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The OME Data Model specification
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Open Microscopy Environment
OME XML Schema June 2012
Author: Ilya G. Goldberg, Andrew J Patterson
The OME element is a container for all information objects accessible by OME.
These information objects include descriptions of the imaging experiments
and the people who perform them, descriptions of the microscope, the resulting
images and how they were acquired, the analyses performed on those images,
and the analysis results themselves.
An OME file may contain any or all of this information.
With the creation of the Metadata Only Companion OME-XML and Binary Only OME-TIFF files
the top level OME node has changed slightly.
It can EITHER:
Contain all the previously expected elements
OR:
Contain a single BinaryOnly element that points at
its Metadata Only Companion OME-XML file.
Pointer to an external metadata file. If this element is
present, then no other metadata may be present in this file,
i.e. this file is a place-holder.
Filename of the OME-XML metadata file for this
binary data. If the file cannot be found, a search can be
performed based on the UUID.
The unique identifier of another OME-XML block
whose metadata describes the binary data in this file. This UUID
is considered authoritative regardless of mismatches in the
filename.
This unique identifier is used to keep track of multi part files.
It allows the links between files to survive renaming.
While OPTIONAL in the general case this is REQUIRED in a
MetadataOnly Companion to a collection of BinaryOnly files.
This is the name of the creating application of the OME-XML
and preferably its full version.
e.g "CompanyName, SoftwareName, V2.6.3456"
This is optional but we hope it will be set by applications
writing out OME-XML from scratch.
Images
This element describes the actual image and its meta-data.
The elements that are references (ending in Ref or Settings) refer to
elements defined outside of the Image element. Ref elements are simple
links, while Settings elements are links with additional values.
If any of the required Image attributes or elements are missing, its
guaranteed to be an invalid document. The required attributes and
elements are ID and Pixels.
ExperimenterRef is required for all Images with well formed LSIDs.
ImageType is a vendor-specific designation of the type of image this is.
Examples of ImageType include 'STK', 'SoftWorx', etc.
The Name attributes are in all cases the name of the element
instance. In this case, the name of the image, not necessarily the filename.
PixelSize* is in microns[um].
The acquisition date of the Image.
The element contains a string in the ISO 8601 dateTime format (i.e. 1988-04-07T18:39:09)
A description for the image. [plane text multi-line string]
Pixels
NOTE: Pixels is DEPRECATED, but it is still required.
This is just notice that the contents of Pixels will be
moved up to Image in the next release. This is because there
has only been 1 Pixels object in each Image for some time.
The concept of multiple Pixels sets for one Image failed to
take off. It is therefore redundant.
The Image will be unreadable if any of the required Pixel attributes are missing.
The Pixels themselves are stored within the file compressed by plane, and encoded in Base64.
The Pixels element must contain a list of BinData, each containing a single plane of pixels.
These Pixels elements, when read in document order, must produce a 5-D pixel array
of the size specified in this element, and in the dimension order specified by 'DimensionOrder'.
The order in which the individual planes of data are interleaved.
The variable type used to represent each pixel in the image.
Dimensional size of pixel data array [units:none]
Dimensional size of pixel data array [units:none]
Dimensional size of pixel data array [units:none]
Dimensional size of pixel data array [units:none]
Dimensional size of pixel data array [units:none]
Physical size of a pixel in microns[um].
Physical size of a pixel in microns[um].
Physical size of a pixel in microns[um].
TimeIncrement is used for time series that have a global
timing specification instead of per-timepoint timing info.
For example in a video stream. The unit is seconds[s].
Planes
The Plane object holds microscope stage and image timing data
for a given channel/z-section/timepoint.
This optional element is a hash of the plane's image data.
It is a choice between all the support hash types.
Currently the only method supported is SHA1.
The Z-section this plane is for. [units:none]
This is numbered from 0.
The timepoint this plane is for. [units:none]
This is numbered from 0.
The channel this plane is for. [units:none]
This is numbered from 0.
Units are seconds since the beginning of the experiment [s]
Units are seconds [s]
The X position of the stage. [units are in the microscope reference frame]
The Y position of the stage. [units are in the microscope reference frame]
The Z position of the stage. [units are in the microscope reference frame]
Channels
There must be one per channel in the Image, even for a single-plane image.
