedLayer attribute) colored_last() (in module neu_glance.state) COLORMAP_SHADER (in module neu_glance.shaders) colors_by_property() (in module neu_glance.state) columns (neu_draw.backends.legend.LegendOverlay attribute) combine() (in module neu_mark.tables) command() (neu_draw.video.Orbit method) commit() (neu_morpho.metrics_db.MetricsDB method) compare() (in module neu_eval.compare) (in module neu_mark.explore) (in module neu_mark.roi_survey) (in module neu_morpho.measure.tables) compartment_counts() (neu_morpho.metrics_db.MetricsDB method) compartment_graph() (in module neu_morpho.measure.paths) complete_tables() (in module neu_mark.tables) Completeness (class in neu_eval.assign) completeness() (in module neu_eval.assign) component_sizes() (in module neu_proc.ops.measure) components() (in module neu_morpho.measure.paths) composites() (in module neu_mark.roi_survey) compressed_morton_code() (in module neu_vol.sharded) compressor (neu_vol.profiles.StorageProfile attribute) compressor_level (neu_vol.profiles.StorageProfile attribute) con (neu_morpho.metrics_db.MetricsDB attribute) Config (class in neu_mark.config) ConfigKeyError ConfigProblem connections() (in module neu_mark.tables) consecutive (neu_morpho.ops.manifest.FailureBreaker attribute) consumed() (neu_mark.rules.Rule method) (neu_mark.rules.RuleSet method) container_sources() (in module neu_vol.ops.write) containment() (in module neu_mark.roi_survey) contains() (neu_lib.grid.BBox method) Contingency (class in neu_eval.overlap) contingency (neu_eval.compare.Report attribute) contingency() (in module neu_eval.overlap) controller (neu_draw.backends.pygfx.View attribute) convert() (in module neu_vol.ops.convert) COORD_DTYPE (in module neu_mark.tables) copy() (neu_lib.piece.Piece method) count_bodies() (in module neu_morpho.fragments) count_components() (in module neu_morpho.mesh) COUNT_INSTANCE (in module neu_mark.dvid) count_labels() (in module neu_morpho.measure.sweep) counts (neu_eval.overlap.Contingency attribute) counts() (blockrun.manifest.Manifest method) counts_by_kind() (in module neu_eval.disagree) coverage() (in module neu_mark.explore) (neu_mark.rules.RuleSet method) covering() (in module neu_eval.assign) cpu_only() (in module neu_proc.ops.backend) create() (neu_vol.backends.tensorstore.TensorStoreBackend class method) create_volume() (in module neu_vol.ops.create) credentials() (in module neu_vol.webknossos) credentials_path() (in module neu_vol.webknossos) crop() (neu_lib.piece.Piece method) (neu_lib.skeleton.Skeleton method) crop_at_scale() (neu_morpho.metrics_db.MetricsDB method) crop_origin_nm() (in module neu_morpho.coords) CropBackend (class in neu_vol.backends.view) CSV_COLUMNS (in module neu_glance.layers) cumulative_factors() (in module neu_vol.pyramid) cursor (neu_glance.movie.animate.Timeline attribute)

D

data_api() (in module neu_vol.webknossos) DATA_AXES (in module neu_draw.orbit) data_bbox (neu_draw.scene.LinesDrawable property) (neu_draw.scene.MeshDrawable property) (neu_draw.scene.Placed property) (neu_draw.scene.PointsDrawable property) data_bounds() (neu_glance.serving.Server method) dataset_info() (in module neu_vol.webknossos) dataset_summary() (in module neu_vol.webknossos) datasets() (in module neu_vol.backends.hdf5) DATASTORE_API_VERSION (in module neu_vol.webknossos) db_path (neu_morpho.pipeline.Plan property) decimation_fraction (neu_morpho.config.MeshConfig attribute) decode_group() (in module neu_mark.annotations) decode_list_of_long() (in module neu_vol.webknossos) decode_single() (in module neu_mark.annotations) deep_merge() (in module blockrun.dask_config) DEFAULT_BACKGROUND (in module neu_draw.backends.vector) DEFAULT_BATCH (in module neu_morpho.measure.skeletons) DEFAULT_BLOCK (in module neu_morpho.measure.sweep) DEFAULT_BLOCK_BYTES (in module neu_vol.ops.maskvalue) (in module neu_vol.ops.pack) DEFAULT_COMPARTMENTS (in module neu_morpho.measure.tables) DEFAULT_CONTAINED (in module neu_mark.roi_survey) DEFAULT_COPY_BLOCK (in module neu_morpho.ops.export_roi_seg) DEFAULT_CREDENTIALS (in module neu_vol.webknossos) DEFAULT_DATASET (in module neu_vol.ops.pack) DEFAULT_EASE (in module neu_glance.movie.animate) default_exclude() (in module neu_eval.adjudicate) DEFAULT_GAP (in module neu_draw.layout) DEFAULT_HASH (in module neu_vol.sharded) DEFAULT_KEY_BOUNDARIES (in module neu_mark.dvid) default_map_path() (in module neu_vol.ops.relabel) default_mapping() (in module neu_vol.webknossos) DEFAULT_MAX_BYTES (in module neu_vol.piece) DEFAULT_MAX_LEVELS (in module neu_vol.ops.create) DEFAULT_MAX_OVERLAP (in module neu_mark.roi_layers) DEFAULT_MAX_REGION_BYTES (in module neu_vol.ops.relabel) DEFAULT_MAX_TAGS (in module neu_mark.segprops) DEFAULT_OFFSET_FIELD (in module neu_vol.ops.pack) DEFAULT_PANEL (in module neu_draw.backends.legend) default_path() (in module neu_draw.toolbar) DEFAULT_PREFIX (in module neu_draw.toolbar) default_progress_path() (in module neu_vol.location) default_properties() (in module neu_mark.annsource) DEFAULT_RELATIONSHIP (in module neu_glance.layers) DEFAULT_SIZE (in module neu_draw.backends.pygfx) DEFAULT_STAGES (in module neu_morpho.pipeline) DEFAULT_THREADS (in module neu_draw.sources) (in module neu_mark.dvid) (in module neu_morpho.measure.skeletons) default_view() (in module neu_glance.state) DEFAULT_VIEWER (in module neu_glance.state)

DEFAULT_VOXEL_NM (in module neu_morpho.measure.sweep) DEFAULT_VOXEL_SIZE_FIELD (in module neu_vol.ops.pack) DENSE_CELL_LIMIT (in module neu_eval.overlap) describe() (in module neu_mark.roi_layers) (in module neu_vol.source_metadata) (neu_mark.rules.RuleSet method) describe_datasets() (in module neu_vol.backends.hdf5) describe_scales() (in module neu_vol.scales) DESCRIBED_ATTRIBUTES (in module neu_vol.backends.hdf5) Description (class in neu_vol.report) description (neu_mark.rules.Rule attribute) detect_backend() (in module neu_vol.detect) detect_file_backend() (in module neu_vol.detect) diameter_stats() (in module neu_morpho.measure.metrics) dilate() (in module neu_proc.ops.dilate) DIM (in module neu_draw.backends.legend) directory (neu_draw.video.Orbit attribute) display_color() (in module neu_draw.backends.pygfx) done_blocks() (neu_morpho.metrics_db.MetricsDB method) done_compartment_blocks() (neu_morpho.metrics_db.MetricsDB method) done_keys() (blockrun.manifest.Manifest method) done_skel_bodies() (neu_morpho.metrics_db.MetricsDB method) DONE_STATUSES (in module neu_vol.ops.progress) done_sweep_blocks() (neu_morpho.metrics_db.MetricsDB method) download() (in module neu_vol.transfer) downsample_schedule() (in module neu_vol.pyramid) draco_quantization_bits (neu_morpho.config.MeshConfig attribute) draw() (neu_draw.backends.legend.LegendOverlay method) Drawable (in module neu_draw.scene) DRAWABLE_KINDS (in module neu_draw.scene) drawables (neu_draw.backends.legend.LegendEntry attribute) (neu_draw.scene.Scene attribute) drop (neu_mark.rules.Rule attribute) dropping() (neu_mark.rules.RuleSet method) drops (neu_mark.rules.RuleSet property) dst (neu_morpho.config.OutputConfig attribute) (neu_morpho.pipeline.Plan attribute) dtype (neu_lib.piece.Piece property) (neu_vol.backends.base.ArrayBackend property) (neu_vol.backends.cloudvolume.CloudVolumeBackend property) (neu_vol.backends.dvid.DVIDBackend property) (neu_vol.backends.hdf5.HDF5Backend property) (neu_vol.backends.imagestack.ImageStackBackend property) (neu_vol.backends.mapped.MappedBackend property) (neu_vol.backends.tensorstore.TensorStoreBackend property) (neu_vol.backends.view.CropBackend property) (neu_vol.backends.view.MaskBackend property) (neu_vol.backends.view.RemapBackend property) (neu_vol.backends.webknossos.WebknossosBackend property) duration (neu_glance.movie.animate.Timeline property) dust() (in module neu_proc.ops.dust) DVID_AXES (in module neu_mark.tables) dvid_roi_region() (in module neu_morpho.measure.paths) DVIDBackend (class in neu_vol.backends.dvid)

E

ease (neu_glance.movie.animate.Tween attribute) ease() (in module neu_glance.movie.animate) EASES (in module neu_draw.orbit) EASINGS (in module neu_glance.movie.animate) edges (neu_lib.skeleton.Skeleton attribute) ELEMENT_CLASSES (in module neu_vol.webknossos) elements_to_frames() (in module neu_mark.tables) empty() (neu_lib.grid.BBox class method) enabled (in module neu_proc.ops.backend) enclose() (neu_glance.serving.Server method) ENCODE_ARGS (in module neu_draw.video) encode_args() (in module neu_draw.video) encode_group() (in module neu_mark.annotations) encode_list_of_long() (in module neu_vol.webknossos) ENCODE_MODES (in module neu_draw.video) encode_single() (in module neu_mark.annotations) encode_skeleton() (in module neu_morpho.precomputed) ENCODING (in module neu_glance.serving) end (neu_glance.movie.animate.Tween attribute) END_LAYERS (in module neu_glance.sources) end_layers() (in module neu_glance.sources)

enrich_connections() (in module neu_mark.tables) enrich_for_source() (in module neu_mark.ops) ensure_aws_credentials() (in module neu_vol.aws) ensure_credentials() (in module neu_vol.location) entries (neu_draw.backends.legend.LegendOverlay attribute) entry() (neu_draw.backends.legend.LegendOverlay method) enum_property() (in module neu_mark.annotations) ENV_CREDENTIALS (in module neu_vol.webknossos) ENV_VAR (in module neu_mark.config) error (neu_eval.voxel.Rand property) exclude() (neu_lib.skeleton.Skeleton method) existing_levels() (in module neu_vol.source_metadata) exists() (in module neu_vol.location) expand() (in module neu_vol.ops.naming) explain() (neu_mark.rules.RuleSet method) export_groups (neu_draw.scene.Scene attribute) export_roi_seg() (in module neu_morpho.ops.export_roi_seg) extra (neu_morpho.config.OutputConfig attribute) (neu_morpho.pipeline.Plan attribute) EXTRA_CONTROLS (in module neu_draw.backends.pygfx) extract_roi() (in module neu_vol.ops.roi)

