Skip to content

statebuilder

Classes:

  • ChainedStateBuilder –

    Builds a collection of states that sequentially add annotations based on a sequence of dataframes.

  • StateBuilder –

    A class for schematic mapping data frames into neuroglancer states.

ChainedStateBuilder(statebuilders)

Builds a collection of states that sequentially add annotations based on a sequence of dataframes.

Parameters:

  • statebuilders (list) –

    List of DataStateBuilders, in same order as dataframes will be passed

Methods:

  • render_state –

    Generate a single neuroglancer state by addatively applying an ordered collection of

render_state(data_list=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None, client=None)

Generate a single neuroglancer state by addatively applying an ordered collection of dataframes to an collection of StateBuilder renders. Parameters data_list : Collection of DataFrame. The order must match the order of StateBuilders contained in the class on creation. base_state : JSON neuroglancer state (optional, default is None). Used as a base state for adding everything else to. return_as: ['url', 'viewer', 'html', 'json', 'short']. optional, default='url'. Sets how the state is returned. Note that if a viewer is returned, the state is not reset to default. url_prefix: string, optional (default is https://neuromancer-seung-import.appspot.com). Overrides the default neuroglancer url for url generation. link_text: string, optional (default is 'Neuroglancer Link'). Text to use for the link when returning as html. target_site: string, optional (default is None). Target Neuroglancer category: either "seunglab" or "mainline"/"cave-explorer"/"spelunker". Will be looked up automatically based on url_prefix, if used. client: caveclient.CAVEclient, optional (default is None). A caveclient to get defaults from. Defaults to None, which falls back on the last statebuilder.

StateBuilder(layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)

A class for schematic mapping data frames into neuroglancer states.

Parameters:

  • layers (list of nglui.statebuilder.layers.LayerConfigBase, default: [] ) –

    List of layers to add. Defaults to [].

  • base_state (dict, default: None ) –

    JSON state to add to. Defaults to None.

  • url_prefix (str, default: None ) –

    http(s) path to Neuroglancer deployment to use. Defaults to None, which will use https://neuromancer-seung-import.appspot.com

  • state_server (str, default: None ) –

    State server to post links to. Defaults to None.

  • resolution (list of float, default: None ) –

    3-element vector controlling the viewer resolution. Defaults to None. If None and a client is set, uses the client viewer resolution.

  • view_kws (dict, default: {} ) –

    Dictionary controlling view parameters. Defaults to {}.

    Keys are: show_slices : bool, optional Sets if slices are shown in the 3d view. Defaults to False. layout : str, optional xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines : bool, optional Determines if the axis lines are shown in the middle of each view. show_scale_bar : bool, optional Toggles showing the scale bar. orthographic : bool, optional Toggles orthographic view in the 3d pane. position : list of float, optional (length-3) Determines the centered location. zoom_image : float, optional Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float, optional Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list of float, optional Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.

  • client (CAVEclient, default: None ) –

    A caveclient to get defaults from. Defaults to None.

  • target_site (str, default: None ) –

    Target Neuroglancer category: either "seunglab" or "mainline"/"cave-explorer"/"spelunker". Defaults to None. Will be looked up automatically based on ngl_url, if used.

Methods:

  • initialize_state –

    Generate a new Neuroglancer state with layers as needed for the schema.

  • render_state –

    Build a Neuroglancer state out of a DataFrame.

initialize_state(base_state=None, target_site=None)

Generate a new Neuroglancer state with layers as needed for the schema.

Parameters:

  • base_state (str, default: None ) –

    Optional initial state to build on, described by its JSON. By default None.

render_state(data=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None, client=None)

Build a Neuroglancer state out of a DataFrame.

Parameters:

  • data (DataFrame, default: None ) –

    DataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.