And information about how each of them was acquired is stored in the various optional *Ref elements. Each Logical Channel is composed of one or more
ChannelComponents. For example, an entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrum
constituting a ChannelComponent of the FTIR Logical Channel. An RGB image where the Red, Green and Blue components do not reflect discrete probes but are
instead the output of a color camera would be treated similarly - one Logical channel with three ChannelComponents in this case.
The total number of ChannelComponents for a set of pixels must equal SizeC.
The IlluminationType attribute is a string enumeration which may be set to 'Transmitted', 'Epifluorescence', 'Oblique', or 'NonLinear'.
The user interface logic for labeling a given channel for the user should use the first existing attribute in the following sequence:
Name -> Fluor -> EmissionWavelength -> ChannelComponent/Index.
A name for the channel that is suitable be presented to the user.
The number of samples the detector takes to form each pixel value.
The SamplesPerPixel attribute is the number of channel components in the logical channel. [units:none]
The method of illumination used to capture the channel.
The optional PinholeSize attribute allows specifying adjustable
pin hole diameters for confocal microscopes (units microns[um]).
AcquisitionMode describes the type of microscopy performed for each channel
ContrastMethod describes the technique used to achieve contrast for each channel
Excitation wavelength of excitation for a particular channel, in nanometres[nm].
Emission wavelength of excitation for a particular channel, in nanometres[nm].
The Fluor attribute is used for fluorescence images.
This is the name of the fluorophore used to produce this channel [plain text string]
The NDfilter attribute is used to specify the combined effect of any neutral density filters used. [units optical density expressed as a PercentFraction]
The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by. [units:none]
A color used to render this channel - encoded as RGBA
The default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value)
NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.
MetadataOnlyMarkers
This place holder means there is on pixel data in this file.
TiffDataBlocks
This described the location of the pixel data in a tiff file.
This must be used when the IFDs are located in another file.
Note: It is permissible for this to be self referential.
This can be used when the IFDs are located in another file.
The / (forward slash) is used as the path separator.
A relative path is recommended. However an absolute path can be specified.
Default is to use the file the ome-xml data has been pulled from.
Note: It is permissible for this to be self referential. The file image1.tiff
may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"
Gives the IFD(s) for which this element is applicable. Indexed from 0.
Default is 0 (the first IFD). [units:none]
Gives the Z position of the image plane at the specified IFD. Indexed from 0.
Default is 0 (the first Z position). [units:none]
Gives the T position of the image plane at the specified IFD. Indexed from 0.
Default is 0 (the first T position). [units:none]
Gives the C position of the image plane at the specified IFD. Indexed from 0.
Default is 0 (the first C position). [units:none]
Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing
Pixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFF
file, unless an IFD is specified, in which case the default is 1. [units:none]
StageLabels
The StageLabel is used to specify a name and position for a stage position in the microscope's reference frame.
The X position of the stage label. [units are in the microscope reference frame]
The Y position of the stage label. [units are in the microscope reference frame]
The Z position of the stage label. [units are in the microscope reference frame]
MicrobeamManipulations
Defines a microbeam operation type and the region of the image it was applied to.
The LightSourceRef element is a reference to a LightSource specified in the Instrument element which was used for a technique other than illumination for
the purpose of imaging. For example, a laser used for photobleaching.
A description for the Microbeam Manipulation. [plane text multi-line string]
The type of manipulation performed.
Instruments
This element describes the instrument used to capture the Image.
It is primarily a container for manufacturer's model and catalog
numbers for the Microscope, LightSource, Detector, Objective and
Filters components.
The Objective element contains the additional elements LensNA and Magnification.
The Filters element can be composed either of separate excitation,
emission filters and a dichroic mirror or a single filter set.
Within the Image itself, a reference is made to this one Filter element.
There may be multiple light sources, detectors, objectives and filters on a microscope.
Each of these has their own ID attribute, which can be referred to from Channel.
It is understood that the light path configuration can be different
for each channel, but cannot be different for each timepoint or
each plane of an XYZ stack.
Microscopes The microscope's manufacturer specification.
ImagingEnvironments
This describes the environment that the biological sample was in
during the experiment.
The Temperature is in Celsius[C].
AirPressure is in millibars[mbar].