F

f_score (neu_eval.voxel.Rand property) faces (neu_lib.mesh.Mesh attribute) facet_order() (in module neu_mark.segprops) facets() (in module neu_mark.segprops) factor_from() (neu_lib.scale.ScaleInfo method) FADE_FROM (in module neu_glance.movie.animate) FAILED (in module neu_morpho.ops.manifest) failure() (neu_morpho.ops.manifest.FailureBreaker method) FailureBreaker (class in neu_morpho.ops.manifest) FANOUT (in module neu_morpho.fragments) fetch() (in module neu_mark.roi_layers) fetch_all() (in module neu_mark.roi_survey) fetch_all_body_annotations() (in module neu_mark.dvid) fetch_all_points() (in module neu_mark.dvid) fetch_bodies() (in module neu_mark.ops) fetch_body_annotations() (in module neu_mark.dvid) fetch_mapping_tables() (in module neu_vol.ops.wk_mappings) fetch_points() (in module neu_mark.dvid) (in module neu_mark.ops) fetch_roi_ranges() (in module neu_vol.dvid) fetch_synapse_counts() (in module neu_mark.dvid) fetch_synapse_counts_for() (in module neu_mark.dvid) fetch_voxel_counts() (in module neu_mark.dvid) ffmpeg_command() (in module neu_glance.movie.rendering) FFMPEG_ENV (in module neu_draw.video) figure() (in module neu_draw.backends.vector) FILENAME (in module neu_mark.config) (in module neu_vol.ops.provenance) fill (neu_draw.vectorfile.Markers attribute) (neu_draw.vectorfile.Rect attribute) (neu_draw.vectorfile.Text attribute) fill_gaps (neu_mark.roi_layers.Layer attribute) fill_holes (neu_mark.roi_layers.Layer attribute) FILL_METHODS (in module neu_proc.ops.offset) filter_blocks() (in module neu_morpho.roi) find() (in module neu_mark.config) find_browser() (in module neu_glance.movie.rendering) find_ffmpeg() (in module neu_draw.video) finest (neu_morpho.pipeline.Plan attribute) finest_first() (in module neu_vol.scales) finest_populated_scale() (in module neu_vol.detect) FIT_MARGIN (in module neu_glance.state) flat_component_sizes() (in module neu_proc.ops.measure) FONT_FAMILY (in module neu_draw.vectorfile) font_size (neu_draw.scene.Legend attribute)

format (neu_vol.profiles.StorageProfile attribute) FORMAT_MARKERS (in module neu_vol.detect) format_report() (in module neu_mark.annsource) (in module neu_mark.roi_survey) (in module neu_mark.segprops) FORMATS (in module neu_draw.toolbar) (in module neu_mark.io) fps (neu_draw.video.Orbit attribute) (neu_glance.movie.animate.Timeline attribute) fragment_format (neu_morpho.config.MeshConfig attribute) fragment_path() (in module neu_morpho.fragments) FRAGMENT_SHARE (in module neu_eval.disagree) fragmentation (neu_eval.assign.Completeness property) fragmentation() (in module neu_eval.assign) Frame (class in neu_lib.frame) frame (neu_glance.served_layer.ServedLayer attribute) (neu_lib.piece.Piece attribute) (neu_lib.scale.ScaleInfo attribute) (neu_vol.dvid.RoiVolume attribute) frame() (neu_draw.backends.pygfx.View method) (neu_vol.report.Description method) FRAME_ATTRIBUTES (in module neu_vol.backends.hdf5) FRAME_ATTRS (in module neu_vol.ops.pack) frame_count (neu_glance.movie.animate.Timeline property) frame_on() (neu_glance.movie.animate.Timeline method) frame_path() (in module neu_glance.movie.rendering) FRAME_PATTERN (in module neu_draw.video) frames (neu_draw.video.Orbit attribute) frames() (neu_glance.movie.animate.Timeline method) from_array() (neu_glance.served_layer.ServedLayer class method) from_hdf5() (neu_glance.served_layer.ServedLayer class method) from_json() (neu_glance.movie.animate.Timeline class method) (neu_glance.movie.animate.Tween class method) from_module() (in module neu_mark.rules) from_piece() (neu_glance.served_layer.ServedLayer class method) from_points() (neu_lib.grid.BBox class method) from_precomputed() (neu_lib.mesh.Mesh class method) (neu_lib.skeleton.Skeleton class method) from_source() (neu_glance.served_layer.ServedLayer class method) from_swc() (neu_lib.skeleton.Skeleton class method) from_volume() (neu_glance.served_layer.ServedLayer class method) frustum_area_nm2() (in module neu_morpho.measure.metrics) frustum_mesh() (in module neu_lib.tube) frustum_volume_nm3() (in module neu_morpho.measure.metrics) func (neu_mark.rules.Rule attribute)

G

GAP (in module neu_draw.backends.legend) gaussian_halo() (in module neu_proc.ops.kernels) GAUSSIAN_TRUNCATE (in module neu_proc.ops.kernels) geometry() (in module neu_vol.backends.dvid) (in module neu_vol.backends.webknossos) GEOMETRY_FLOATS (in module neu_mark.annotations) get() (neu_draw.scene.Scene method) get_backend() (in module neu_draw.backends) get_bbox() (neu_morpho.metrics_db.MetricsDB method) get_profile() (in module neu_vol.profiles) get_reducer() (in module neu_vol.pyramid) glyph (neu_draw.backends.legend.LegendEntry attribute) GLYPH_WIDTH (in module neu_draw.backends.legend) gpu_available() (in module neu_proc.ops.backend) GPU_FLAGS (in module neu_glance.movie.rendering) GRAYSCALE_SHADER (in module neu_glance.shaders) Grid (class in neu_mark.roi_layers)

grid_changes() (in module neu_morpho.ops.manifest) grid_frame() (in module neu_mark.roi_layers) grid_mismatch() (in module neu_morpho.ops.manifest) grid_record() (in module neu_morpho.ops.manifest) GridChanged GRIDS (in module neu_vol.ops.align) Group (class in neu_draw.vectorfile) group (neu_draw.backends.legend.LegendEntry attribute) (neu_draw.backends.legend.LegendOverlay attribute) (neu_draw.backends.pygfx.View attribute) group() (neu_draw.scene.Scene method) (neu_glance.movie.animate.Timeline method) group_counts() (in module neu_morpho.ops.manifest) group_row_color (neu_draw.scene.Legend attribute) groups (neu_draw.scene.Legend attribute) (neu_glance.movie.animate.Timeline attribute) guarded() (in module neu_morpho.ops.manifest)

H

h (neu_draw.vectorfile.Image attribute) (neu_draw.vectorfile.Rect attribute) has_placeholder() (in module neu_vol.ops.naming) hdf5_dataset_name() (in module neu_vol.ops.pack) HDF5_EXTENSIONS (in module neu_vol.backends.hdf5) HDF5Backend (class in neu_vol.backends.hdf5) header_lines() (neu_vol.report.Description method) headless_browser() (in module neu_glance.movie.rendering) HEADLESS_FLAGS (in module neu_glance.movie.rendering) headline() (neu_eval.compare.Report method)

hi (neu_lib.grid.BBox attribute) (neu_mark.roi_layers.Region property) hi_array (neu_lib.grid.BBox property) highlight() (neu_draw.backends.legend.LegendOverlay method) highlight_color (neu_draw.scene.Legend attribute) HIGHLIGHT_ROW_ALPHA (in module neu_draw.backends.legend) highlighted (neu_draw.backends.legend.LegendEntry attribute) (neu_draw.backends.legend.LegendOverlay property) hold() (neu_glance.movie.animate.Timeline method) HUNGARIAN_MAX_LABELS (in module neu_eval.assign)

I

idempotent() (in module blockrun.engine) identical() (in module neu_mark.roi_survey) identity() (neu_lib.frame.Frame class method) IDENTITY_TRANSFORM (in module neu_morpho.precomputed) ids (neu_mark.roi_layers.Spec attribute) ignore (neu_mark.roi_layers.Spec attribute) ignore_a (neu_eval.overlap.Contingency attribute) ignore_b (neu_eval.overlap.Contingency attribute) illustrator_id() (in module neu_draw.vectorfile) Image (class in neu_draw.vectorfile) IMAGE_EXTENSIONS (in module neu_vol.backends.imagestack) image_shader() (in module neu_glance.shaders) IMAGE_SHADERS (in module neu_glance.shaders) ImageStackBackend (class in neu_vol.backends.imagestack) in_notebook() (in module neu_draw.backends.pygfx) index (blockrun.engine.Block attribute) INDEX (in module neu_vol.ops.wk_mappings) index (neu_lib.scale.ScaleInfo attribute) index_segments() (in module neu_morpho.ops.index_segments) indices (neu_draw.backends.legend.LegendEntry attribute) ingest_image_stack() (in module neu_vol.ops.ingest) InsideFn (in module neu_lib.skeleton) install_quiet_stores() (in module neu_draw.logs) installed() (in module neu_draw.logs) instance_info() (in module neu_vol.dvid) instance_type() (in module neu_vol.dvid) instances (neu_mark.config.Config attribute) instances() (in module neu_mark.explore) interpolate_color_map() (in module neu_glance.movie.animate)

interpolate_hex_color() (in module neu_glance.movie.animate) interpolate_linear() (in module neu_glance.movie.animate) interpolate_orbit() (in module neu_glance.movie.animate) interpolate_quaternion() (in module neu_glance.movie.animate) interpolate_step() (in module neu_glance.movie.animate) interpolate_zoom() (in module neu_glance.movie.animate) interpolate_zoom_by() (in module neu_glance.movie.animate) INTERPOLATORS (in module neu_glance.movie.animate) intersect() (neu_lib.grid.BBox method) intersects() (in module neu_morpho.roi) iou() (in module neu_eval.assign) is_benign() (in module neu_vol.logs) is_complete() (in module neu_morpho.ops.manifest) is_container (neu_vol.report.Description property) is_descriptor() (in module neu_vol.mapped) is_done() (blockrun.manifest.Manifest method) is_empty() (neu_lib.grid.BBox method) is_gpu_array() (in module neu_proc.ops.backend) is_group (neu_draw.backends.legend.LegendEntry attribute) is_isotropic (neu_lib.frame.Frame property) is_local() (in module neu_vol.location) is_region_stored() (neu_vol.backends.tensorstore.TensorStoreBackend method) is_segmentation (neu_lib.piece.Piece property) is_systemic() (in module neu_morpho.ops.manifest) is_transient() (in module neu_vol.retry) is_url() (in module neu_vol.dvid) (in module neu_vol.webknossos) is_written() (in module neu_glance.movie.rendering) iso_date() (in module neu_vol.webknossos) iter_blocks() (in module blockrun.engine)