  • base_state (dict, default: None ) –

    Initial state to build on, expressed as Neuroglancer JSON. By default None

  • return_as (['url', 'viewer', 'html', 'json', 'dict', 'short'], default: 'url' ) –

    Choice of output types. Note that if a viewer is returned, the state is not reset. url : Returns the raw url describing the state viewer : Returns an EasyViewer object holding the state information html : Returns an HTML link to the url, useful for notebooks. json : Returns a JSON string describing the state. dict : Returns a dict version of the JSON state. short : Posts the state to the state server and returns a short link. Requires a client. By default 'url'

  • url_prefix (str, default: None ) –

    Neuroglancer URL prefix to use. By default None, for which it will open with the class default.

  • link_text (str, default: 'Neuroglancer Link' ) –

    Text to use for the link when returning as html, by default 'Neuroglancer Link'

  • target_site (str, default: None ) –

    Target Neuroglancer category: either "seunglab" or one of "mainline"/"cave-explorer"/"spelunker". Defaults to None. Will be looked up automatically based on ngl_url, if used and a client is set.

  • client (CAVEclient, default: None ) –

    A caveclient to get defaults from. Defaults to None, which falls back on the statebuilder.

Returns:

  • string or Viewer –

    A link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data.

Classes:

AnnotationLayerConfig(name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)

Bases: LayerConfigBase

Configuration class for annotation layers

Parameters:

  • name (str, default: None ) –

    Layer name. By default, 'annos'

  • color (str, default: None ) –

    Hex color code with an initial #. By default, None

  • linked_segmentation_layer (str, default: None ) –

    Name of a linked segmentation layer for selected ids. By default, None

  • mapping_rules ((PointMapper, LineMapper, SphereMapper or list), default: [] ) –

    One rule or a list of rules mapping data to annotations. By default, []

  • array_data (bool, default: False ) –

    If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.

  • tags (list, default: None ) –

    List of tags for the layer.

  • active (bool, default: True ) –

    If True, makes the layer selected. Default is True (unlike for image/segmentation layers).

ImageLayerConfig(source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)

Bases: LayerConfigBase

Image layer configuration class.

This provides the rules for setting up an image layer in neuroglancer.

Parameters:

  • source (str) –

    Cloudpath to an image source

  • name (str, default: None ) –

    Name of the image layer. By default, 'img'.

  • active (bool, default: False ) –

    If True, makes the layer active in neuroglancer. Default is False.

  • contrast_controls (bool, default: False ) –

    If True, gives the layer a user-controllable brightness and contrast shader. Default is False.

  • black (float, default: 0.0 ) –

    If contrast_controls is True, sets the default black level. Default is 0.0.

  • white (float, default: 1.0 ) –

    If contrast_controls is True, sets the default white level. Default is 1.0.

LayerConfigBase(name, type, source, color, active)

Base class for configuring layers

Parameters:

  • name (str) –

    Layer name for reference and display

  • type (str) –

    Layer type. Usually handled by the subclass

  • source (str) –

    Datasource for the layer

  • color (str) –

    Hex string (with starting hash).

  • active ((bool)) –

    If True, becomes a selected layer.

SegmentationLayerConfig(source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None, mapping_set=None, segment_properties=None, skeleton_source=None, skeleton_shader=None)

Bases: LayerConfigBase

Configuration class for segmentation layers

Parameters:

  • source (str) –

    Segmentation source

  • name ((str, optional), default: None ) –

    Layer name.

  • selected_ids_column (str or list-like, optional., default: None ) –

    Column name (or list of column names) to use for selected ids.

  • fixed_ids (list-like, optional., default: None ) –

    List of root ids to select directly.

  • fixed_id_colors (list-like, optional., default: None ) –

    List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.

  • color_column (str, optional., default: None ) –

    at the begining.

    Column to use for color values for selected objects. Values should be RGB hex strings with a

  • active (bool, optional., default: False ) –

    If True, makes the layer selected. Default is False.

  • alpha_selected –

    Opacity of selected segmentations in the image layer. Optional, default is 0.3.

  • alpha_3d –

    Opacity of meshes. Optional, default is 1.

  • alpha_unselected –

    Opacity of unselected segments. Optional, default is 0.

