Compliant File Specification
This was developed in conjunction with the April 2010 release of the OME-XML Model
A "compliant" specification OME file has been defined. This is not the minimum required for the display of an image (for this, see Minimum Specification). This is the information we feel a file should contain to authoritatively describe an imaging experiment. A key point is that an 'OME Compliant' file is as complete as possible, but only contains metadata relevant to a specific imaging experiment. The expectation is not that every field is filled out regardless of the experiment, but that all of the fields listed below that are relevant to an experiment are completed. As an example, PockelCellSetting would not be used in most wide-field microscopy experiments, but would be mandatory for many multi-photon imaging experiments. Thus the OME Compliant Specification should be used as a 'best-effort' spec, to describe as completely as possible a specific imaging experiment. The goal of that 'best-effort' should be to document an experiment as completely as possible, so another person could, with the same sample and microscope, reproduce the data recorded in the file.
Two samples of this structure are shown below. They were generated by opening a propriety file (Olympus .oib and DeltaVision .dv, respectively) in ImageJ using the Bio-Formats plugin with the Display OME-XML Metadata option checked. We then manually added a few addition attributes to the files to make them compliant.
Sample structure one:
<?xml version="1.0" encoding="UTF-8"?>
<OME:OME xmlns:ROI="http://www.openmicroscopy.org/Schemas/ROI/2010-04"
xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2010-04"
xmlns:BIN="http://www.openmicroscopy.org/Schemas/BinaryFile/2010-04"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2010-04
http://www.openmicroscopy.org/Schemas/OME/2010-04/ome.xsd">
<OME:Image ID="Image:0" Name="Series 1">
<OME:AcquiredDate>2008-02-06T13:43:19</OME:AcquiredDate>
<OME:Description>An example OME compliant file, based on Olympus.oib</OME:Description>
<OME:Pixels DimensionOrder="XYCZT" ID="Pixels:0"
PhysicalSizeX="0.207" PhysicalSizeY="0.207" PhysicalSizeZ="0.0"
SizeC="3" SizeT="16" SizeX="1024" SizeY="1024" SizeZ="1"
TimeIncrement="120.1302" Type="uint16">
<OME:Channel EmissionWavelength="523" ExcitationWavelength="488" ID="Channel:0:0"
IlluminationType="Epifluorescence" Name="CH1" SamplesPerPixel="1"
PinholeSize="103.5" AcquisitionMode="LaserScanningConfocalMicroscopy"/>
<OME:Channel EmissionWavelength="578" ExcitationWavelength="561" ID="Channel:0:1"
IlluminationType="Epifluorescence" Name="CH3" SamplesPerPixel="1"
PinholeSize="127.24" AcquisitionMode="LaserScanningConfocalMicroscopy"/>
<OME:Channel ExcitationWavelength="488" ID="Channel:0:2"
IlluminationType="Transmitted"
ContrastMethod="DIC" Name="TD1" SamplesPerPixel="1"
AcquisitionMode="LaserScanningConfocalMicroscopy"/>
<BIN:BinData BigEndian="false" Length="0"/>
</OME:Pixels>
</OME:Image>
</OME:OME>
Sample structure two:
<?xml version="1.0" encoding="UTF-8"?>
<OME:OME xmlns:ROI="http://www.openmicroscopy.org/Schemas/ROI/2010-04"
xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2010-04"
xmlns:BIN="http://www.openmicroscopy.org/Schemas/BinaryFile/2010-04"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2010-04
http://www.openmicroscopy.org/Schemas/OME/2010-04/ome.xsd">
<OME:Instrument ID="Instrument:0">
<OME:Detector ID="Detector:0:0" Model="COOLSNAP_HQ / ICX285" Type="CCD"/>
<OME:Objective ID="Objective:10002" Immersion="Oil" LensNA="1.4" Manufacturer="Olympus"
NominalMagnification="100"/>
</OME:Instrument>
<OME:Image ID="Image:1" Name="example_R3D_D3D.dv">
<OME:AcquiredDate>2005-01-28T13:50:08</OME:AcquiredDate>
<OME:Description>An example OME compliant file,
based on a wide-field microscope image</OME:Description>
<OME:ObjectiveSettings ID="Objective:10002" Medium="Oil" RefractiveIndex="1.52"
CorrectionCollar="7"/>
<OME:Pixels DimensionOrder="XYCZT" ID="Pixels:1" PhysicalSizeX="0.06631"