J

join() (in module neu_vol.location)

joint_counts() (in module neu_morpho.measure.compartments)

K

KAPPA (in module neu_draw.vectorfile) keep (neu_mark.rules.RuleSet attribute) keep_pairs() (neu_eval.overlap.Contingency method) key (neu_lib.scale.ScaleInfo attribute) key() (in module neu_vol.sharded) key_ranges() (in module neu_mark.dvid) keyvalues_to_frame() (in module neu_mark.tables) kind (neu_glance.movie.animate.Tween attribute) (neu_glance.served_layer.ServedLayer attribute) (neu_lib.piece.Piece attribute) (neu_mark.roi_layers.Layer property)

KIND_ATTR (in module neu_vol.ops.pack) kind_counts (neu_eval.compare.Report property) kind_for() (in module neu_glance.movie.animate) KIND_GROUPS (in module neu_draw.backends.vector) KINDS (in module neu_eval.disagree) (in module neu_glance.layers) (in module neu_lib.piece) kinds (neu_draw.backends.legend.LegendEntry property) KNOWN (in module neu_draw.backends)

L

label (neu_draw.backends.legend.LegendEntry attribute) (neu_draw.scene.LinesDrawable attribute) (neu_draw.scene.MeshDrawable attribute) (neu_draw.scene.PointsDrawable attribute) (neu_mark.roi_layers.Layer attribute) (neu_mark.rules.Rule attribute) (neu_mark.rules.RuleSet attribute) label_of() (in module neu_draw.scene) label_point_rois() (in module neu_mark.dvid) label_width (neu_draw.backends.legend.LegendEntry property) labeled_regions() (in module neu_vol.ops.occupancy) labels (neu_draw.backends.legend.LegendOverlay property) (neu_draw.scene.Scene property) (neu_eval.compare.Report attribute) (neu_eval.overlap.Contingency attribute) (neu_vol.dvid.RoiVolume attribute) LAST (in module neu_draw.viewstate) last_prefix (in module neu_draw.toolbar) last_suffix (in module neu_draw.toolbar) Layer (class in neu_mark.roi_layers) layer() (neu_mark.roi_layers.Spec method) layer_base() (in module neu_vol.webknossos) LAYER_COLORS (in module neu_glance.config) LAYER_DEFAULTS (in module neu_glance.movie.animate) LAYER_DISPLAY (in module neu_glance.config) LAYER_FLAGS (in module neu_glance.config) layer_pixels() (in module neu_draw.backends.vector) layer_record() (in module neu_vol.webknossos) layer_rois() (in module neu_mark.roi_layers) LAYER_SUBSOURCES (in module neu_glance.config) LAYER_SWITCHES (in module neu_glance.config) LAYER_TABS (in module neu_glance.config) layer_volume() (in module neu_glance.sources) layers (neu_mark.roi_layers.Spec attribute) layout() (neu_draw.backends.legend.LegendEntry method) (neu_draw.backends.legend.LegendOverlay method) LAYOUTS (in module neu_glance.state) lcm_grid() (in module neu_lib.grid) Legend (class in neu_draw.scene) legend (neu_draw.backends.pygfx.View attribute) (neu_draw.scene.Scene attribute) LEGEND_LOCATIONS (in module neu_draw.scene) LegendEntry (class in neu_draw.backends.legend) LegendOverlay (class in neu_draw.backends.legend) level0_chunking() (in module neu_vol.source_metadata) level_factor() (in module neu_vol.scales) level_progress() (in module neu_vol.ops.progress) level_scale_translation() (in module neu_vol.pyramid) level_shape() (in module neu_vol.backends.dvid) level_spec() (in module neu_vol.source_metadata) LIGHTS (in module neu_draw.backends.animation) like() (in module neu_proc.ops.backend) like_extent() (in module neu_mark.roi_survey) limit_bodies (neu_morpho.pipeline.Plan attribute) LINE (in module neu_mark.annotations) LinesDrawable (class in neu_draw.scene) link_subresources() (in module neu_vol.ops.subresources) list_bodies() (in module neu_morpho.fragments) list_datasets() (in module neu_vol.webknossos) list_keys() (in module neu_vol.location) lo (neu_lib.grid.BBox attribute) (neu_mark.roi_layers.Grid attribute) (neu_mark.roi_layers.Region attribute)

lo_array (neu_lib.grid.BBox property) load() (blockrun.manifest.Manifest method) (in module neu_glance.config) (in module neu_mark.bodies) (in module neu_mark.config) (neu_draw.viewstate.ViewState class method) load_allowlist() (in module neu_morpho.allowlist) load_bodies() (in module neu_morpho.measure.tables) load_config() (in module blockrun.dask_config) load_layer() (in module neu_glance.state) load_segment_properties() (in module neu_morpho.measure.tables) load_spec() (in module neu_mark.roi_layers) load_state() (in module neu_glance.state) load_table() (in module neu_vol.mapped) load_view_file() (in module neu_draw.viewstate) local_copy() (in module neu_vol.backends.hdf5) local_layer() (in module neu_glance.layers) local_path() (in module neu_vol.location) locate() (in module neu_eval.disagree) (neu_vol.sharded.ShardReader method) location (neu_draw.scene.Legend attribute) (neu_vol.sharded.ShardReader attribute) location_spec() (in module neu_vol.mapped) (in module neu_vol.source_metadata) locked (neu_mark.config.Config attribute) lod_decimation_factor (neu_morpho.config.MeshConfig attribute) log (in module neu_morpho.pipeline) (in module neu_vol.webknossos) log_bin_edges() (in module neu_morpho.measure.sweep) log_histogram() (in module neu_morpho.measure.tables) logger (in module neu_glance.serving) (in module neu_mark.annsource) (in module neu_mark.dvid) (in module neu_mark.io) (in module neu_mark.ops) (in module neu_mark.roi_layers) (in module neu_mark.roi_survey) (in module neu_mark.rules) (in module neu_mark.segprops) (in module neu_morpho.ops.export_roi_seg) (in module neu_morpho.ops.meshify) (in module neu_morpho.precomputed) (in module neu_proc.ops.backend) (in module neu_vol.detect) (in module neu_vol.ops.convert) (in module neu_vol.ops.create) (in module neu_vol.ops.ingest) (in module neu_vol.ops.maskvalue) (in module neu_vol.ops.pack) (in module neu_vol.ops.provenance) (in module neu_vol.ops.rebuild) (in module neu_vol.ops.roi) (in module neu_vol.ops.wk_mappings) (in module neu_vol.ops.write) (in module neu_vol.piece) (in module neu_vol.retry) (in module neu_vol.source_metadata) logical_size() (neu_draw.backends.pygfx.View method) LONG_URL (in module neu_glance.state)