  • split_point_map –

    If not None, provides an object to map the dataframe input to multicut points. Default is None.

  • view_kws (dict, optional., default: None ) –

    Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.

  • timestamp (float or datetime, optional., default: None ) –

    Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.

  • mapping_set (str, optional., default: None ) –

    Name of the mapping set, the key in the data dictionary for statebuilder. Optional, default is None.

  • segment_properties –

    Location of a segment properties file. Optional, default is None.

  • skeleton_source –

    Location of a skeleton source. Optional, default is None.

  • skeleton_shader –

    Shader function for rendering skeletons, if set with skeleton_source. Optional, default is None.

Methods:

add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, mapping_set=None)

Add rules for selecting active segment ids and their colors

Parameters:

  • selected_ids_column (str, default: None ) –

    Dataframe column to use for adding selected segment ids to the segmentation layer, by default None

  • fixed_ids (int or list, default: None ) –

    Add one or more segment ids to be active, independent of the data, by default None

  • fixed_id_colors (list, default: None ) –

    Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None

  • color_column (str, default: None ) –

    Dataframe column to use for adding selected segment colors, by default None

  • mapping_set (str, default: None ) –

    Name of the mapping set, the key in the data dictionary for statebuilder, by default None

Modules:

  • ev_base –

Classes:

  • BoundingBoxMapper –

    Sets rules to map dataframes to bounding box annotations

  • LineMapper –

    Sets rules to map dataframes to line annotations

  • PointMapper –

    Sets rules to map dataframes to point annotations

  • SelectionMapper –

    Class for configuring object selections based on root id

  • SphereMapper –

    Sets rules to map dataframes to sphere annotations

  • SplitPointMapper –

    Mapper to create split points in a segmentation layer.

BoundingBoxMapper(point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)

Bases: AnnotationMapperBase

Sets rules to map dataframes to bounding box annotations

Parameters:

  • point_column_a (str, default: None ) –

    Column name with 3d position data for the first point of the bounding box. Must be set if array_data is False (the default)

  • point_column_b (str, default: None ) –

    Column name with 3d position data for the second point of the bounding box. Must be set if array_data is False (the default)

  • description_column (str, default: None ) –

    Column name with string data for annotation descriptions

  • linked_segmentation_column (str, default: None ) –

    Column name for root ids to link to annotations

  • tag_column (str, default: None ) –

    Column name for categorical tag data. Tags must match those set in the annotation layer.

  • group_column (str, default: None ) –

    Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.

  • set_position (bool, default: True ) –

    If set to True, moves the position to center on the first point in the data (using point_column_a).

  • multipoint –

    If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.

  • collapse_groups –

    If True, groups are toggled closed in the annotation view.

  • mapping_set –

    If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.

LineMapper(point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)

Bases: AnnotationMapperBase

Sets rules to map dataframes to line annotations

Parameters:

  • point_column_a (str, default: None ) –

    Column name with 3d position data for the first point of the line. Must be set if array_data is False (the default)

  • point_column_b (str, default: None ) –

    Column name with 3d position data for the first point of the line. Must be set if array_data is False (the default)

  • description_column (str, default: None ) –

    Column name with string data for annotation descriptions

  • linked_segmentation_column (str, default: None ) –

    Column name for root ids to link to annotations

  • tag_column (str, default: None ) –

    Column name for categorical tag data. Tags must match those set in the annotation layer.

  • group_column (str, default: None ) –

    Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.

  • set_position (bool, default: True ) –

    If set to True, moves the position to center on the first point in the data (using point_column_a).

  • multipoint –

    If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.

  • collapse_groups –

    If True, groups are toggled closed in the annotation view.

  • mapping_set –

    If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.

PointMapper(point_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)

Bases: AnnotationMapperBase

Sets rules to map dataframes to point annotations

Parameters:

  • point_column (str, default: None ) –

    Column name with 3d position data

  • description_column (str, default: None ) –

    Column name with string data for annotation descriptions

  • linked_segmentation_column (str, default: None ) –

    Column name for root ids to link to annotations

  • tag_column (str, default: None ) –

    Column name for categorical tag data. Tags must match those set in the annotation layer.