PhysicalSizeY="0.06631" PhysicalSizeZ="0.2"
SizeC="3" SizeT="1" SizeX="480" SizeY="480" SizeZ="5"
Type="int16">
<OME:Channel EmissionWavelength="457" ExcitationWavelength="360" ID="Channel:1:0"
NDFilter="0.5" Name="DAPI" SamplesPerPixel="1" Fluor="DAPI"
IlluminationType="Epifluorescence" ContrastMethod="Fluorescence"
AcquisitionMode="WideField" Color="65535">
<OME:DetectorSettings Binning="1x1" Gain="0.5" ID="Detector:0:0"
ReadOutRate="10.0"/>
</OME:Channel>
<OME:Channel EmissionWavelength="528" ExcitationWavelength="490" ID="Channel:1:1"
NDFilter="0.0" Name="FITC" SamplesPerPixel="1" Fluor="GFP"
IlluminationType="Epifluorescence" ContrastMethod="Fluorescence"
AcquisitionMode="WideField" Color="16711935">
<OME:DetectorSettings Binning="1x1" Gain="0.5" ID="Detector:0:0"
ReadOutRate="10.0"/>
</OME:Channel>
<OME:Channel EmissionWavelength="617" ExcitationWavelength="555" ID="Channel:1:2"
NDFilter="0.0" Name="RD-TR-PE" SamplesPerPixel="1" Fluor="TRITC"
IlluminationType="Epifluorescence" ContrastMethod="Fluorescence"
AcquisitionMode="WideField" Color="4278190335">
<OME:DetectorSettings Binning="1x1" Gain="0.5" ID="Detector:0:0"
ReadOutRate="10.0"/>
</OME:Channel>
<BIN:BinData BigEndian="false" Length="0"/>
<OME:Plane DeltaT="0.0" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.496" TheC="0" TheT="0" TheZ="0"/>
<OME:Plane DeltaT="0.294" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.696" TheC="0" TheT="0" TheZ="1"/>
<OME:Plane DeltaT="0.587" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.896" TheC="0" TheT="0" TheZ="2"/>
<OME:Plane DeltaT="0.881" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-22.096" TheC="0" TheT="0" TheZ="3"/>
<OME:Plane DeltaT="1.174" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-22.296" TheC="0" TheT="0" TheZ="4"/>
<OME:Plane DeltaT="9.625" ExposureTime="0.3" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.496" TheC="1" TheT="0" TheZ="0"/>
<OME:Plane DeltaT="10.12" ExposureTime="0.3" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.696" TheC="1" TheT="0" TheZ="1"/>
<OME:Plane DeltaT="10.613" ExposureTime="0.3" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.896" TheC="1" TheT="0" TheZ="2"/>
<OME:Plane DeltaT="11.106" ExposureTime="0.3" PositionX="3316.37" PositionY="-646.46"
PositionZ="-22.096" TheC="1" TheT="0" TheZ="3"/>
<OME:Plane DeltaT="11.599" ExposureTime="0.3" PositionX="3316.37" PositionY="-646.46"
PositionZ="-22.296" TheC="1" TheT="0" TheZ="4"/>
<OME:Plane DeltaT="25.447" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.496" TheC="2" TheT="0" TheZ="0"/>
<OME:Plane DeltaT="25.739" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.696" TheC="2" TheT="0" TheZ="1"/>
<OME:Plane DeltaT="26.033" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-21.896" TheC="2" TheT="0" TheZ="2"/>
<OME:Plane DeltaT="26.326" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-22.096" TheC="2" TheT="0" TheZ="3"/>
<OME:Plane DeltaT="26.619" ExposureTime="0.1" PositionX="3316.37" PositionY="-646.46"
PositionZ="-22.296" TheC="2" TheT="0" TheZ="4"/>
</OME:Pixels>
</OME:Image>
</OME:OME>
The data (BinData element content) in these sample was removed for reasons of length.
Alternative valid forms:
- would have a OME:TiffData block instead of the BIN:BinData block. This would be used in the header of an OME-TIFF file.
- would have a OME:MetadataOnly block instead of the BIN:BinData block. This would ONLY be acceptable if the image data of the file CANNOT for technical reasons, be represented in an OME file.
Definitions of values stored
Image
Describes the actual image and its metadata.
AcquiredDate
The acquisition date of the Image.
Description
A multi-line description for the image.
Name
A short description for the image. This would be
used to, for example, select the image from a list.
ImagingEnvironment
Describes the environment that the biological sample
was in during the experiment.
AirPressure
AirPressure in millibars[mbar].