M

main (neu_draw.backends.legend.LegendOverlay attribute) Manifest (class in blockrun.manifest) manifest_counts() (in module neu_vol.ops.progress) MappedBackend (class in neu_vol.backends.mapped) mappings() (in module neu_vol.webknossos) MARKER (in module neu_vol.mapped) marker (neu_draw.scene.PointsDrawable attribute) MARKER_ALIASES (in module neu_draw.scene) Markers (class in neu_draw.vectorfile) MARKERS (in module neu_draw.scene) mask (neu_mark.roi_layers.Region attribute) mask() (neu_vol.dvid.RoiVolume method) mask_predicate() (in module neu_lib.predicates) MASK_TAG (in module neu_vol.backends.view) mask_values() (in module neu_vol.ops.maskvalue) MaskBackend (class in neu_vol.backends.view) Match (class in neu_eval.assign) match_rate() (in module neu_mark.tables) max_consecutive (neu_morpho.ops.manifest.FailureBreaker attribute) max_consecutive_failures (neu_morpho.pipeline.Plan attribute) MAX_EDT_VOXELS (in module neu_eval.disagree) MAX_EMBED_BYTES (in module neu_mark.rules) MAX_FACETS (in module neu_mark.segprops) max_overlap (neu_mark.roi_layers.Spec attribute) max_radius_nm() (in module neu_morpho.measure.metrics) MAX_SPLIT_DEPTH (in module neu_mark.dvid) MAX_WIDTH_FRACTION (in module neu_draw.backends.legend) maximal_boxes() (in module neu_vol.ops.occupancy) mean_cross_section() (in module neu_morpho.measure.sweep) mean_downsample() (in module neu_vol.pyramid) measure() (neu_draw.backends.legend.LegendOverlay method) measure_skeleton() (in module neu_morpho.measure.metrics) MemoryCache (class in neu_draw.cache) merge (neu_eval.voxel.Voi attribute) merge_into() (in module neu_glance.state) merge_properties() (in module neu_morpho.measure.tables) Mesh (class in neu_lib.mesh) mesh (neu_draw.scene.MeshDrawable attribute) mesh_block() (in module neu_morpho.mesh) mesh_body_ids() (in module neu_vol.readback) mesh_dir (neu_morpho.config.OutputConfig attribute) mesh_metrics() (in module neu_morpho.mesh) mesh_out() (neu_morpho.config.OutputConfig method) mesh_scale (neu_morpho.config.MeshConfig attribute) mesh_smoothing (neu_morpho.pipeline.Plan attribute) mesh_transform() (in module neu_vol.readback) MeshConfig (class in neu_morpho.config) MeshDrawable (class in neu_draw.scene) meshify() (in module neu_morpho.ops.meshify) meta() (blockrun.manifest.Manifest method) metadata (neu_vol.sharded.ShardReader attribute) METADATA_KEY (in module neu_mark.io) method (neu_eval.assign.Match attribute) METHODS (in module neu_proc.ops.dilate) metrics_db (neu_morpho.pipeline.Plan attribute) MetricsDB (class in neu_morpho.metrics_db) min_iou (neu_eval.assign.Match attribute) min_segment_voxels (neu_morpho.config.MeshConfig attribute) MIN_TAG_ALLOWANCE (in module neu_mark.segprops) min_voxels (neu_morpho.pipeline.Plan attribute) MIN_WIDTH (in module neu_draw.backends.legend) misaligned_axes() (in module neu_lib.grid) (neu_lib.grid.BBox method) MISSING (in module neu_vol.dvid) MissingSubresource mode_downsample() (in module neu_vol.pyramid) MODES (in module neu_lib.grid) module blockrun blockrun.dask_config blockrun.dask_runner blockrun.engine blockrun.manifest neu_draw neu_draw.backends neu_draw.backends.animation neu_draw.backends.legend neu_draw.backends.pygfx neu_draw.backends.vector neu_draw.cache neu_draw.colors neu_draw.layout neu_draw.logs neu_draw.orbit neu_draw.scene neu_draw.sources neu_draw.toolbar neu_draw.vectorfile neu_draw.video neu_draw.viewstate neu_eval neu_eval.adjudicate neu_eval.assign neu_eval.compare neu_eval.disagree neu_eval.overlap neu_eval.tables neu_eval.voxel neu_glance neu_glance.config neu_glance.layers neu_glance.movie neu_glance.movie.animate neu_glance.movie.rendering neu_glance.served_layer neu_glance.serving neu_glance.shaders neu_glance.sources neu_glance.state neu_lib neu_lib.frame neu_lib.grid neu_lib.mesh neu_lib.piece neu_lib.predicates neu_lib.scale neu_lib.skeleton neu_lib.tube neu_lib.vec neu_mark neu_mark.annotations neu_mark.annsource neu_mark.bodies neu_mark.config neu_mark.dvid neu_mark.explore neu_mark.io neu_mark.notebook neu_mark.ops neu_mark.roi_layers neu_mark.roi_survey neu_mark.rules neu_mark.segprops neu_mark.tables neu_morpho neu_morpho.allowlist neu_morpho.config neu_morpho.coords neu_morpho.fragments neu_morpho.measure neu_morpho.measure.compartments neu_morpho.measure.driver neu_morpho.measure.metrics neu_morpho.measure.paths neu_morpho.measure.skeletons neu_morpho.measure.sweep neu_morpho.measure.tables neu_morpho.mesh neu_morpho.metrics_db neu_morpho.occupancy neu_morpho.ops neu_morpho.ops.export_roi_seg neu_morpho.ops.index_segments neu_morpho.ops.manifest neu_morpho.ops.meshify neu_morpho.pipeline neu_morpho.precomputed neu_morpho.roi neu_morpho.run_records neu_proc neu_proc.ops neu_proc.ops.backend neu_proc.ops.dilate neu_proc.ops.dust neu_proc.ops.kernels neu_proc.ops.measure neu_proc.ops.offset neu_proc.ops.opening neu_vol neu_vol.aws neu_vol.backends neu_vol.backends.base neu_vol.backends.cloudvolume neu_vol.backends.dvid neu_vol.backends.hdf5 neu_vol.backends.imagestack neu_vol.backends.mapped neu_vol.backends.tensorstore neu_vol.backends.view neu_vol.backends.webknossos neu_vol.detect neu_vol.dvid neu_vol.location neu_vol.logs neu_vol.mapped neu_vol.ngff neu_vol.ops neu_vol.ops.align neu_vol.ops.convert neu_vol.ops.create neu_vol.ops.ingest neu_vol.ops.maskvalue neu_vol.ops.naming neu_vol.ops.occupancy neu_vol.ops.pack neu_vol.ops.progress neu_vol.ops.provenance neu_vol.ops.rebuild neu_vol.ops.relabel neu_vol.ops.roi neu_vol.ops.subresources neu_vol.ops.wk_mappings neu_vol.ops.write neu_vol.piece neu_vol.profiles neu_vol.pyramid neu_vol.readback neu_vol.report neu_vol.retry neu_vol.scales neu_vol.sharded neu_vol.source_metadata neu_vol.transfer neu_vol.webknossos

morton_bits() (in module neu_vol.sharded) multi (neu_mark.rules.Rule attribute) murmurhash3_x86_128_low64() (in module neu_vol.sharded)

N

n_a (neu_eval.overlap.Contingency property) n_a_kept (neu_eval.assign.Completeness attribute) n_b (neu_eval.overlap.Contingency property) n_b_kept (neu_eval.assign.Completeness attribute) n_ignored (neu_eval.overlap.Contingency attribute) n_matched (neu_eval.assign.Match property) n_pairs (neu_eval.overlap.Contingency property) n_scored (neu_eval.overlap.Contingency property) name (neu_draw.scene.LinesDrawable attribute) (neu_draw.scene.MeshDrawable attribute) (neu_draw.scene.PointsDrawable attribute) (neu_draw.vectorfile.Group attribute) (neu_glance.served_layer.ServedLayer attribute) (neu_lib.mesh.Mesh attribute) (neu_lib.piece.Piece attribute) (neu_lib.skeleton.Skeleton attribute) (neu_mark.roi_layers.Layer attribute) (neu_mark.rules.Rule attribute) names (neu_draw.backends.legend.LegendEntry property) (neu_draw.scene.Scene property) (neu_mark.roi_layers.Spec attribute) (neu_mark.rules.RuleSet property) (neu_vol.dvid.RoiVolume attribute) names_remote_hdf5() (in module neu_vol.backends.hdf5) natural_key() (in module neu_mark.segprops) ndim (neu_lib.grid.BBox property) ndimage_for() (in module neu_proc.ops.backend) near() (in module neu_mark.explore) near_points_region() (in module neu_morpho.measure.paths) needs (neu_mark.rules.Rule property) nested() (neu_draw.vectorfile.Group method) NestedRois neu_draw module neu_draw.backends module neu_draw.backends.animation module neu_draw.backends.legend module neu_draw.backends.pygfx module neu_draw.backends.vector module neu_draw.cache module neu_draw.colors module neu_draw.layout module neu_draw.logs module neu_draw.orbit module neu_draw.scene module neu_draw.sources module neu_draw.toolbar module neu_draw.vectorfile module neu_draw.video module neu_draw.viewstate module neu_eval module neu_eval.adjudicate module neu_eval.assign module neu_eval.compare module neu_eval.disagree module neu_eval.overlap module neu_eval.tables module neu_eval.voxel module neu_glance module neu_glance.config module neu_glance.layers module neu_glance.movie module neu_glance.movie.animate module neu_glance.movie.rendering module neu_glance.served_layer module neu_glance.serving module neu_glance.shaders module neu_glance.sources module neu_glance.state module neu_lib module neu_lib.frame module neu_lib.grid module neu_lib.mesh module neu_lib.piece module neu_lib.predicates module neu_lib.scale module neu_lib.skeleton module neu_lib.tube module neu_lib.vec module neu_mark module neu_mark.annotations module neu_mark.annsource module neu_mark.bodies module neu_mark.config module neu_mark.dvid module neu_mark.explore module neu_mark.io module neu_mark.notebook module neu_mark.ops module neu_mark.roi_layers module neu_mark.roi_survey module neu_mark.rules module neu_mark.segprops module neu_mark.tables module neu_morpho module neu_morpho.allowlist module neu_morpho.config module neu_morpho.coords module neu_morpho.fragments module neu_morpho.measure module neu_morpho.measure.compartments module neu_morpho.measure.driver module

neu_morpho.measure.metrics module neu_morpho.measure.paths module neu_morpho.measure.skeletons module neu_morpho.measure.sweep module neu_morpho.measure.tables module neu_morpho.mesh module neu_morpho.metrics_db module neu_morpho.occupancy module neu_morpho.ops module neu_morpho.ops.export_roi_seg module neu_morpho.ops.index_segments module neu_morpho.ops.manifest module neu_morpho.ops.meshify module neu_morpho.pipeline module neu_morpho.precomputed module neu_morpho.roi module neu_morpho.run_records module neu_proc module neu_proc.ops module neu_proc.ops.backend module neu_proc.ops.dilate module neu_proc.ops.dust module neu_proc.ops.kernels module neu_proc.ops.measure module neu_proc.ops.offset module neu_proc.ops.opening module neu_vol module neu_vol.aws module neu_vol.backends module neu_vol.backends.base module neu_vol.backends.cloudvolume module neu_vol.backends.dvid module neu_vol.backends.hdf5 module neu_vol.backends.imagestack module neu_vol.backends.mapped module neu_vol.backends.tensorstore module neu_vol.backends.view module neu_vol.backends.webknossos module neu_vol.detect module neu_vol.dvid module neu_vol.location module neu_vol.logs module neu_vol.mapped module neu_vol.ngff module neu_vol.ops module neu_vol.ops.align module neu_vol.ops.convert module neu_vol.ops.create module neu_vol.ops.ingest module neu_vol.ops.maskvalue module neu_vol.ops.naming module neu_vol.ops.occupancy module neu_vol.ops.pack module neu_vol.ops.progress module neu_vol.ops.provenance module neu_vol.ops.rebuild module neu_vol.ops.relabel module neu_vol.ops.roi module neu_vol.ops.subresources module neu_vol.ops.wk_mappings module neu_vol.ops.write module neu_vol.piece module neu_vol.profiles module neu_vol.pyramid module neu_vol.readback module neu_vol.report module neu_vol.retry module neu_vol.scales module neu_vol.sharded module neu_vol.source_metadata module neu_vol.transfer module neu_vol.webknossos module neuropils (neu_mark.roi_layers.Spec attribute) NEVER_DROP (in module neu_vol.logs) new_run_id() (in module neu_morpho.run_records) next_level() (in module neu_mark.annsource) ng_source() (in module neu_morpho.pipeline) NO_BODY (in module neu_mark.tables) NO_COMPARTMENT (in module neu_morpho.measure.paths) NO_RECORD (in module neu_mark.segprops) NO_ROI (in module neu_mark.annsource) NO_ROI_LABEL (in module neu_mark.annsource) NO_SKELETON (in module neu_morpho.measure.paths) node_dist_sum (neu_morpho.measure.sweep.SweepTotals attribute) node_provenance() (in module neu_vol.dvid) node_radii() (in module neu_morpho.measure.sweep) node_record() (in module neu_mark.dvid) node_summary() (in module neu_vol.dvid) node_voxels (neu_morpho.measure.sweep.SweepTotals attribute) NOMINAL_VIEWPORT_PX (in module neu_glance.state) NoOccupancy norm() (neu_lib.vec.Vec3 method) normalize() (in module neu_mark.explore) normalize_tag() (in module neu_mark.segprops) normals_zyx (neu_lib.mesh.Mesh attribute) notes (neu_glance.movie.animate.Timeline attribute) NullCache (class in neu_draw.cache) num_lods (neu_morpho.config.MeshConfig attribute)