  • group_column (str, default: None ) –

    Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.

  • set_position (bool, default: True ) –

    If set to True, moves the position to center on the first point in the data.

  • multipoint –

    If True, permits multiple points in a given row, sharing data in other columns. Default is False.

  • collapse_groups –

    If True, groups are toggled closed in the annotation view.

  • mapping_set –

    If given, assumes data is passed as a dictionary and uses this string to as the key for the data to use.

SelectionMapper(data_columns=None, fixed_ids=None, fixed_id_colors=None, color_column=None, mapping_set=None)

Class for configuring object selections based on root id

Parameters:

  • data_columns (str or list, default: None ) –

    Name (or list of names) of the data columns to get ids from. Default is None.

  • fixed_ids (list, default: None ) –

    List of ids to select irrespective of data.

  • fixed_id_colors (list, default: None ) –

    List of colors associated with the fixed ids list.

  • color_column (str, default: None ) –

    Column name with color data per row

  • mapping_set (str, default: None ) –

    If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use. Note that using a mapping_set for one Mapper requires all Mappers use them. You cannot mix and match specificed mapping sets and ordered lists.

Methods:

  • selected_ids –

    Uses the rules to generate a list of ids from a dataframe.

selected_ids(data)

Uses the rules to generate a list of ids from a dataframe.

SphereMapper(center_column=None, radius_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, z_multiplier=0.1, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)

Bases: AnnotationMapperBase

Sets rules to map dataframes to sphere annotations

Parameters:

  • center_column (str, default: None ) –

    Column name with 3d position data for the center of the sphere

  • radius_column (str, default: None ) –

    Column name with a radius for the sphere (in nm)

  • description_column (str, default: None ) –

    Column name with string data for annotation descriptions

  • linked_segmentation_column (str, default: None ) –

    Column name for root ids to link to annotations

  • tag_column (str, default: None ) –

    Column name for categorical tag data. Tags must match those set in the annotation layer.

  • group_column (str, default: None ) –

    Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.

  • set_position (bool, default: True ) –

    If set to True, moves the position to center on the first point in the data.

  • multipoint –

    If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.

  • collapse_groups –

    If True, groups are toggled closed in the annotation view.

  • mapping_set –

    If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.

SplitPointMapper(id_column, point_column, team_column, team_names=['red', 'blue'], supervoxel_column=None, focus=True, mapping_set=None)

Mapper to create split points in a segmentation layer.

Parameters:

  • id_column (str) –

    Column name for segment ids. The id column must contain the same id in all rows.

  • point_column (str) –

    Name of the column containing points in space.

  • team_column (str) –

    Name of the column describing the team for the points. The contents of the column should have two values, by default "red" and "blue".

  • team_names (list, default: ['red', 'blue'] ) –

    List of two values for the team names used in the team column. The first is mapped to red points, the second blue. Default is ["red", "blue"].

  • supervoxel_column (str or None, default: None ) –

    Name of a column providing supervoxel ids. If None (default), the supervoxel must be looked up on the server.

  • focus (bool, default: True ) –

    If True, sets the focus on the split tool and sets the position to the center of split points. Default is True.

Returns:

  • SplitPointMapper instance to pass to a segmentation layer. –

.helpers

Functions:

  • from_client –

    Generate basic image and segmentation layers from a FrameworkClient

  • make_line_statebuilder –

    Generate a state builder that puts points on a single column with a linked segmentaton id

  • make_neuron_neuroglancer_link –

    function to create a neuroglancer link view of a neuron, optionally including inputs and outputs

  • make_point_statebuilder –

    Generate a state builder that puts points on a single column with a linked segmentaton id

  • make_pre_post_statebuilder –

    Function to generate ChainedStateBuilder with optional pre and post synaptic

  • make_state_url –

    Generate a url from a neuroglancer state via a state server.

