n5

n5 data source

The "n5" data source allows Neuroglancer to directly read n5 format datasets, using the following data source URL syntax:

n5://FILE_URL, where FILE_URL is a URL to the directory containing the attributes.json metadata file using any supported file protocol.

Both single-scale and multi-scale datasets are supported.

Dimension names may be specified using the axes metadata attribute; if present, the axes attribute must be an array of strings, specifying the name of each dimension in the same order as the dimensions attribute.

As a Neuroglancer-specific extension, coordinate arrays may be specified using the coordinateArrays metadata attribute; if present, the coordinateArrays attribute must be an object, where the keys correspond to dimension names in axes and the values are arrays of strings specifying the coordinate labels starting at 0. For example:

{
  "dimensions": [10000, 10000, 5],
  "dataType": "uint8",
  "blockSize": [512, 512, 1],
  "compression": { "type": "raw" },
  "axes": ["x", "y", "c"],
  "coordinateArrays": {
    "c": ["A", "B", "C", "D", "E"]
  }
}

For mutli-scale datasets, both the n5-viewer and bigdataviewer-n5 formats are supported. FILE_URL must specify a directory with the following contents:

• attributes.json: Specifies the multi-scale metadata with the following attributes:
  • "downsamplingFactors": array of arrays, where downsamplingFactors[i] is an array specifying the downsampling factor for each dimension of scale i. For example, [[1, 1, 1], [2, 2, 1], [4, 4, 1]] indicates that there are three downsampling levels, where scale s0 is full resolution, scale s1 is downsampled by 2 in the first two dimensions and 1 in the third dimension, and scale s2 is downsampled by 4 in the first two dimensions and 1 in the third dimensions. For compatibility with n5-viewer, this attribute may also be named scales.
  • "resolution": Array of numbers specifying the size along each dimension of a single voxel at the base resolution, in the units specified by "units". For example, if "resolution" is [4, 4, 30] and "units" is ["nm", "nm", "nm"], then the first two dimensions have a voxel size of 4nm and the third dimension has a voxel size of 30nm.
  • "units": Array of strings specifying the units in which "resolution" is specified for each dimension. May be "m" (for meters), "s" (for seconds), or "Hz" (Hertz) with any SI prefix. May be an empty string to indicate a unit-less dimension.
  • "pixelResolution": For compatibility with n5-viewer, may be specified in place of "resolution" and "units". Must be an object with the following properties:
    • "unit": String specifying the unit for all dimensions.
    • "dimensions": Array of numbers specifying the voxel size for each dimension, in the specified unit.
• s0/: directory containing dataset for base resolution.
• s1/: directory containing dataset for first downsampling level.
• sN/: directory containing dataset for Nth downsampling level.

Supported compression types:

• raw
• blosc
• gzip

Supported data types:

• uint8
• int8
• uint16
• int16
• uint32
• int32
• uint64
• float32