O

occupancy_dilate (neu_morpho.pipeline.Plan attribute) occupancy_scale (neu_morpho.pipeline.Plan attribute) occupancy_spec (neu_morpho.pipeline.Plan attribute) occupancy_voxel_size (neu_morpho.pipeline.Plan attribute) occupied_blocks() (in module neu_morpho.occupancy) occupied_cells() (in module neu_vol.ops.occupancy) of() (neu_lib.vec.Vec3 class method) of_kind() (neu_draw.scene.Scene method) offset() (in module neu_proc.ops.offset) offset_by() (neu_draw.scene.Placed method) (neu_draw.scene.Scene method) offset_zyx_nm (neu_draw.scene.LinesDrawable attribute) (neu_draw.scene.MeshDrawable attribute) (neu_draw.scene.PointsDrawable attribute) OK (in module neu_morpho.measure.paths) OldFragmentLayout ome_levels() (in module neu_vol.scales) ome_multiscale() (in module neu_vol.scales) ome_unit() (in module neu_vol.ngff) on_change() (neu_draw.scene.Scene method) (neu_glance.serving.Server method) on_click() (neu_glance.serving.Server method) ON_OVERLAP (in module neu_mark.dvid) opacity (neu_glance.served_layer.ServedLayer attribute) open() (neu_vol.backends.cloudvolume.CloudVolumeBackend class method) (neu_vol.backends.dvid.DVIDBackend class method) (neu_vol.backends.hdf5.HDF5Backend class method) (neu_vol.backends.imagestack.ImageStackBackend class method) (neu_vol.backends.mapped.MappedBackend class method) (neu_vol.backends.tensorstore.TensorStoreBackend class method) (neu_vol.backends.view.CropBackend class method) (neu_vol.backends.view.MaskBackend class method) (neu_vol.backends.view.RemapBackend class method) (neu_vol.backends.webknossos.WebknossosBackend class method)

open_backend() (in module neu_vol.backends.base) open_blocks (neu_mark.roi_layers.Layer attribute) open_bodies_source() (in module neu_mark.dvid) open_counts_source() (in module neu_mark.dvid) open_hdf5() (in module neu_vol.backends.hdf5) open_kvstore() (in module neu_vol.sharded) open_node() (in module neu_mark.roi_layers) open_or_create() (neu_vol.backends.tensorstore.TensorStoreBackend class method) open_points_source() (in module neu_mark.dvid) open_source() (in module neu_mark.dvid) open_viewer() (in module neu_glance.movie.rendering) opening() (in module neu_proc.ops.opening) OPTIONAL_COLUMNS (in module neu_glance.layers) optional_rois() (neu_mark.roi_layers.Spec method) options (neu_draw.toolbar.Toolbar attribute) Orbit (class in neu_draw.video) orbit() (in module neu_draw.backends.animation) (neu_draw.backends.pygfx.View method) (neu_glance.movie.animate.Timeline method) origin_nm (neu_lib.frame.Frame attribute) (neu_lib.piece.Piece property) (neu_lib.scale.ScaleInfo property) origin_voxel (neu_lib.piece.Piece property) other_format_markers() (in module neu_vol.detect) other_manifests() (in module neu_vol.ops.progress) output (neu_draw.video.Orbit attribute) output_dimensions() (in module neu_glance.layers) OutputConfig (class in neu_morpho.config) overlap (neu_mark.roi_layers.Layer attribute) overlaps (neu_vol.dvid.RoiVolume attribute) overlaps() (in module neu_mark.roi_survey) override() (neu_mark.rules.RuleSet method)

P

pack_hdf5() (in module neu_vol.ops.pack) pack_hdf5_datasets() (in module neu_vol.ops.pack) PAD (in module neu_draw.backends.legend) paint() (in module neu_mark.roi_layers) pair_voi() (in module neu_eval.voxel) panel_color (neu_draw.scene.Legend attribute) PARAMS_FILE (in module neu_draw.backends.animation) parse() (in module neu_glance.config) parse_node_url() (in module neu_mark.roi_layers) parse_roi() (in module neu_morpho.roi) parse_spec() (in module neu_mark.roi_layers) parse_url() (in module neu_glance.state) (in module neu_vol.dvid) (in module neu_vol.webknossos) parts (neu_vol.sharded.ShardReader attribute) past_extent() (in module neu_mark.roi_survey) path (blockrun.manifest.Manifest attribute) (neu_draw.toolbar.Toolbar attribute) (neu_glance.movie.animate.Tween attribute) (neu_mark.config.Config attribute) path_distances() (in module neu_morpho.measure.paths) pd_isna() (in module neu_mark.annsource) pending_frames() (in module neu_glance.movie.rendering) per_axis() (in module neu_proc.ops.kernels) per_label_frame() (in module neu_eval.tables) per_label_voi() (in module neu_eval.voxel) PERMANENT_MARKERS (in module neu_vol.retry) physical_box() (in module neu_morpho.coords) pick_shader() (in module neu_glance.shaders) Piece (class in neu_lib.piece) piece (neu_glance.served_layer.ServedLayer property) piece_name() (in module neu_vol.piece) pivot() (in module neu_draw.orbit) pixel_ratio (neu_draw.backends.pygfx.View property) Placed (class in neu_draw.scene) placed_at() (neu_draw.scene.Placed method) Plan (class in neu_morpho.pipeline) PLAN (in module neu_morpho.run_records) plan() (in module neu_morpho.pipeline) (neu_draw.backends.legend.LegendOverlay method) plan_mask_values() (in module neu_vol.ops.maskvalue) plan_relabel() (in module neu_vol.ops.relabel) plan_sharding() (in module neu_vol.sharded) plan_spatial() (in module neu_mark.annsource)

plan_subvolume_write() (in module neu_vol.ops.write) plan_volume() (in module neu_vol.ops.create) planned_blocks (neu_morpho.pipeline.Plan attribute) planned_blocks() (in module neu_morpho.run_records) plate (neu_draw.backends.legend.LegendEntry attribute) PNG_MAGIC (in module neu_glance.movie.rendering) PNG_SIGNATURE (in module neu_draw.backends.animation) POINT (in module neu_mark.annotations) POINT_INSTANCE (in module neu_mark.dvid) POINT_TABLES (in module neu_mark.ops) points() (in module neu_mark.notebook) (neu_glance.serving.Server method) points_from_table() (in module neu_draw.sources) PointsDrawable (class in neu_draw.scene) POLICIES (in module neu_mark.roi_layers) pool() (in module neu_eval.overlap) pose() (in module neu_draw.orbit) position (neu_glance.serving.Click attribute) (neu_glance.serving.Server property) POSITION_GROUPS (in module neu_glance.layers) position_index() (in module neu_mark.tables) positions() (in module neu_glance.layers) positions_xyz() (in module neu_mark.tables) positions_zyx() (in module neu_mark.tables) positions_zyx_nm (neu_draw.scene.PointsDrawable attribute) precision (neu_eval.voxel.Rand attribute) precomputed_chunks_are_gzipped() (in module neu_vol.detect) precomputed_create_spec() (in module neu_vol.profiles) PRECOMPUTED_GZ (in module neu_vol.detect) precomputed_info() (in module neu_vol.scales) precomputed_level() (in module neu_vol.scales) PRECOMPUTED_PROFILE (in module neu_morpho.ops.export_roi_seg) prefix (neu_mark.rules.Rule attribute) print_encode_hint() (in module neu_glance.movie.rendering) PROBABILITY_SHADER (in module neu_glance.shaders) profile_for() (in module neu_vol.ops.create) PROFILES (in module neu_vol.profiles) progress_path (neu_morpho.config.OutputConfig attribute) project() (in module neu_draw.backends.vector) properties() (in module neu_mark.roi_layers) PROPERTY_KINDS (in module neu_glance.movie.animate) PROPERTY_TYPES (in module neu_mark.annotations) provenance() (in module neu_mark.rules) (in module neu_vol.backends.dvid) prune() (neu_draw.vectorfile.Group method)

Q

QUALITATIVE (in module neu_draw.colors) quantization_step_nm() (in module neu_morpho.precomputed) quiet (in module neu_draw.logs)

quiet_reads() (in module neu_draw.logs) (in module neu_vol.logs) quiet_store_logs() (in module neu_vol.logs) quiet_stores() (in module neu_draw.logs)