  • make_synapse_neuroglancer_link –

    Generate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.

  • make_url_robust –

    Generate a url from a neuroglancer state. If too long, return through state server,

  • package_state –

    Automate creating a state from a statebuilder and

  • segment_property_link –

    Returns a basic link to a default neuroglancer state and segment properties.

  • sort_dataframe_by_root_id –

    Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.

from_client(client, image_name=None, segmentation_name=None, contrast=None, use_skeleton_service=False)

Generate basic image and segmentation layers from a FrameworkClient

Parameters:

  • client (CAVEclient) –

    A CAVEclient with a specified datastack

  • image_name (str, default: None ) –

    Name for the image layer, by default None.

  • segmentation_name (str, default: None ) –

    Name for the segmentation layer, by default None

  • contrast (list - like or False, default: None ) –

    Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.

  • use_skeleton_service (bool, default: False ) –

    If True, uses a skeleton service, if advertised, with the segmentation. Defaults to False.

Returns:

  • image_layer ( ImageLayerConfig ) –

    Image layer with default values from the client

  • seg_layer ( ImageLayerConfig ) –

    Segmentation layer with default values from the client

make_line_statebuilder(client, point_column_a='pre_pt_position', point_column_b='post_pt_position', linked_seg_column='pt_root_id', description_column=None, tag_column=None, data_resolution=None, group_column=None, contrast=None, view_kws=None, point_layer_name='lines', color=None, split_positions=False)

Generate a state builder that puts points on a single column with a linked segmentaton id

Parameters:

  • client (CAVEclient) –

    CAVEclient configured for the datastack desired

  • point_column_a (str, default: 'pre_pt_position' ) –

    column in dataframe to pull points from. Defaults to "pre_pt_position".

  • point_column_b (str, default: 'post_pt_position' ) –

    column in dataframe to pull points from. Defaults to "post_pt_position".

  • linked_seg_column (str, default: 'pt_root_id' ) –

    column to link to segmentation, None for no column. Defaults to "pt_root_id".

  • group_column (str, or list, default: None ) –

    column(s) to group annotations by, None for no grouping (default=None)

  • tag_column (str, default: None ) –

    column to use for tags, None for no tags (default=None)

  • description_column (str, default: None ) –

    column to use for descriptions, None for no descriptions (default=None)

  • contrast (list, default: None ) –

    Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.

  • view_kws (dict, default: None ) –

    dictionary of view keywords to configure neuroglancer view

  • split_positions (bool, default: False ) –

    whether the position column into x,y,z columns. Defaults to False.

Returns:

  • StateBuilder –

    A statebuilder to make points with linked segmentations

function to create a neuroglancer link view of a neuron, optionally including inputs and outputs

Parameters:

  • client (CAVEclient) –

    A CAVEclient configured for the datastack to visualize.

  • root_ids (Iterable[int]) –

    The root_ids to build the visualization around.

  • return_as (str, default: 'html' ) –

    How to return the URL or state. Valid options are: - 'html': Returns an IPython HTML element. - 'json': Returns a dictionary representing the Neuroglancer state. - 'url': Returns a URL string. Defaults to 'html'.

  • shorten (str, default: 'always' ) –

    Whether to shorten the link. Valid options are: - 'always': Always shorten the link. - 'if_long': Shorten the link if it exceeds MAX_URL_LENGTH. - 'never': Never shorten the link. Defaults to 'if_long'.

  • show_inputs (bool, default: False ) –

    Whether to include input synapses. Defaults to False.

  • show_outputs (bool, default: False ) –

    Whether to include output synapses. Defaults to False.

  • sort_inputs (bool, default: True ) –

    Whether to sort input synapses by presynaptic root id, ordered by synapse count. Defaults to True.

  • sort_outputs (bool, default: True ) –

    Whether to sort output synapses by presynaptic root id, ordered by postsynaptic synapse count. Defaults to True.

  • sort_ascending (bool, default: False ) –

    If sorting, whether to sort ascending (lowest synapse count to highest). Defaults to False.