Humidity around the sample [units:none]
A fraction, as a value from 0.0 to 1.0.
Carbon Dioxide concentration around the sample [units:none]
A fraction, as a value from 0.0 to 1.0.
Projects
The Project ID is required.
Datasets can be grouped into projects using a many-to-many relationship.
A Dataset may belong to one or more Projects by including one or more ProjectRef elements which refer to Project IDs.
Projects do not directly contain images - only by virtue of containing datasets, which themselves contain images.
A description for the project. [plane text multi-line string]
ExperimenterGroups
The ExperimenterGroupID is required.
Information should ideally be specified for at least one Leader as a contact for the group.
The Leaders are themselves Experimenters.
A description for the group. [plane text multi-line string]
Leaders
Contact information for a ExperimenterGroup leader specified using a reference
to an Experimenter element defined elsewhere in the document.
Datasets
An element specifying a collection of images that are always processed together.
Images can belong to more than one Dataset, and a Dataset may contain more than one Image.
Images contain one or more DatasetRef elements to specify what datasets they belong to.
Once a Dataset has been processed in any way, its collection of images cannot be altered.
The ExperimenterRef and ExperimenterGroupRef elements specify the person and group this Dataset belongs to.
Projects may contain one or more Datasets, and Datasets may belong to one or more Projects.
This relationship is specified by listing DatasetRef elements within the Project element.
A description for the dataset. [plane text multi-line string]
A name for the dataset that is suitable be presented to the user.
Experiments
This element describes the type of experiment. The required Type attribute must contain one or more entries from the following list:
FP FRET Time-lapse 4-D+ Screen Immunocytochemistry FISH Electrophysiology Ion-Imaging Colocalization PGI/Documentation
FRAP Photoablation Optical-Trapping Photoactivation Fluorescence-Lifetime Spectral-Imaging Other
FP refers to fluorescent proteins, PGI/Docuemntation is not a 'data' image.
The optional Description element may contain free text to further describe the experiment.
A description for the experiment. [plane text multi-line string]
This is a link to the Experimenter who conducted the experiment
A term to describe the type of experiment.
Experimenters
This element describes a person who performed an imaging experiment.
This person may also be a user of the OME system, in which case the UserName element contains their login name.
Experimenters may belong to one or more groups which are specified using one or more ExperimenterGroupRef elements.
First name, sometime called christian name or given name or forename. [plain text string]
Any other names. [plain text string]
A person's last name sometimes called surname or family name. [plain text string]
A person's email address. [valid email address as string]
A person's Institution
The organizing structure that people belong to other than groups. A university, or company, etc.
We do not specify a department element, and do not mean for Institution to be used in this way.
We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed location
and of being more recognizable than a group of experimenters. [plain text string]
This is the username of the experimenter (in a 'unix' or 'database' sense). [plain text string]
This is the base from which many microscope components are extended. E.g Objective, Filter etc.
Provides attributes for recording common properties of these components such as Manufacturer name, Model etc,
all of which are optional.
The manufacturer of the component. [plain text string]
The Model of the component. [plain text string]
The serial number of the component. [plain text string]
The lot number of the component. [plain text string]
Binary contents coded in hexadecimal (20 characters long)
A simple type that restricts the value to an integer between 0 and 9223372036854775807 (inclusive).
A simple type that restricts the value to an integer between 0 and 2,147,483,647 (inclusive).
A simple type that restricts the value to an integer between 1 and 2,147,483,647 (inclusive).
A simple type that restricts the value to a float between >0 and max 32-bit float {i.e. (2−2^-23) × 2^27 ≈ 3.4 × 10^38}
A simple type that restricts the value to a float between 0 and 1 (inclusive).
This is a unique ID for the file but does not conform to the ID pattern used in the rest of the file.
The rest of the IDs are either an full LSID or an internal ID which is a string that is simply unique in this file.
As the UniversallyUniqueIdentifier is used from outside this file to identify it having the same ID in another file could cause problems.
A UUID is 32 hexadecimal digits, in 5 groups, 8-4-4-4-12, separated by hyphens
e.g. urn:uuid:3e450fae-b8f2-4d35-aa54-702168b2487f
There are methods to generate these in most modern languages.
http://www.ietf.org/rfc/rfc4122.txt
The number size/kind used to represent a pixel
A simple type that identifies itself as a Color, the value is an integer between -2,147,483,648 and 2,147,483,647 (inclusive).