CO2Percent
%CO2 as a percent-fractions from 0.0 to 1.0 [%].
Humidity
Humidity as a percent-fraction from 0.0 to 1.0 [%].
Temperature
Temperature [degrees Celsius].
ObjectiveSettings
Describes any settings on or around the objective
CorrectionCollar
An adjustable ring on the objective that corrects
for changes in immersion medium refractive imdex. Arbitrary scale and
unitless.
Medium
A description of a Medium used for the lens. e.g.,
Oil, Water, WaterDipping, Air, Multi, Glycerol, Other
RefractiveIndex
Refractive index is that of the immersion medium.
Pixels
Defines the location and paramater sof the Pixels,
the actual binary image data
DimensionOrder
The order in which the individual planes of data are
interleaved. e.g., XYZCT, XYZTC, XYCTZ, XYCZT, XYTCZ, XYTZC
PhysicalSizeX
}
PhysicalSizeY
Physical size in x, y, z of a pixel in microns[um]
PhysicalSizeZ
SizeC
}
SizeT
SizeX
Dimensional size x, y, z, c, t of pixel data array
SizeY
SizeZ
TimeIncrement
Used for time series that have a global timing
specification instead of per-timepoint timing info, e.g., a video stream.
[s].
Type
The variable type used to represent each pixel in
the image. e.g., int8, int16, int32, uint8, uint16, uint32, float, bit,
double, complex, double-complex
BinData
If the pixel data is stored dierctly in the XML it
is enclosed in BinData Elements
TiffData
If the pixel data is stored in an OME-TIFF file it
is described by TiffData Elements
FirstC
}
FirstT
FirstZ
The TiffData element describes how the
TIFF IFD numbers are mapped to the Pixels.
IFD
PlaneCount
UUID
The TiffData UUID and Filename are used for
multi-file datasets to maintain connections between the files
FileName
Channel
AcquisitionMode
AcquisitionMode describes the type of microscopy
performed. e.g., WideField, LaserScanningMicroscopy, LaserScanningConfocal,
SpinningDiskConfocal, SlitScanConfocal, MultiPhotonMicroscopy,
StructuredIllumination, SingleMoleculeImaging, TotalInternalReflection,
FluorescenceLifetime, SpectralImaging, FluorescenceCorrelationSpectroscopy,
NearFieldScanningOpticalMicroscopy, SecondHarmonicGenerationImaging, Other
Color
A color used render this channel
ContrastMethod
The technique used to achieve contrast. e.g.,
Brightfield, Phase, DIC, HoffmanModulation, ObliqueIllumination,
PolarizedLight, Darkfield, Fluorescence, Other
EmissionWavelength
Emission wavelength of excitation for a particular
channel, in nanometres [nm].
ExcitationWavelength
Excitation wavelength of excitation for a particular
channel, in nanometres [nm].
Fluor
The name of the fluorophore used to produce this
channel.
IlluminationType
The method of illumination used to capture the
channel. e.g., Transmitted, Epifluorescence, Oblique, NonLinear, Other
Name
A short name for the channel, used to, for example,
identify the channel from a list.
NDFilter
Specifies the combined effect of any neutral density
filters used. [% Transmittance]
PinholeSize
Specifies adjustable pin hole diameters for confocal
microscopes (microns [um]).
PockelCellSetting
Amount the polarization of the beam introduced by
Pockel Cell, if any.
SamplesPerPixel
The number of samples the detector takes to form
each pixel value.
DetectorSettings
Binning
Represents the number of pixels that are combined to
form larger pixels. e.g., 1x1, 2x2, 4x4, 8x8, Other
Gain
The Gain of the detector.
Offset
The Offset of the detector.
ReadOutRate
Detector read speed (MHz)
Voltage
The Voltage of the detector. volts[V]
LightSourceSettings
Attenuation
The Attenuation of the light source. [%]
Wavelength
The Wavelength of the light source. [nm]
Plane
DeltaT
Elapsed time since the beginning of the experiment
[s]
ExposureTime
Elapsed time during image recording. [s]
PositionX
}
PositionY
The x, y, z position of the stage. [µm]
PositionZ
StageLabel
Name
Short name for this stage location This would be
used to, for example, identify the channel from a list.
X
}
Y
The labeled x, y, z position of the stage.
[µm]
Z
©2010 Linkert et al. Figure originally published as Figure 2, Linkert et al (2010), J. Cell Biol. 189(5):777-782
(http://jcb.rupress.org/content/189/5/777)