  • input_color (list(float) or str, default: DEFAULT_POSTSYN_COLOR ) –

    Color of input synapse points as an RGB list [0, 1], hex string, or common name.

  • output_color (list(float) or str, default: DEFAULT_PRESYN_COLOR ) –

    Color of output synapse points as an RGB list [0, 1], hex string, or common name.

  • contrast (list, default: None ) –

    List of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.

  • timestamp (datetime, default: None ) –

    Timestamp to use for the query. Defaults to None, which will use the materialized version.

  • view_kws (dict, default: None ) –

    Dictionary containing viewer settings for Neuroglancer. See nglui.StateBuilder for options. See the previous docstring for details on available keys.

  • point_column (str, default: 'ctr_pt_position' ) –

    Column to pull synapse positions from. Defaults to "ctr_pt_position".

  • pre_pt_root_id_col (str, default: 'pre_pt_root_id' ) –

    Column to pull presynaptic IDs for synapses from. Defaults to "pre_pt_root_id".

  • post_pt_root_id_col (str, default: 'post_pt_root_id' ) –

    Column to pull postsynaptic IDs for synapses from. Defaults to "post_pt_root_id".

  • input_layer_name (str, default: 'syns_in' ) –

    Name of the layer for input synapses. Defaults to "syns_in".

  • output_layer_name (str, default: 'syns_out' ) –

    Name of the layer for output synapses. Defaults to "syns_out".

  • ngl_url (str, default: None ) –

    URL of the Neuroglancer instance to use. Defaults to the default viewer set in the datastack.

  • link_text (str, default: 'Neuroglancer Link' ) –

    Text to use for the HTML return. Defaults to 'Neuroglancer Link'.

Raises:

  • ValueError –

    If the specified point column is not present in the synapse table.

Returns:

  • IPython.HTML, str, or dict –

    Representation of the Neuroglancer state, depending on the return_as parameter.

make_point_statebuilder(client, point_column='pt_position', linked_seg_column='pt_root_id', data_resolution=None, group_column=None, tag_column=None, description_column=None, contrast=None, view_kws=None, point_layer_name='pts', color=None, split_positions=False)

Generate a state builder that puts points on a single column with a linked segmentaton id

Parameters:

  • client (CAVEclient) –

    CAVEclient configured for the datastack desired

  • point_column (str, default: 'pt_position' ) –

    Column in dataframe to pull points from. Defaults to "pt_position".

  • linked_seg_column (str, default: 'pt_root_id' ) –

    column to link to segmentation, None for no column. Defaults to "pt_root_id".

  • group_column (str, or list, default: None ) –

    column(s) to group annotations by, None for no grouping (default=None)

  • tag_column (str, optional), default: None ) –

    column to use for tags, None for no tags (default=None)

  • description_column (str, default: None ) –

    column to use for descriptions, None for no descriptions (default=None)

  • contrast (list, default: None ) –

    Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.

  • view_kws (dict, default: None ) –

    dictionary of view keywords to configure neuroglancer view

  • split_positions (bool, default: False ) –

    whether the position column into x,y,z columns. Defaults to False.

Returns:

  • StateBuilder –

    A statebuilder to make points with linked segmentations

make_pre_post_statebuilder(client, show_inputs=False, show_outputs=False, contrast=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', dataframe_resolution_pre=None, dataframe_resolution_post=None, input_layer_name='syns_in', output_layer_name='syns_out', input_layer_color=DEFAULT_POSTSYN_COLOR, output_layer_color=DEFAULT_PRESYN_COLOR, split_positions=False)

Function to generate ChainedStateBuilder with optional pre and post synaptic annotation layers

Parameters:

  • client (CAVEclient) –

    a CAVEclient configured for datastack to visualize

  • show_inputs (bool, default: False ) –

    whether to show input synapses. Defaults to False.

  • show_outputs (bool, default: False ) –

    whether to show output synapses.. Defaults to False.

  • contrast (list, default: None ) –

    Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.

