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.

• pixelResolution: number[] or object
  • physical scale factors and units (see Physical space)
• downsamplingFactors: number[]
  • factors by which the image is downsampled (see Downsampling)

BigCat

This metadata specification is used by BigCat, the predecessor to Paintera.

Example

{
    "resolution": [ ],
    "offset": [ ],
    "downsamplingFactors": [ ]
}

• resolution: number[]
  • physical scale factors (see Physical space)
• offset: number[]
  • physical translation (see Physical space)
• downsamplingFactors: number[]
  • factors by which the image is downsampled (see Downsampling)

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 space)
• translate: number[]
  • physical translation (see physical space)

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
  • The name or title of the image (see ImagePlus.getTitle
• fps: number (float)
  • the frames per second (see Calibration.fps)
• frameInterval: number (float)
  • spacing of the tim axis (see Calibration.frameInterval)
• pixelWidth: number (float)
  • pixel spacing of the x axis (see Calibration.pixelWidth)
  • corresponds to scale[0] in (Physical space)
• pixelHeight: number (float)
  • pixel spacing of the y axis (see Calibration.pixelHeight)
  • corresponds to scale[1] in (Physical space)
• pixelDepth: number (float)
  • pixel spacing of the z axis (see Calibration.pixelDepth)
  • corresponds to scale[2] in (Physical space)
• xOrigin: number (float)
  • the origin of the x axis (see Calibration.xOrigin)
  • corresponds to translate[0] in (Physical space)
• yOrigin: number (float)
  • the origin of the x axis (see Calibration.yOrigin)
  • corresponds to translate[1] in (Physical space)
• zOrigin: number (float)
  • the origin of the x axis (see Calibration.zOrigin)
  • corresponds to translate[2] in (Physical space)
• numChannels: number (integer)
  • the number of channels (see ImagePlus.getNChannels)
• numSlices: number (integer)
  • the number of z slices (see ImagePlus.getNSlices)
• numFrames: number (integer)
  • the number of frames / time points (see ImagePlus.getNFrames)
• type: number (integer)
  • the data type of the image (see ImagePlus.getType)
• unit: string
  • the physical unit (see Calibration.getUnit)
• properties: object
  • the image's properties (see ImagePlus.getProperties)

Ome-Ngff

This information refers to Version 0.3 of the ome-ngff specification.o

Multiscale metadata example

Example:

{
    "multiscales": [
        {
            "axes": [ "z", "y", "x" ],
            "datasets": [
                { "path": "s0" },
                { "path": "s1" },
                { "path": "s2" }
            ],
            "metadata": {
                "order": 0,
                "preserve_range": true,
                "scale": [ 0.5, 0.5, 0.5 ]
            },
            "name": "zyx",
            "type": "skimage.transform._warps.rescale",
            "version": "0.3"
        }
    ]
}

In this example the dataset pixel scales are:

• s0 : [1.0, 1.0, 1.0]
• s1 : [2.0, 2.0, 2.0]
• s2 : [4.0, 4.0, 4.0]

All of these scales are at arbitrary (pixel) units.

Concepts

Physical space

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]

Downsampling

The N5-viewer and BigCat dialects assume downsampling is done in a particular way such that it affects both the scale and translation of the physical space. Given a scale and downsamplingFactors discrete coordinates are mapped to physical space with:

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

similar to the above.