Skip to content

Latest commit

 

History

History
65 lines (51 loc) · 3.74 KB

skeletons.md

File metadata and controls

65 lines (51 loc) · 3.74 KB
Raw

Skeleton representation of segmented objects

A skeleton representation of some or all segmented objects may be specified as a directory tree consisting of the following files:

  • info file in JSON format specifying the metadata.
  • For each segment ID for which there is a skeleton representation, a segment data file specifying the encoded skeleton for a single segment.

The actual storage of the manifest and mesh fragment data depends on whether the unsharded or sharded format is used.

Skeleton info JSON file format

The info file is a JSON-format text file. The root value must be a JSON object with the following members:

  • "@type": Must be "neuroglancer_skeletons".
  • "transform": JSON array of 12 numbers specifying a 4x3 homogeneous coordinate transform from the "stored model" coordinate space to a "model" coordinate space. The "stored model" coordinate space is arbitrary. The "model" coordinate space should be in nanometers. If using a "radius" attribute, the scaling applied by "transform" should be uniform.
  • "vertex_attributes": JSON array specifying additional per-vertex attributes, where each array element is a JSON object with the following members:
    • "id": Attribute identifier, must be a unique, non-empty JSON string.
    • "data_type": JSON string specifying the data type, must be one of "float32", "int8", "uint8", "int16", "uint16", "int32", "uint32".
    • "num_components": JSON number specifying the number of components per vertex.
  • "sharding": If specified, indicates that the mesh is stored using the sharded format. Must be a sharding specification. If not specified, the unsharded storage representation is used.
  • "segment_properties": Optional. If specified, it must be a string value specifying the name of the subdirectory containing a segment properties representation. Note that Neuroglancer only uses these segment properties if this skeleton source is specified as a data source directly. If it is specified indirectly via the "skeletons" property in a multi-scale volume, then you must instead specify the properties using use the "segment_properties" member in the volume's info file.

The special vertex attribute id of "radius" may be used to indicate the radius in "stored model" units; it should have a "data_type" of "float32" and "num_components" of 1.

Encoded skeleton file format

The skeleton representation for a single segment ID is a binary file with the following format:

  • num_vertices: uint32le, specifies the number of vertices.
  • num_edges: uint32le, specifies the number of edges.
  • vertex_positions: 3*num_vertices float32le, as a C-order [num_vertices, 3] array specifying the x, y, and z vertex positions in "stored model" coordinates.
  • edges: 2*num_edges uint32le, as a C-order [num_edges, 2] array specifying the source and target vertex index in the range [0, num_vertices).
  • For each additional attribute in vertex_attributes:
    • attribute_data: num_vertices * num_components elements of the specified data_type in little-endian format.

Unsharded storage of encoded skeleton data

If the unsharded format is used, the encoded skeleton data is stored as a separate file within the same directory as the info file under the name <segment-id>, where <segment-id> is the base-10 segment ID.

Sharded storage of encoded skeleton data

If the sharded format is used, the encoded skeleton data is retrieved using the segment ID as the key. The shard files are stored in the same directory as the info file.