  • view_kws (dict, default: None ) –

    view_kws to configure statebuilder, see nglui.StateBuilder. Defaults to None. keys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in.

  • point_column (str, default: 'ctr_pt_position' ) –

    column to pull points for synapses from. Defaults to "ctr_pt_position".

  • pre_pt_root_id_col (str, default: 'pre_pt_root_id' ) –

    column to pull pre synaptic ids for synapses from. Defaults to "pre_pt_root_id".

  • post_pt_root_id_col (str, default: 'post_pt_root_id' ) –

    column to pull post synaptic ids for synapses from. Defaults to "post_pt_root_id".

  • input_layer_name (str, default: 'syns_in' ) –

    name of layer for inputs. Defaults to "syns_in".

  • output_layer_name (str, default: 'syns_out' ) –

    name of layer for outputs. Defaults to "syns_out".

  • split_positions (bool, default: False ) –

    whether the position column is split into x,y,z columns. Defaults to False.

Returns:

  • ChainedStateBuilder –

    An instance of a ChainedStateBuilder configured to accept a list starting with None followed by optionally synapse input dataframe followed by optionally synapse output dataframe.

make_state_url(df, sb, client, ngl_url=None, target_site=None)

Generate a url from a neuroglancer state via a state server.

Parameters:

  • df (DataFrame) –

    Dataframe to pass through statebuilder

  • sb (StateBuilder) –

    Statebuilder to use to render data for link

  • client (CAVEclient) –

    CAVEclient configured with a state server

  • ngl_url (str, default: None ) –

    Neuroglancer deployment URL, by default None

  • target_site (str, default: None ) –

    Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.

Returns:

  • str –

    Url to the uploaded neuroglancer state.

Generate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.

Parameters:

  • synapse_df (DataFrame) –

    DataFrame where each row represents a synapse.

  • client (CAVEclient) –

    A CAVEclient instance.

  • return_as (str, default: 'html' ) –

    How to return the URL. Valid options are: - 'html': Returns an IPython HTML element. - 'url': Returns a URL string. - 'json': Returns a dictionary representing the Neuroglancer state. Defaults to 'html'.

  • shorten (str, default: 'always' ) –

    Whether to shorten the link. Valid options are: - 'always': Always shorten the link. - 'if_long': Shorten the link if it exceeds MAX_URL_LENGTH. - 'never': Never shorten the link. Defaults to 'always'.

  • contrast (list, default: None ) –

    List of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.

  • point_column (str, default: 'ctr_pt_position' ) –

    Column in the DataFrame containing synapse positions. Defaults to 'ctr_pt_position'.

  • dataframe_resolution (list, default: None ) –

    List of length 3, specifying the resolution units of the position column. If None, attempts to get the resolution from DataFrame metadata or client.info.viewer_resolution().

  • group_connections (bool, default: True ) –

    Whether to group synapses within the same connection (between the same neurons). Defaults to True.

  • link_pre_and_post (bool, default: True ) –

    Whether to link the synapse annotations to the pre- and post-synaptic partners. Defaults to True.

  • ngl_url (str, default: None ) –

    URL of the Neuroglancer instance to use. Defaults to client.info.viewer_site() or DEFAULT_NGL.

  • view_kws (dict, default: None ) –

    Dictionary containing viewer settings for Neuroglancer. Available keys: - show_slices: Boolean, sets if slices are shown in the 3D view. - layout: str, specifies the viewer layout (e.g., 'xy-3d', '4panel'). - show_axis_lines: Boolean, determines if axis lines are shown. - show_scale_bar: Boolean, toggles the scale bar. - orthographic: Boolean, toggles orthographic view in the 3D pane. - position: 3-element vector, sets the centered location. - zoom_image: float, zoom level for the imagery in nm per voxel. - zoom_3d: float, zoom level for the 3D pane.

  • pre_post_columns (list, default: None ) –

    List of two strings, specifying the column names for pre- and post-synaptic root_ids. Defaults to ['pre_pt_root_id', 'post_pt_root_id'].