The value is a signed 32 bit encoding of RGBA so "-1" is #FFFFFFFF or solid white.
NOTE: Prior to the 2012-06 schema the default values were incorrect and produced a transparent red not solid white.
Objectives
A description of the microscope's objective lens.
Required elements include the lens numerical aperture,
and the magnification, both of which a floating
point (real) numbers.
The values are those that are fixed for a particular
objective: either because it has been manufactured to
this specification or the value has been measured on
this particular objective.
Correction: This is the type of correction coating applied to this lens.
Immersion: This is the types of immersion medium the lens is designed to
work with. It is not the same as 'Medium' in ObjectiveRef (a
single type) as here Immersion can have compound values like 'Multi'.
LensNA: The numerical aperture of the lens (as a float)
NominalMagnification: The specified magnification e.g. x10
CalibratedMagnification: The measured magnification e.g. x10.3
WorkingDistance: WorkingDistance of the lens. The Units are microns[um].
The correction applied to the lens
The immersion medium the lens is designed for
The numerical aperture of the lens expressed as a floating point (real) number.
Expected range 0.02 - 1.5 [units:none]
The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. [units:none]
The magnification of the lens as measured by a calibration process- i.e. '59.987' for a 60X lens. [units:none]
The working distance of the lens expressed as a floating point (real) number. Units are microns[um].
Records whether or not the objective was fitted with an Iris. [flag]
Detectors
The type of detector used to capture the image.
The Detector ID can be used as a reference within the Channel element in the Image element.
Each attribute now has an indication of what type of detector
it applies to. This is preparatory work for cleaning up and
possibly splitting this object into sub-types.
The Detector Gain for this detector, as a float. [units:none] {used:CCD,EMCCD,PMT}
The Voltage of the detector (e.g. PMT voltage) as a float. volts[V] {used:PMT}
The Detector Offset. [units:none] {used:CCD,EMCCD}
The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}
Gain applied to the detector signal.
This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] {used:EMCCD#EMGain}
The Type of detector. E.g. CCD, PMT, EMCCD etc.
FilterSets Filter set manufacturer specification
ExcitationFilters
The Filters placed in the Excitation light path.
EmissionFilters
The Filters placed in the Emission light path.
Filters
A filter is either an excitation or emission filters.
There should be one filter element specified per wavelength in the image.
The channel number associated with a filter set is specified in Channel.
It is based on the FilterSpec type, so has the required attributes Manufacturer, Model, and LotNumber.
It may also contain a Type attribute which may be set to
'LongPass', 'ShortPass', 'BandPass', 'MultiPass',
'Dichroic', 'NeutralDensity', or 'Other'.
It can be associated with an optional FilterWheel - Note: this is not the same as a FilterSet
A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string]
TransmittanceRanges
This records the range of wavelengths that are transmitted by the filter. It also records the maximum amount of light transmitted.
CutIn is the wavelength below which there is less than 50% transmittance for a filter. Units: nanometres[nm].
CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units: nanometres[nm].
CutInTolerance Units: nanometres[nm],
CutOutTolerance Units: nanometres[nm],
The amount of light the filter transmits at a maximum [units:none]
A fraction, as a value from 0.0 to 1.0.
Dichroics The dichromatic beamsplitter or dichroic mirror used for this filter combination.
LightPaths A description of the light path
ExcitationFilters
The Filters placed in the Excitation light path.
EmissionFilters
The Filters placed in the Emission light path.
LightSources
The lightsource for the instrument. An instrument may have several light sources.
The type of lightsource is specified by one of the child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'.
Each of the light source types has its own Type attribute to further differentiate the light source
(eg, Nd-YAG for Laser or Hg for Arc).
A LightSource ID must be specified for each light source, and the individual
light sources can be referred to by their LightSource IDs (eg from Channel).
The light-source power. units milliwatts[mW]
Lasers
Laser types are specified using two attributes - the Type and the LaserMedium.
The Laser element may contain a Pump sub-element which refers to
a LightSource used as a laser pump.
Type is the general category of laser.
The Medium attribute specifies the actual lasing medium
for a given laser type.