R

radii_nm (neu_lib.skeleton.Skeleton attribute) Rand (class in neu_eval.voxel) rand() (in module neu_eval.voxel) read() (neu_vol.sharded.ShardReader method) read_annotation() (in module neu_mark.annsource) read_annotation_csv() (in module neu_glance.layers) read_annotation_info() (in module neu_glance.sources) read_body_fragments() (in module neu_morpho.fragments) read_body_mesh() (in module neu_vol.readback) read_body_skel_fragments() (in module neu_morpho.fragments) read_body_skeleton() (in module neu_vol.readback) read_bytes() (in module neu_vol.location) read_chunks (neu_vol.backends.mapped.MappedBackend property) (neu_vol.backends.tensorstore.TensorStoreBackend property) read_descriptor() (in module neu_vol.mapped) read_disagreements() (in module neu_eval.tables) read_embedded_provenance() (in module neu_mark.io) READ_FORMATS (in module neu_mark.io) read_json() (in module neu_vol.location) read_level_voxel_sizes() (in module neu_vol.source_metadata) read_one() (in module neu_vol.sharded) read_only (neu_morpho.metrics_db.MetricsDB attribute) read_piece() (in module neu_vol.piece) read_range() (in module neu_vol.location) (neu_vol.sharded.ShardReader method) read_region() (neu_vol.backends.base.ArrayBackend method) (neu_vol.backends.cloudvolume.CloudVolumeBackend method) (neu_vol.backends.dvid.DVIDBackend method) (neu_vol.backends.hdf5.HDF5Backend method) (neu_vol.backends.imagestack.ImageStackBackend method) (neu_vol.backends.mapped.MappedBackend method) (neu_vol.backends.tensorstore.TensorStoreBackend method) (neu_vol.backends.view.CropBackend method) (neu_vol.backends.view.MaskBackend method) (neu_vol.backends.view.RemapBackend method) (neu_vol.backends.webknossos.WebknossosBackend method) read_related() (in module neu_mark.annsource) read_scales() (in module neu_vol.scales) read_segment_properties() (in module neu_glance.sources) read_source_metadata() (in module neu_vol.source_metadata) read_stage_meta() (neu_morpho.metrics_db.MetricsDB method) read_table() (in module neu_mark.io) read_tables() (in module neu_mark.io) read_zarr_json() (in module neu_vol.scales) reads_quiet (in module neu_vol.logs) reason (neu_morpho.ops.manifest.FailureBreaker attribute) rebuild_pyramid() (in module neu_vol.ops.rebuild) rebuild_view() (in module neu_morpho.run_records) recall (neu_eval.voxel.Rand attribute) recolor() (neu_draw.backends.legend.LegendOverlay method) (neu_draw.scene.Scene method) record() (blockrun.manifest.Manifest method) (in module neu_glance.movie.rendering) record_meta() (blockrun.manifest.Manifest method) record_relationships() (in module neu_glance.layers) record_size() (in module neu_mark.annotations) record_stage_meta() (neu_morpho.metrics_db.MetricsDB method) Rect (class in neu_draw.vectorfile) rects_for() (neu_draw.backends.legend.LegendOverlay method) REDUCERS (in module neu_vol.pyramid) REFERENCE_PREFIX (in module neu_mark.config) refine() (in module neu_mark.dvid) refresh() (neu_draw.backends.legend.LegendEntry method) (neu_draw.backends.legend.LegendOverlay method) (neu_draw.backends.pygfx.View method) region (blockrun.engine.Block attribute) Region (class in neu_mark.roi_layers) (in module blockrun.engine) (in module neu_vol.backends.base) region_from_ranges() (in module neu_mark.roi_layers) REGION_PIECES (in module neu_morpho.measure.paths) register_backend() (in module neu_vol.backends.base) REL_KEYS (in module neu_mark.annsource) relabel() (in module neu_vol.ops.relabel) (neu_draw.backends.legend.LegendOverlay method) (neu_draw.scene.Scene method) relabel_sides() (neu_eval.overlap.Contingency method) RELATIONS (in module neu_mark.explore) RELATIONSHIP_PREFIX (in module neu_glance.layers) relayout() (neu_draw.backends.legend.LegendOverlay method) release_backends() (in module neu_vol.backends.base) remainder() (neu_mark.rules.Rule method) (neu_mark.rules.RuleSet method)

REMAP_TAG (in module neu_vol.backends.view) RemapBackend (class in neu_vol.backends.view) remember_prefix() (in module neu_draw.toolbar) remove_quiet_stores() (in module neu_draw.logs) rename() (neu_draw.scene.Scene method) render() (in module neu_glance.layers) render_state() (in module neu_glance.movie.rendering) rendered (neu_draw.video.Orbit attribute) renderer (neu_draw.backends.legend.LegendOverlay attribute) (neu_draw.backends.pygfx.View attribute) RenderProblem Report (class in neu_eval.compare) REQUEST_CHUNK (in module neu_vol.backends.webknossos) request_draw() (neu_draw.backends.pygfx.View method) require() (neu_mark.rules.RuleSet method) require_chunked_volume() (in module neu_vol.detect) require_local_path() (in module neu_vol.backends.hdf5) require_one_array() (in module neu_vol.source_metadata) require_populated_scale() (in module neu_vol.detect) require_sync() (in module neu_mark.dvid) rescale() (in module neu_glance.layers) RESERVED (in module neu_mark.rules) reset() (blockrun.manifest.Manifest method) (neu_draw.backends.pygfx.View method) reset_compartments() (neu_morpho.metrics_db.MetricsDB method) reset_index() (neu_morpho.metrics_db.MetricsDB method) reset_skel() (neu_morpho.metrics_db.MetricsDB method) reset_sweep() (neu_morpho.metrics_db.MetricsDB method) resolve() (in module neu_draw.cache) (in module neu_mark.roi_layers) (neu_mark.config.Config method) resolve_config() (in module blockrun.dask_config) resolve_dataset_id() (in module neu_vol.webknossos) resolve_keep() (in module neu_morpho.measure.driver) resolve_labelsz() (in module neu_mark.dvid) resolve_marker() (in module neu_draw.scene) resolve_max_levels() (in module neu_vol.ops.rebuild) resolve_node() (in module neu_vol.dvid) resolve_offset() (in module neu_vol.ops.write) resolve_partner_bodies() (in module neu_mark.tables) resolve_roi_set() (in module neu_vol.dvid) resolve_source() (in module neu_vol.ops.pack) resolve_tag_limit() (in module neu_mark.segprops) resolved() (neu_glance.movie.animate.Timeline method) restore_view() (neu_draw.backends.pygfx.View method) restrict() (neu_eval.overlap.Contingency method) resume (neu_morpho.pipeline.Plan attribute) RGB_SHADER (in module neu_glance.shaders) RGBA (in module neu_draw.colors) (in module neu_draw.vectorfile) rgba (neu_draw.vectorfile.Image attribute) roi (neu_morpho.pipeline.Plan attribute) roi_block_mask() (in module neu_morpho.measure.sweep) ROI_BLOCK_VOXELS (in module neu_vol.dvid) ROI_DESCRIPTIONS (in module neu_mark.annsource) roi_frame() (in module neu_vol.dvid) ROI_INSTANCE (in module neu_vol.dvid) roi_scale (neu_morpho.pipeline.Plan attribute) roi_set() (in module neu_mark.notebook) (neu_mark.config.Config method) roi_sets (neu_mark.config.Config attribute) ROI_UNSPECIFIED (in module neu_mark.dvid) roi_values() (in module neu_mark.annsource) roi_volume() (in module neu_vol.dvid) rois (neu_mark.roi_layers.Layer attribute) (neu_morpho.pipeline.Plan attribute) RoiVolume (class in neu_vol.dvid) rounded() (neu_lib.vec.Vec3 method) row_color (neu_draw.scene.Legend attribute) ROW_HEIGHT (in module neu_draw.backends.legend) row_text (neu_draw.backends.legend.LegendEntry property) rows (neu_eval.compare.Report attribute) rows() (in module neu_eval.disagree) Rule (class in neu_mark.rules) rule() (in module neu_mark.rules) rule_set() (neu_mark.config.Config method) rule_sets (neu_mark.config.Config attribute) rules (neu_mark.rules.RuleSet attribute) RuleSet (class in neu_mark.rules) run() (in module neu_mark.roi_survey) (in module neu_morpho.pipeline) run_encode() (in module neu_draw.video) RUNS (in module neu_morpho.run_records) runs() (in module neu_morpho.run_records)

S

S3_SINGLE_PUT_BYTES (in module neu_vol.transfer) sample_ids() (in module neu_eval.disagree) save() (in module neu_draw.backends.vector) (neu_draw.backends.pygfx.View method) (neu_draw.viewstate.ViewState method) save_pdf() (neu_draw.backends.pygfx.View method) save_svg() (neu_draw.backends.pygfx.View method) save_view() (neu_draw.backends.pygfx.View method) save_view_file() (in module neu_draw.viewstate) SAVED (in module neu_draw.viewstate) scalar() (neu_mark.rules.Rule method) scale_cost() (in module neu_morpho.ops.export_roi_seg) scale_holds_data() (in module neu_vol.detect) scale_is_empty() (in module neu_vol.detect) scale_roi() (in module neu_morpho.roi) scale_spec() (in module neu_vol.scales) scale_stores_chunks() (in module neu_vol.detect) ScaleInfo (class in neu_lib.scale) scales (neu_morpho.pipeline.Plan attribute) scales() (in module neu_draw.sources) SCATTER_FACTOR (in module neu_eval.compare) SCATTER_MIN_VOXELS (in module neu_eval.compare) scattered_labels() (in module neu_eval.compare) Scene (class in neu_draw.scene) scene (neu_draw.backends.legend.LegendOverlay attribute) (neu_draw.backends.pygfx.View attribute) scene_data (neu_draw.backends.legend.LegendOverlay attribute) (neu_draw.backends.pygfx.View attribute) SCHEME (in module neu_vol.webknossos) scheme (neu_mark.config.Config attribute) SCREEN_AXES (in module neu_draw.orbit) (in module neu_glance.movie.animate) screenshot() (neu_glance.serving.Server method) seconds (neu_glance.movie.animate.Tween attribute) seg_encoding (neu_morpho.pipeline.Plan attribute) seg_scales (neu_morpho.pipeline.Plan attribute) seg_scales() (in module neu_morpho.run_records) segment_boxes() (in module neu_glance.sources) segment_color() (in module neu_glance.shaders) segment_ids() (in module neu_glance.sources) segment_labels() (in module neu_glance.sources) segment_properties() (in module neu_mark.ops) segment_tags() (in module neu_glance.sources) Segments (class in neu_draw.vectorfile) segments (neu_draw.vectorfile.Segments attribute) segments() (neu_lib.skeleton.Skeleton method) segments_with_meshes() (in module neu_glance.sources) select_bodies() (in module neu_mark.notebook) select_segments() (in module neu_glance.sources) selected_segments() (neu_glance.serving.Server method) SelectionChanged semantic_label_names() (in module neu_morpho.measure.compartments) SEPARATOR (in module neu_mark.segprops) sequence() (neu_glance.movie.animate.Timeline method) serve() (in module neu_glance.serving) ServedLayer (class in neu_glance.served_layer) ServeProblem Server (class in neu_glance.serving) server (neu_mark.config.Config attribute) SERVER_FORMATS (in module neu_vol.ops.pack) set() (neu_glance.movie.animate.Timeline method) set_alpha() (neu_draw.backends.pygfx.View method) (neu_draw.scene.Scene method) set_color() (neu_draw.scene.Scene method) set_kwargs() (neu_mark.rules.Rule method) set_visible() (neu_draw.backends.legend.LegendOverlay method) sets() (neu_glance.movie.animate.Timeline method) shader (neu_glance.served_layer.ServedLayer attribute) shader_color_control() (in module neu_glance.shaders) shader_control_names() (in module neu_glance.config) ShaderProblem SHADERS (in module neu_glance.shaders) shape (blockrun.engine.Block property) Shape (in module neu_draw.vectorfile) shape (neu_draw.vectorfile.Markers attribute) (neu_lib.grid.BBox property) (neu_lib.piece.Piece property) (neu_lib.scale.ScaleInfo attribute) (neu_mark.roi_layers.Grid attribute) (neu_vol.backends.base.ArrayBackend property) (neu_vol.backends.cloudvolume.CloudVolumeBackend property) (neu_vol.backends.dvid.DVIDBackend property) (neu_vol.backends.hdf5.HDF5Backend property) (neu_vol.backends.imagestack.ImageStackBackend property) (neu_vol.backends.mapped.MappedBackend property) (neu_vol.backends.tensorstore.TensorStoreBackend property) (neu_vol.backends.view.CropBackend property) (neu_vol.backends.view.MaskBackend property) (neu_vol.backends.view.RemapBackend property) (neu_vol.backends.webknossos.WebknossosBackend property) shape_csvs() (in module neu_eval.tables) SHAPE_OF (in module neu_eval.tables) shard (neu_vol.profiles.StorageProfile attribute) shard_location() (in module neu_vol.sharded) sharded (neu_morpho.config.MeshConfig attribute) sharding_spec() (in module neu_vol.sharded) ShardReader (class in neu_vol.sharded) show() (in module neu_draw) (in module neu_draw.backends.pygfx) siblings() (in module neu_mark.roi_survey) SINGLE_LEVEL_FORMATS (in module neu_vol.detect) size (neu_draw.scene.PointsDrawable attribute) (neu_draw.vectorfile.Markers attribute) (neu_draw.vectorfile.Text attribute) (neu_draw.video.Orbit attribute) (neu_draw.viewstate.ViewState attribute) (neu_lib.grid.BBox property) (neu_mark.roi_layers.Region property) sizes() (in module neu_proc.ops.measure) skel_chunked_dir (neu_morpho.config.OutputConfig attribute) skel_counts() (neu_morpho.metrics_db.MetricsDB method) Skeleton (class in neu_lib.skeleton) skeleton (neu_draw.scene.LinesDrawable attribute) skeleton_columns() (in module neu_morpho.measure.skeletons)

