N5 Metadata Dialects

N5 Metadata Dialects

This page contains a list and description of known n5 metadata dialects.

N5-viewer

The n5-viewer metadata style is briefly described here.

Dataset-level attributes

Datasets may contain a pixelResolution field that is either

"pixelResolution": {
   "unit": "um",
   "dimensions": []
}

or

"pixelResolution": []

Datasets may contain a downsamplingFactors field.

COSEM

The COSEM metadata style is described here.

Dataset-level attributes

Datasets shall contain a transform field that describes how the discrete pixel grid should be arranged in physical space.

"transform": {
    "axes": [ ], 
    "units": [ ],
    "scale": [ ],
    "translate": [ ]
}

All fields below must have lengths equal to the dimensionality of the n5 dataset they describe.

• axes: String[]
  • gives a label to axis indexes
  • examples: ["x","y","z"], ["z","y","x"]
• units: String[]
  • the physical
  • examples ["nm","nm","nm"], ["microns","microns","microns"]
• scale: number[]
  • physical scale factors (see physical spacing)
• translate: number[]
  • physical translation (see physical spacing)

Physical spacing

Call the 0th, 1st, and 2nd dimensions of the dataset i, j, and k, respectively. Then if axis: ["x","y","z"], then The discrete point at (i,j,k), should be mapped to the physical point (x,y,z) as follows:

x = (scale[0] * i) + translate[0]
y = (scale[1] * j) + translate[1]
z = (scale[2] * k) + translate[2]

ImageJ

The ImageJ metadata dialect mirrors the metadata stored in ImageJ's ImagePlus class. Images of up to five dimensions are supported, i.e. 3D, multi-channel, time-series can be described with this dialect. This standard does not support multiscale datasets.

Dataset-level attributes

• name: string
• fps: number (float)
• frameInterval: number (float)
• pixelWidth: number (float)
• pixelHeight: number (float)
• pixelDepth: number (float)
• xOrigin: number (float)
• yOrigin: number (float)
• zOrigin: number (float)
• numChannels: number (integer)
• numSlices: number (integer)
• numFrames: number (integer)
• type: number (integer)
• unit: string
• properties: object