The Wavelength of the laser in nanometres[nm]
FrequencyMultiplication that may be specified. [units:none]
Whether or not the laser is Tuneable [flag]
The Pulse mode of the laser.
If true the laser has a PockelCell to rotate the polarization of the beam. [flag]
The is the rate in Hz at which the laser pulses if
the Pulse type is 'Repetitive'. hertz[Hz]
Arcs
The Arc element is used to describe various kinds of Arc lamps - Hg, Xe, HgXe.
The Power of the Arc is now stored in the LightSource.
The type of Arc lamp.
Filaments
The Filament element is used to describe various kinds of filament bulbs such as Incadescent or Halogen.
The Power of the Filament is now stored in the LightSource.
The type of filament.
LightEmittingDiodes
The LightEmittingDiode element is used to describe
various kinds of LED lamps.
As the LightEmittingDiode is inside a LightSource it already has
available the values from ManufacturerSpec
(Manufacturer, Model, SerialNumber, LotNumber)
And the values from LightSource which includes Power in milliwatts
We have looked at extending this element but have had a problem
producing a generic solution.
Possible attributes talked about adding include:
Power in lumens - but this is complicated by multi-channel
devices like CoolLED where each channel's power is different
Wavelength Range - not a simple value so would require
multiple attributes or a child element
Angle of Projection - this would be further affected by the
optics used for filtering the naked LED or that combine
power from multiple devices
These values are further affected if you over-drive the LED
resulting in a more complex system
Another issue is that LED's may not be used directly for
illumination but as drivers for secondary emissions from doped
fiber optics. This would require the fiber optics to be modeled.
Thanks to Paul Goodwin of Applied Precision of information about
this topic.
Pumps
The Pump element is a reference to a LightSource. It is used within the Laser element to specify the light source for the laser's pump (if any).
Reference is an empty complex type that is contained and extended by all the *Ref elements and also the Settings Complex Type
Each *Ref element defines an attribute named ID of simple type *ID and no other information
Each simple type *ID is restricted to the base type LSID with an appropriate pattern
The ImageRef element is a reference to a OME:Image element.
There may be one or more of these in a Dataset.
This empty element has a required Project ID attribute that refers to Projects defined within the OME element.
This empty element has a required Experimenter ID and an optional DocumentID attribute which refers to one of the Experimenters defined within OME.
This empty element has a reference (the ExperimenterGroup ID attribute) to a ExperimenterGroup defined within OME.
This empty element can be used (via the required Instrument ID attribute) to refer to an Instrument defined within OME.
The DatasetRef element refers to a Dataset by specifying the Dataset ID attribute.
One or more DatasetRef elements may be listed within the Image element to specify what Datasets
the Image belongs to.
Settings is an empty complex type that is contained and extended by all the *Settings elements
Each *Settings element defines an attribute named ID of simple type *ID and the other information that is needed.
Each simple type *ID is restricted to the base type LSID with an appropriate pattern
LightSourceSettingsCombinations
The Attenuation of the light source [units:none]
A fraction, as a value from 0.0 to 1.0.
The Wavelength of the light source. nanometres[nm]
DetectorSettingsCombinations
This holds the setting applied to a detector as well as a
reference to the detector.
The ID is the detector used in this case.
Each attribute now has an indication of what type of detector
it applies to. This is preparatory work for cleaning up and
possibly splitting this object into sub-types.
The Offset of the detector. [units none] {used:CCD,EMCCD}
The Gain of the detector. [units:none] {used:CCD,EMCCD,PMT}
The Voltage of the detector. volts[V] {used:PMT}
The speed at which the detector can count pixels. {used:CCD,EMCCD}
Units of ReadOutRate is MHz. This is the bytes per second that
can be read from the detector (like a baud rate). megahertz[MHz]
Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD}
ObjectiveSettingsCombinations
This holds the setting applied to an objective as well as a
reference to the objective.
The ID is the objective used in this case.
The CorrectionCollar is normally an adjustable ring on the
objective. Each has an arbitrary scale on it so the values
is unit-less. [units:none]
A description of a Medium used for the lens.
The Medium is the actual immersion medium used in this case.
The RefractiveIndex is that of the immersion medium. This is
a ratio so it also unit-less. [units:none]
Either LSID or internal consistent IDs for the file
See: http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/id-and-lsid