pymaid.get_connectors_in_bbox

pymaid.get_connectors_in_bbox(bbox, unit='NM', limit=None, restrict_to=False, ret='COORDS', remote_instance=None, **kwargs)[source]

Retrieves connectors within given bounding box.

Parameters:

  • bbox (list-like | dict | pymaid.Volume) –

    Coordinates of the bounding box. Can be either:

    1. List/np.array: [[left, right], [top, bottom], [z1, z2]]

    2. Dictionary {'left': int|float, 'right': ..., ...}

  • unit ('NM' | 'PIXEL') – Unit of your coordinates. Attention: ‘PIXEL’ will also assume that Z1/Z2 is in slices. By default, a X/Y resolution of 3.8nm and a Z resolution of 35nm is assumed. Pass ‘xy_res’ and ‘z_res’ as **kwargs to override this.

  • limit (int, optional) – Limit the number of connectors returned.

  • restrict_to (list, optional) – List of skeleton IDs to return connectors for.

  • ret (‘IDS’ |’COORDS’ | ‘LINKS’) – Connector data to be returned. See below for explanation.

  • remote_instance (CatmaidInstance) – If not passed directly, will try using global.

Returns:

  • pandas.DataFrame – If ret="COORDS" (default): DataFrame in which each row represents a connector:

    connector_id x y z

    0 1 ..

  • list – If ret="IDS": list of connector IDs.

  • pandas.DataFrame – If ret="LINKS": DataFrame in which each row represents a connector. Please note that connectors can show up multiple times - once for each link.

    connector_id x y z skeleton confidence creator_id ..

    0 1 ..

    0 1 ..