skeleton_dir (neu_morpho.config.OutputConfig attribute) skeleton_graph() (in module neu_morpho.measure.paths) skeleton_out() (neu_morpho.config.OutputConfig method) skeleton_to_physical() (in module neu_morpho.coords) skeleton_transform() (in module neu_vol.readback) skeleton_tube() (in module neu_lib.tube) SKELETON_VERTEX_ATTRIBUTES (in module neu_morpho.precomputed) slices() (neu_lib.grid.BBox method) sliders (neu_draw.toolbar.Toolbar attribute) SLOW_REQUEST_S (in module neu_vol.backends.webknossos) smoothing_iterations (neu_morpho.config.MeshConfig attribute) snapshot() (neu_draw.backends.pygfx.View method) sole_dataset() (in module neu_vol.backends.hdf5) somatic_labels() (in module neu_morpho.measure.compartments) SOMATIC_NAMES (in module neu_morpho.measure.compartments) sort_properties() (in module neu_mark.annotations) source (neu_mark.roi_layers.Layer attribute) (neu_mark.rules.RuleSet attribute) source() (in module neu_mark.notebook) source_levels() (in module neu_morpho.ops.export_roi_seg) source_provenance() (in module neu_vol.ops.provenance) source_spec() (in module neu_vol.ops.write) SourceProblem spatial_axes() (in module neu_vol.scales) SPATIAL_KEY (in module neu_mark.annsource) spatial_shape (neu_lib.piece.Piece property) Spec (class in neu_mark.roi_layers) spec (neu_draw.backends.legend.LegendEntry attribute) (neu_draw.backends.legend.LegendOverlay attribute) spec_kvstore() (in module neu_vol.location) spec_names_path() (in module neu_vol.backends.base) spec_url() (in module neu_vol.dvid) (in module neu_vol.webknossos) SpecError split (neu_eval.voxel.Voi attribute) split() (neu_glance.movie.animate.Timeline method) split_at() (neu_lib.skeleton.Skeleton method) split_rects() (in module neu_draw.backends.legend) split_segment_layer() (in module neu_glance.state) split_table_path() (in module neu_mark.io) split_tokens() (in module neu_mark.explore) src (neu_morpho.pipeline.Plan attribute) stage() (in module neu_proc.ops.backend) stage_counts() (neu_morpho.metrics_db.MetricsDB method) STAGE_DOC (in module neu_morpho.pipeline) StageAborted staged_output() (in module neu_vol.backends.hdf5) StageRunner (in module neu_morpho.pipeline) STAGES (in module neu_morpho.pipeline) stages (neu_morpho.pipeline.Plan attribute) stale_frames() (in module neu_glance.movie.rendering) StaleManifest start (neu_glance.movie.animate.Tween attribute) start_dask() (in module blockrun.dask_runner) state (neu_glance.serving.Click attribute) state() (neu_glance.serving.Server method) state_url() (in module neu_glance.state) StateProblem status (neu_draw.toolbar.Toolbar attribute) status() (blockrun.manifest.Manifest method) STATUSES (in module neu_morpho.measure.paths) stop (neu_glance.movie.animate.Tween property) stop() (neu_glance.serving.Server method) stop_serving() (in module neu_glance.serving) StorageProfile (class in neu_vol.profiles) stored_axes() (neu_vol.backends.hdf5.HDF5Backend method) (neu_vol.backends.view.RemapBackend method) stored_chunks() (in module neu_vol.ops.progress) stored_kind() (neu_vol.backends.hdf5.HDF5Backend method) stored_offset() (neu_vol.backends.hdf5.HDF5Backend method) (neu_vol.backends.view.RemapBackend method) stored_units() (neu_vol.backends.hdf5.HDF5Backend method) stored_voxel_size() (neu_vol.backends.hdf5.HDF5Backend method) (neu_vol.backends.view.RemapBackend method) stroke (neu_draw.vectorfile.Markers attribute) (neu_draw.vectorfile.Segments attribute) stroke_width (neu_draw.vectorfile.Markers attribute) SUBDIR (in module neu_mark.config) (in module neu_mark.segprops) subresource_dir() (in module neu_draw.sources) SUBRESOURCE_TYPES (in module neu_vol.ops.subresources) subset_layers() (in module neu_glance.state) success() (neu_morpho.ops.manifest.FailureBreaker method) SUFFIX (in module blockrun.dask_config) summarise() (in module neu_mark.bodies) summarize() (in module neu_eval.adjudicate) (in module neu_eval.compare) (in module neu_morpho.measure.tables) SUMMARY (in module neu_morpho.run_records) summary (neu_eval.compare.Report attribute) summary() (in module neu_eval.assign) (in module neu_eval.voxel) superimpose() (neu_draw.scene.Scene method) superimpose_offsets() (in module neu_draw.layout) surface_area_nm2() (in module neu_morpho.mesh) survey() (in module neu_mark.roi_survey) sweep_compartments() (in module neu_morpho.measure.compartments) sweep_skeletons() (in module neu_morpho.measure.skeletons) sweep_volumes() (in module neu_morpho.measure.driver) SweepTotals (class in neu_morpho.measure.sweep) SYNAPSE_COLORINGS (in module neu_glance.shaders) synapse_colorings() (in module neu_glance.shaders) synapse_counts() (in module neu_mark.notebook) synapse_distance_table() (in module neu_morpho.measure.paths) synapse_distances() (in module neu_morpho.measure.paths) SYNAPSE_FILTERS (in module neu_glance.shaders) synapse_filters() (in module neu_glance.shaders) synapse_points() (in module neu_draw.sources) SYNAPSE_SHADER (in module neu_glance.shaders) synapse_shader() (in module neu_glance.shaders) SYNAPTIC_RELS (in module neu_mark.tables) sync() (neu_draw.backends.legend.LegendOverlay method) synced_instances() (in module neu_vol.dvid) synchronize() (in module neu_proc.ops.backend)

T

T (in module neu_vol.retry) (neu_eval.overlap.Contingency property) TABLE_BATCH (in module neu_vol.webknossos) table_bytes() (in module neu_vol.mapped) table_lines() (neu_vol.report.Description method) table_name() (in module neu_mark.io) TAG (in module neu_vol.backends.cloudvolume) (in module neu_vol.backends.dvid) (in module neu_vol.backends.hdf5) (in module neu_vol.backends.imagestack) (in module neu_vol.backends.view) (in module neu_vol.backends.webknossos) (in module neu_vol.mapped) tag (neu_mark.rules.Rule attribute) tag_for() (in module neu_mark.segprops) tagged (neu_mark.rules.RuleSet property) TAGS (in module neu_vol.backends.tensorstore) target (neu_draw.scene.Camera attribute) task_total() (in module neu_vol.ops.progress) tbar_fanout() (in module neu_mark.annsource) TensorStoreBackend (class in neu_vol.backends.tensorstore) test() (neu_mark.rules.Rule method) Text (class in neu_draw.vectorfile) text (neu_draw.backends.legend.LegendEntry attribute) (neu_draw.vectorfile.Text attribute) text() (neu_vol.report.Description method) text_color (neu_draw.scene.Legend attribute) thickness (neu_draw.scene.LinesDrawable attribute) thin_pairs() (in module neu_eval.disagree) Timeline (class in neu_glance.movie.animate) TIMEOUT_S (in module neu_vol.webknossos) to_cpu() (in module neu_proc.ops.backend) (neu_lib.piece.Piece method) to_csv() (neu_morpho.metrics_db.MetricsDB method) to_frame() (neu_eval.overlap.Contingency method) to_gpu() (in module neu_proc.ops.backend) to_json() (neu_glance.movie.animate.Timeline method) (neu_glance.movie.animate.Tween method) to_kvstore() (in module neu_vol.location)

to_nm() (neu_lib.frame.Frame method) (neu_lib.piece.Piece method) to_numpy() (neu_lib.piece.Piece method) to_pdf() (in module neu_draw.vectorfile) to_rgba() (in module neu_draw.colors) to_spec() (neu_vol.backends.base.ArrayBackend method) (neu_vol.backends.cloudvolume.CloudVolumeBackend method) (neu_vol.backends.dvid.DVIDBackend method) (neu_vol.backends.hdf5.HDF5Backend method) (neu_vol.backends.imagestack.ImageStackBackend method) (neu_vol.backends.mapped.MappedBackend method) (neu_vol.backends.tensorstore.TensorStoreBackend method) (neu_vol.backends.view.CropBackend method) (neu_vol.backends.view.MaskBackend method) (neu_vol.backends.view.RemapBackend method) (neu_vol.backends.webknossos.WebknossosBackend method) to_svg() (in module neu_draw.vectorfile) to_voxel() (neu_lib.frame.Frame method) to_voxels() (in module neu_proc.ops.kernels) to_xyz() (in module neu_lib.frame) toggle() (neu_draw.backends.legend.LegendEntry method) (neu_draw.backends.legend.LegendOverlay method) toggle_highlight() (neu_draw.backends.legend.LegendEntry method) (neu_draw.backends.legend.LegendOverlay method) tokens() (in module neu_mark.explore) Toolbar (class in neu_draw.toolbar) top_level() (in module neu_mark.roi_layers) topology() (in module neu_morpho.measure.metrics) total (neu_eval.voxel.Voi property) (neu_morpho.ops.manifest.FailureBreaker attribute) TRANSIENT_MARKERS (in module neu_vol.retry) translate() (neu_lib.grid.BBox method) (neu_lib.mesh.Mesh method) (neu_lib.skeleton.Skeleton method) tree (neu_mark.roi_layers.Layer attribute) TS_FORMAT (in module neu_draw.toolbar) Tween (class in neu_glance.movie.animate) tween() (neu_glance.movie.animate.Timeline method) tweens (neu_glance.movie.animate.Timeline attribute)

U

ui (neu_draw.backends.pygfx.View attribute) UNFILTERED_WARN_BODIES (in module neu_morpho.pipeline) UNFINISHED (in module neu_morpho.run_records) unfinished_stages() (in module neu_morpho.run_records) unhighlight() (neu_draw.backends.legend.LegendOverlay method) union() (in module neu_lib.predicates) (in module neu_mark.roi_layers) (neu_lib.grid.BBox method) unique_names() (in module neu_glance.state) unknown_keys() (in module blockrun.dask_config) unmatched_a() (neu_eval.assign.Match method) unmatched_b() (neu_eval.assign.Match method)

unparsed() (in module neu_mark.explore) (neu_mark.rules.RuleSet method) UNREACHABLE (in module neu_morpho.measure.paths) UnsupportedSubresource up (neu_draw.scene.Camera attribute) update_bodies() (neu_morpho.metrics_db.MetricsDB method) update_body() (neu_morpho.metrics_db.MetricsDB method) upload() (in module neu_vol.transfer) url (neu_glance.serving.Server property) url() (neu_mark.config.Config method) used_rois() (neu_mark.roi_layers.Spec method) uuid (neu_mark.config.Config attribute)

V

VALID_QUANTIZATION_BITS (in module neu_morpho.precomputed) validate_attrs() (in module neu_vol.ngff) value_at() (neu_glance.movie.animate.Tween method) value_color() (in module neu_glance.shaders) values (neu_glance.serving.Click attribute) values() (neu_mark.rules.Rule method) VARIANTS (in module neu_morpho.measure.tables) variants() (in module neu_mark.explore) Vec3 (class in neu_lib.vec) VERDICT_COLUMN (in module neu_eval.adjudicate) verdict_names() (in module neu_eval.adjudicate) verdict_tally (neu_eval.compare.Report attribute) VERDICTS (in module neu_eval.adjudicate) verify() (in module neu_mark.annsource) verify_compartments() (in module neu_morpho.measure.compartments) verify_spatial() (in module neu_mark.annsource) vertices_zyx_nm (neu_lib.mesh.Mesh attribute) (neu_lib.skeleton.Skeleton attribute) video (neu_draw.video.Orbit attribute) View (class in neu_draw.backends.pygfx) view (neu_draw.toolbar.Toolbar attribute) view() (neu_glance.movie.animate.Timeline method) (neu_mark.roi_layers.Grid method) view_angle (neu_draw.scene.Camera attribute) VIEW_DEFAULTS (in module neu_glance.movie.animate) VIEW_KEYS (in module neu_glance.config) viewer (neu_glance.serving.Server attribute) viewport (neu_draw.backends.legend.LegendOverlay attribute) views (in module neu_draw.viewstate)

ViewState (class in neu_draw.viewstate) visibility (neu_draw.backends.legend.LegendEntry property) visible (neu_draw.scene.Legend attribute) (neu_draw.scene.LinesDrawable attribute) (neu_draw.scene.MeshDrawable attribute) (neu_draw.scene.PointsDrawable attribute) Voi (class in neu_eval.voxel) voi() (in module neu_eval.voxel) volume_dir() (neu_morpho.config.OutputConfig method) volume_exists() (in module neu_morpho.precomputed) volume_extent() (in module neu_glance.sources) volume_frame() (in module neu_draw.sources) volume_info() (in module neu_draw.sources) volume_layer() (in module neu_glance.sources) volume_nm3() (neu_morpho.measure.sweep.SweepTotals method) volume_roi_region() (in module neu_morpho.measure.paths) volume_to_voxels() (in module neu_proc.ops.kernels) VolumeDrawable (class in neu_draw.scene) volumes (neu_glance.serving.Server attribute) voxel (neu_glance.serving.Click property) voxel_box() (neu_lib.frame.Frame method) voxel_nm (neu_morpho.measure.sweep.SweepTotals attribute) voxel_size (neu_lib.scale.ScaleInfo property) (neu_vol.backends.dvid.DVIDBackend attribute) (neu_vol.backends.mapped.MappedBackend property) (neu_vol.backends.webknossos.WebknossosBackend attribute) voxel_size_nm (neu_lib.frame.Frame attribute) (neu_lib.piece.Piece property) voxel_size_nm() (neu_glance.movie.animate.Timeline method) voxel_volume_nm3 (neu_morpho.measure.sweep.SweepTotals property)

W

w (neu_draw.vectorfile.Image attribute) (neu_draw.vectorfile.Rect attribute) wait_for_browser() (in module neu_glance.movie.rendering) walk() (neu_draw.vectorfile.Group method) warning_lines() (neu_vol.report.Description method) warnings (neu_eval.compare.Report attribute) WEBGL_SKELETON_ATTRIBUTE_DTYPES (in module neu_morpho.precomputed) WebknossosBackend (class in neu_vol.backends.webknossos) weighted_histogram() (in module neu_morpho.measure.sweep) weighted_quantile() (in module neu_morpho.measure.metrics) widget (neu_draw.toolbar.Toolbar attribute) width (neu_draw.backends.legend.LegendOverlay property) (neu_draw.scene.Legend attribute) (neu_draw.vectorfile.Segments attribute) with_frame() (neu_lib.piece.Piece method) with_kind() (neu_lib.piece.Piece method) with_name() (neu_lib.piece.Piece method) with_retry() (in module neu_vol.retry) with_source_options() (in module neu_vol.ops.convert) WK_API_VERSION (in module neu_vol.webknossos) work() (neu_morpho.config.OutputConfig method) work_dir (neu_morpho.config.OutputConfig attribute) (neu_morpho.pipeline.Plan attribute) world_axis() (in module neu_draw.orbit) world_objects (neu_draw.backends.legend.LegendEntry attribute) write() (in module neu_draw.vectorfile) (in module neu_mark.annsource) (in module neu_mark.segprops) (in module neu_vol.ops.provenance) write_all() (in module neu_vol.sharded) write_allowlist() (neu_morpho.metrics_db.MetricsDB method) write_body_multires() (in module neu_morpho.precomputed) write_body_skeleton() (in module neu_morpho.precomputed) write_bytes() (in module neu_vol.location)

write_descriptor() (in module neu_vol.mapped) write_disagreements() (in module neu_eval.tables) write_effective_config() (in module blockrun.dask_config) write_failures() (in module neu_morpho.ops.manifest) write_fragment() (in module neu_morpho.fragments) write_group_metadata() (in module neu_vol.ngff) write_hdf5_array() (in module neu_vol.ops.pack) write_json() (in module neu_vol.location) write_layer() (in module neu_mark.roi_layers) write_mesh_info() (in module neu_morpho.precomputed) write_piece() (in module neu_vol.piece) write_provenance() (in module neu_mark.io) write_region() (neu_vol.backends.base.ArrayBackend method) (neu_vol.backends.cloudvolume.CloudVolumeBackend method) (neu_vol.backends.dvid.DVIDBackend method) (neu_vol.backends.hdf5.HDF5Backend method) (neu_vol.backends.imagestack.ImageStackBackend method) (neu_vol.backends.mapped.MappedBackend method) (neu_vol.backends.tensorstore.TensorStoreBackend method) (neu_vol.backends.view.CropBackend method) (neu_vol.backends.view.MaskBackend method) (neu_vol.backends.view.RemapBackend method) (neu_vol.backends.webknossos.WebknossosBackend method) write_run_plan() (in module neu_morpho.run_records) write_run_summary() (in module neu_morpho.run_records) write_selected_bodies() (in module neu_mark.ops) write_skel_fragment() (in module neu_morpho.fragments) write_skeleton_info() (in module neu_morpho.precomputed) write_subvolume() (in module neu_vol.ops.write) write_subvolumes() (in module neu_vol.ops.write) write_summary() (in module neu_eval.tables) write_table() (in module neu_eval.tables) (in module neu_mark.io) (in module neu_morpho.measure.tables)

X

x (neu_draw.vectorfile.Image attribute) (neu_draw.vectorfile.Rect attribute) (neu_draw.vectorfile.Text attribute) (neu_lib.vec.Vec3 attribute)

xy (neu_draw.vectorfile.Markers attribute) xyz (neu_lib.vec.Vec3 property)

Y

y (neu_draw.vectorfile.Image attribute) (neu_draw.vectorfile.Rect attribute) (neu_draw.vectorfile.Text attribute) (neu_lib.vec.Vec3 attribute)

Yes3Cache (class in neu_draw.cache)

Z

z (neu_lib.vec.Vec3 attribute) zarr3_create_spec() (in module neu_vol.profiles) ZARR_METADATA (in module neu_vol.ops.occupancy)

zero() (neu_lib.vec.Vec3 class method) zoom (neu_draw.scene.Camera attribute) zoom() (neu_glance.movie.animate.Timeline method) zyx (neu_lib.vec.Vec3 property)