CustomMetadata.md

Custom metadata

You can specify the format of metadata for exported datasets by selecting the Custom option for the metadata type. A dialog will appear, initialized with the resolution only examples specification. The specification transforms the variables into a new json, formatting the metadata as you desire. The specifcation mapper uses jackson-jq, a java implementation of jq. See also the examples below.

Variables

• name
• xResolution - spatial resolution in x
• yResolution - spatial resolution in y
• zResolution - spatial resolution in z
• tResolution - resolution in time
• xOrigin - spatial origin x
• yOrigin - spatial origin y
• zOrigin - spatial origin z
• tOrigin - origin in time
• xUnit - physical unit of x resolution
• yUnit- physical unit of y resolution
• zUnit- physical unit of z resolution
• tUnit- unit of time resolution
• globalUnit - global spatial resolution unit
• axis0 - label of axis 0
• axis1 - label of axis 1
• axis2 - label of axis 2
• axis3 - label of axis 3
• axis4 - label of axis 4
• otherMetadata - the contents of getProperties

Examples

All examples will show output using the 5d mitosis.tif sample image from ImageJ. Code implementing these examples can be found here.

Spatial resolution in array

{
"resolution" : [ .xResolution, .yResolution, .zResolution ]
}

yields:

{
  "resolution": [
    0.08850000022125,
    0.08850000022125,
    1
  ]
}

COSEM

{
"transform": 
    { 
    "scale": [.xResolution, .yResolution, .zResolution], 
    "translate": [.xOrigin, .yOrigin, .zOrigin], 
    "axes": [.axis0, .axis1, .axis2, .axis3, .axis4], 
    "units": [.xUnit, .yUnit, .zUnit] 
    } 
}

{
"transform" :
    {
    "axes" : ["x","y","c","z","t"],
    "scale" : [0.08850000022125,0.08850000022125,1.0],
    "units" : ["µm","µm","µm"],
    "translate" : [0.0,0.0,0.0]
    }
}