  • neuroglancer_link_text (str, default: 'Neuroglancer Link' ) –

    Text to use in the returned HTML link. Defaults to 'Neuroglancer Link'.

  • color (list(float) or str, default: None ) –

    Color of synapse points as an RGB list [0, 1], hex string, or common name.

  • split_positions (bool, default: False ) –

    Whether the position column is split into x, y, and z columns.

  • target_site (str, default: None ) –

    Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.

Returns:

  • IPython.HTML, str, or dict –

    Representation of the Neuroglancer state, depending on the return_as parameter.

Raises:

  • ValueError –

    If the specified point_column is not found in the DataFrame.

make_url_robust(df, sb, client, shorten='if_long', ngl_url=None, max_url_length=MAX_URL_LENGTH, target_site=None)

Generate a url from a neuroglancer state. If too long, return through state server, othewise return a url containing the data directly.

Parameters:

  • df (DataFrame) –

    Dataframe to pass through statebuilder

  • sb (StateBuilder) –

    Statebuilder to use to render data for link

  • client (CAVEclient) –

    CAVEclient configured with a state server

  • shorten (str, default: 'if_long' ) –

    How to shorten link. one of 'if_long', 'always', 'never'. 'if_long' will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). 'always' will always use the state server to shorten the url 'never' will always return the full url. Defaults to "if_long".

  • ngl_url (str, default: None ) –

    Neuroglancer deployment URL, by default None

  • max_url_length (int, default: MAX_URL_LENGTH ) –

    Maximum length of url to return directly, by default 1_750_000

  • target_site (str, default: None ) –

    Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.

Returns:

  • str –

    URL containing the state created by the statebuilder.

package_state(df, sb, client, shorten='if_long', return_as='url', ngl_url=None, link_text='Neuroglancer Link', target_site=None)

Automate creating a state from a statebuilder and a dataframe, return it in the desired format, shortening if desired.

Parameters:

  • df (DataFrame) –

    Dataframe to pass through statebuilder

  • sb (StateBuilder) –

    Statebuilder to use to render data for link

  • client (CAVEclient) –

    CAVEclient configured with a state server

  • shorten (str, default: 'if_long' ) –

    How to shorten link. one of 'if_long', 'always', 'never'. 'if_long' will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). 'always' will always use the state server to shorten the url 'never' will always return the full url. Defaults to "if_long".

  • return_as (str, default: 'url' ) –

    How to return the state. one of 'html', 'url', 'json'. 'html' will return an ipython clickable link 'url' will return a string with the url 'json' will return the state as a dictionary

  • ngl_url (str, default: None ) –

    Neuroglancer deployment URL, by default None

  • link_text (str, default: 'Neuroglancer Link' ) –

    Text to use for the link, by default "Neuroglancer Link"

  • target_site (str, default: None ) –

    Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.

Returns:

  • (HTML, str or dict) –

    state in format specified by return_as

Returns a basic link to a default neuroglancer state and segment properties.

Parameters:

  • seg_props (SegmentProperties or str) –

    A segment propeties object or a URL to a segment properties.

  • client (CAVEclient) –

    A caveclient object.

  • ngl_url (str, default: None ) –

    URL for a neuroglancer deployment, by default None which uses a default Spelunker deployment.

  • return_as (str, default: 'html' ) –

    Select how the data comes back from statebuilder, by default "html". See statebuilder.render_state for more information.

Returns:

sort_dataframe_by_root_id(df, root_id_column, ascending=False, num_column='n_times', drop=False)

Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.

Parameters:

  • df (DataFrame) –

    dataframe to sort

  • root_id_column (str) –

    Column name to use for sorting root ids

  • ascending (bool, default: False ) –

    Whether to sort ascending (lowest count to highest) or not, by default False

  • num_column (str, default: 'n_times' ) –

    Temporary column name to use for count information, by default 'n_times'

  • drop (bool, default: False ) –

    If True, drop the additional column when returning.

Returns: