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Open Microscopy Environment
OME XML Schema June 2016
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.
Physical size of pixels are microns[µm].
The acquisition date of the Image.
The element contains an xsd:dateTime string based on the ISO 8601 format (i.e. 1988-04-07T18:39:09.359)
YYYY-MM-DDTHH:mm:SS.sssZ
Y - Year
M - Month
D - Day
H - Hour
m - minutes
S - Seconds
s - sub-seconds (optional)
Z - Zone (optional) +HH:mm or -HH:mm or Z for UTC
Note: xsd:dataTime supports a very wide date range with unlimited precision. The full date range
and precision are not typically supported by platform- and language-specific libraries.
Where the supported time precision is less than the precision used by the xsd:dateTime
timestamp there will be loss of precision; this will typically occur via direct truncation
or (less commonly) rounding.
The year value can be large and/or negative. Any value covering the current or last century
should be correctly processed, but some systems cannot process earlier dates.
The sub-second value is defined as an unlimited number of digits after the decimal point.
In Java a minimum of millisecond precision is guaranteed.
In C++ microsecond precision is guaranteed, with nanosecond precision being available on
some platforms.
Time zones are supported, eg '2013-10-24T11:52:33+01:00' for Paris, but in most cases it will
be converted to UTC when the timestamp is written.
A description for the image. [plain-text multi-line string]
Pixels
Pixels is going to be removed in the future, but it is still required.
This is just notice that the contents of Pixels will be
moved up to Image in a future 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 can be stored within the OME-XML compressed by plane, and encoded
in Base64.
Or the Pixels may be stored in TIFF format.
The Pixels element should contain a list of BinData or TiffData, 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'.
All of the values in the Pixels object when present should match the same value
stored in any associated TIFF format (e.g. SizeX should be the same). Where there
is a mismatch our readers will take the value from the TIFF structure as overriding
the value in the OME-XML. This is simply a pragmatic decision as it increases the
likelihood of reading data from a slightly incorrect file.
The order in which the individual planes of data are interleaved.
The variable type used to represent each pixel in the image.
The number of bits within the type storing each pixel that are significant.
e.g. you can store 12 bit data within a 16 bit type.
This does not reduce the storage requirements but can be a useful indicator
when processing or viewing the image data.
How the channels are arranged within the data block:
true if channels are stored RGBRGBRGB...;
false if channels are stored RRR...GGG...BBB...
This is true if the pixels data was written in BigEndian order.
If this value is present it should match the value used in BinData
or TiffData. If it does not a reader should honour the value used
in the BinData or TiffData. This values is useful for MetadataOnly
files and is to allow for future storage solutions.
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. Units are set by PhysicalSizeXUnit.The units of the physical size of a pixel - default:microns[µm].Physical size of a pixel. Units are set by PhysicalSizeYUnit.The units of the physical size of a pixel - default:microns[µm].Physical size of a pixel. Units are set by PhysicalSizeZUnit.The units of the physical size of a pixel - default:microns[µm].
TimeIncrement is used for time series that have a global
timing specification instead of per-timepoint timing info.
For example in a video stream. Units are set by TimeIncrementUnit.
The units of the TimeIncrement - default: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.
Time since the beginning of the experiment.
Units are set by DeltaTUnit.
The units of the DeltaT - default:seconds[s].
The length of the exposure.
Units are set by ExposureTimeUnit.
The units of the ExposureTime - default:seconds[s].
The X position of the stage. Units are set by PositionXUnit.
The units of the X stage position - default:[reference frame].
The Y position of the stage. Units are set by PositionYUnit.
The units of the Y stage position - default:[reference frame].
The Z position of the stage. Units are set by PositionZUnit.
The units of the Z stage position - default:[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 for presentation to the user.
The number of samples the detector takes to form each pixel value. [units:none]
Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings
The method of illumination used to capture the channel.
The optional PinholeSize attribute allows specifying adjustable
pin hole diameters for confocal microscopes. Units are set by PinholeSizeUnit.
The units of the pin hole diameter for confocal microscopes - default:microns[µm].
AcquisitionMode describes the type of microscopy performed for each channel
ContrastMethod describes the technique used to achieve contrast for each channel
Wavelength of excitation for a particular channel. Units are set by ExcitationWavelengthUnit.
The units of the wavelength of excitation - default:nanometres[nm].
Wavelength of emission for a particular channel. Units are set by EmissionWavelengthUnit.
The units of the wavelength of emission - default: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.
The amount of light the filter transmits at a maximum [units:none]
A fraction, as a value from 0.0 to 1.0.
NOTE: This was formerly described as "units optical density expressed as a PercentFraction".
This was how the field had been described in the schema from the beginning but all
the use of it has been in the opposite direction, i.e. as a amount transmitted,
not the amount blocked. This change has been made to make the model reflect this usage.
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 set by XUnit.
The units of the X stage position - default:[reference frame].
The Y position of the stage label. Units are set by YUnit.
The units of the Y stage position - default:[reference frame].
The Z position of the stage label. Units are set by ZUnit.
The units of the Z stage position - default:[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. [plain-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.
MicroscopesThe microscope's manufacturer specification.ImagingEnvironments
This describes the environment that the biological sample was in
during the experiment.
The Temperature is the define units.
The units the Temperature is in - default:Celsius[°C].
AirPressure is the define units.
The units the AirPressure is in - default: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. [plain-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. [plain-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. [plain-text multi-line string]
A name for the dataset that is suitable for presentation 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/Documentation is not a 'data' image.
The optional Description element may contain free text to further describe the experiment.
A description for the experiment. [plain-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]Folders
An element specifying a possibly heterogeneous collection of data.
Folders may contain Folders so that data may be organized within a tree of Folders.
Data may be in multiple Folders but a Folder may not be in more than one other Folder.
A description for the folder. [plain-text multi-line string]
A name for the folder that is suitable for presentation to the user.
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 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 long 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
Maps
This is a Mapping of key/value pairs.
Ms This is a key/value pair used to build up a Mapping. The
Element and Attribute name are kept to single letters to minimize the
length at the expense of readability as they are likely to occur many
times.
Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD}
No binning.2×2 binning.4×4 binning.8×8 binning.Other binning value.
The font family used to draw the text. [enumeration]
Note: these values are all lower case so they match
the standard HTML/CSS values. "fantasy" has been
included for completeness we do not recommended its
regular use.
serif.sans-serif.cursive.fantasy.monospace.
The number size/kind used to represent a pixel
8 bit signed integer.16 bit signed integer.32 bit signed integer.8 bit unsigned integer.16 bit unsigned integer.32 bit unsigned integer.single-precision floating point.double-precision floating point.complex single-precision floating point.complex double-precision floating point.bit mask.
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.
The units used to represent a length
yottameter SI unit.zettameter SI unit. exameter SI unit.petameter SI unit.terameter SI unit.gigameter SI unit.megameter SI unit.kilometer SI unit.hectometer SI unit.decameter SI unit.meter SI unit.decimeter SI unit.centimeter SI unit.millimeter SI unit.micrometer SI unit.nanometer SI unit.picometer SI unit.femtometer SI unit.attometer SI unit.zeptometer SI unit.yoctometer SI unit.ångström SI-derived unit.thou Imperial unit (or mil, 1/1000 inch).line Imperial unit (1/12 inch).inch Imperial unit.foot Imperial unit.yard Imperial unit.terrestrial mile Imperial unit.astronomical unit SI-derived unit. The official term is ua as the SI standard assigned AU to absorbance unit.light year.parsec.typography point Imperial-derived unit (1/72 inch). Use of this unit should be limited to font sizes.pixel abstract unit. This is not convertible to any other length unit without a calibrated scaling factor. Its use should should be limited to ROI objects, and converted to an appropriate length units using the PhysicalSize units of the Image the ROI is attached to.reference frame abstract unit. This is not convertible to any other length unit without a scaling factor. Its use should be limited to uncalibrated stage positions, and converted to an appropriate length unit using a calibrated scaling factor.
The units used to represent a time interval
yottasecond SI unit.zettasecond SI unit.exasecond SI unit.petasecond SI unit.terasecond SI unit.gigasecond SI unit.megasecond SI unit.kilosecond SI unit.hectosecond SI unit.decasecond SI unit.second SI unit.decisecond SI unit.centisecond SI unit.millisecond SI unit.microsecond SI unit.nanosecond SI unit.picosecond SI unit.femtosecond SI unit.attosecond SI unit.zeptosecond SI unit.yoctosecond SI unit.minute SI-derived unit.hour SI-derived unit.day SI-derived unit.
The units used to represent a pressure
yottapascal SI unit.zettapascal SI unit.exapascal SI unit.petapascal SI unit.terapascal SI unit.gigapascal SI unit.megapascal SI unit.kilopascal SI unit.hectopascal SI unit.decapascal SI unit.pascal SI unit. Note the C++ enum is mixed case due to PASCAL being a macro used by the Microsoft C and C++ compiler.decipascal SI unit.centipascal SI unit.millipascal SI unit.micropascal SI unit.nanopascal SI unit.picopascal SI unit.femtopascal SI unit.attopascal SI unit.zeptopascal SI unit.yoctopascal SI unit.bar SI-derived unit.megabar SI-derived unit.kilobar SI-derived unit.decibar SI-derived unit.centibar SI-derived unit.millibar SI-derived unit.standard atmosphere SI-derived unit.pound-force per square inch Imperial unit.torr SI-derived unit.millitorr SI-derived unit.millimetre of mercury SI-derived unit
The units used to represent an angle
degree unit.radian unit.gradian unit.
The units used to represent a temperature
degree Celsius unit.degree Fahrenheit unit.Kelvin unit.degree Rankine unit.
The units used to represent an electric potential
yottavolt unit.zettavolt unit.exavolt unit.petavolt unit.teravolt unit.gigavolt unit.megavolt unit.kilovolt unit.hectovolt unit.decavolt unit.volt unit.decivolt unit.centivolt unit.millivolt unit.microvolt unit.nanovolt unit.picovolt unit.femtovolt unit.attovolt unit.zeptovolt unit.yoctovolt unit.
The units used to represent power
yottawatt unit.zettawatt unit.exawatt unit.petawatt unit.terawatt unit.gigawatt unit.megawatt unit.kilowatt unit.hectowatt unit.decawatt unit.watt unit.deciwatt unit.centiwatt unit.milliwatt unit.microwatt unit.nanowatt unit.picowatt unit.femtowatt unit.attowatt unit.zeptowatt unit.yoctowatt unit.
The units used to represent frequency
yottahertz unit.zettahertz unit.exahertz unit.petahertz unit.terahertz unit.gigahertz unit.megahertz unit.kilohertz unit.hectohertz unit.decahertz unit.hertz unit.decihertz unit.centihertz unit.millihertz unit.microhertz unit.nanohertz unit.picohertz unit.femtohertz unit.attohertz unit.zeptohertz unit.yoctohertz unit.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 correction applied to the lensThe 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]
Note: The type of this has been changed from int to float to allow
the specification of additional lenses e.g. 0.5X lens
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 set by WorkingDistanceUnit.
The units of the working distance - default:microns[µm].
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.
The values stored in Detector represent the fixed values,
variable values modified during the acquisition go in DetectorSettings
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. {used:PMT}
Units are set by VoltageUnit.
The units of the Voltage - default:volts[V].
The Detector Offset. [units:none] {used:CCD,EMCCD}
The fixed 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.
FilterSetsFilter set manufacturer specificationExcitationFilters
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', 'Tuneable' 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 are set by CutInUnit.
The units of the CutIn - default:nanometres[nm].
CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units are set by CutOutUnit.
The units of the CutOut - default:nanometres[nm].
CutInTolerance. Units are set by CutInToleranceUnit.
The units of the CutInTolerance - default:nanometres[nm].
CutOutTolerance. Units are set by CutOutToleranceUnit.
The units of the CutOutTolerance - default: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.
DichroicsThe dichromatic beamsplitter or dichroic mirror used for this filter combination.LightPathsA description of the light pathExcitationFilters
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 are set by PowerUnit.
The units of the Power - default: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. Units are set by WavelengthUnit.
The units of the Wavelength - default: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]
Units are set by RepetitionRateUnit.
The units of the RepetitionRate - default: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.
GenericExcitationSources
The GenericExcitationSource element is used to represent
a source as a collection of key/value pairs, stored
in a Map. The other lightsource objects should
always be used in preference to this if possible.
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).
Rights
The rights holder of this data and the rights held.
The rights holder for this data. [plain-text multi-line string]
e.g. "Copyright (C) 2002 - 2016 Open Microscopy Environment"
The rights held by the rights holder. [plain-text multi-line string]
e.g. "All rights reserved" or "Creative Commons Attribution 3.0 Unported License"
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 an 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.
The FolderRef element refers to a Folder by specifying the Folder ID attribute.
One or more FolderRef elements may be listed within the Folder element to specify what Folders
the Folder contains. This tree hierarchy must be acyclic.
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. Units are set by WavelengthUnit.
The units of the Wavelength of the light source - default: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.
The values stored in DetectorSettings represent the variable values,
fixed values not modified during the acquisition go in Detector.
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. {used:PMT}
Units are set by VoltageUnit.
The units of the Voltage of the detector - default:volts[V]
The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}
The speed at which the detector can count pixels. {used:CCD,EMCCD}
This is the bytes per second that
can be read from the detector (like a baud rate).
Units are set by ReadOutRateUnit.
The units of the ReadOutRate - default:megahertz[Hz].
Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD}
This is the number of sequential frames that get averaged,
to improve the signal-to-noise ratio. [units:none] {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
ExternalsDescribes a file location. Can optionally specify a portion of a file using Offset and a ReadLength.
If Offset and ReadLength are specified in conjuction with Compression, then they point into the uncompressed file.
file locationThe digest of the file specified in href.Specifies the compression scheme used to encode the data.BinDataBlocksThe contents of this element are base64-encoded. These are not CDATA sections, just a base64 stream.Specifies the compression scheme used to encode the data.
This is true if the binary data was written in BigEndian order. This is dependent on the system architecture of the machine that wrote the pixels. True for essentially all modern CPUs other than Intel and Alpha. All Binary data must be written in the same endian order.
Character count attribute for the BinData field. This is the length of the base-64 encoded block. It allows easy skipping of the block when parsing the file. [unit:bytes]
BinaryFilesDescribes a binary file.
Size of the uncompressed file. [unit:bytes]
An unordered collection of annotation attached to objects in the OME data model.
The AnnotationRef element is a reference to an element derived
from the CommonAnnotation element.
Annotations
An annotation from which all others are ultimately derived.
A description for the annotation. [plain-text multi-line string]
We recommend the inclusion of a namespace for annotations you
define. If it is absent then we assume the annotation is to
use our (OME's) default interpretation for this type.
The Annotator is the person who attached this annotation.
e.g. If UserA annotates something with TagB, owned by UserB,
UserA is still the Annotator.
BasicAnnotations
An abstract Basic Annotation from which some others are derived.
NumericAnnotations
An abstract Numeric Annotation from which some others are derived.
TextAnnotations
An abstract Text Annotation from which some others are derived.
TypeAnnotations
An abstract Type Annotation from which some others are derived.
FileAnnotations
A file object annotation
XMLAnnotations
An general xml annotation. The contents of this is not processed as OME XML but should still be well-formed XML.
ListAnnotations
This annotation is a grouping object. It uses the sequence of
annotation refs from the base Annotation to form the list.
CommentAnnotations
A simple comment annotation
LongAnnotations
A simple numerical annotation of type xsd:long
DoubleAnnotations
A simple numerical annotation of type xsd:double
BooleanAnnotations
A simple boolean annotation of type xsd:boolean
TimestampAnnotations
A date/time annotation of type xsd:dateTime
TagAnnotations
A tag annotation (represents a tag or a tagset)
TermAnnotations
A ontology term annotation
MapAnnotations
An map annotation. The contents of this is a list of key/value pairs.
ROIs
A four dimensional 'Region of Interest'.
If they are not used, and the Image has more than one plane,
the entire set of planes is assumed to be included in the ROI.
Multiple ROIs may be specified.
A description for the ROI. [plain-text multi-line string]
The Name identifies the ROI to the user. [plain-text string]
Shapes
The shape element contains a single specific ROI shape and links
that to any channels, and a timepoint and a z-section. It also
records any transform applied to the ROI shape.
This is a matrix used to transform the shape.
The element has 6 xsd:float attributes. If the element
is present then all 6 values must be included.
The color of the fill - encoded as RGBA
The 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.
The rule used to decide which parts of the shape to
fill. [enumeration]
The color of the stroke - encoded as RGBA
The 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.
The width of the stroke. Units are set by StrokeWidthUnit.
The units used for the stroke width.
e.g. "none", "10 20 30 10"
The font family used to draw the text. [enumeration]
Note: these values are all lower case so they match
the standard HTML/CSS values. "fantasy" has been
included for completeness; we do not recommend its
regular use. This attribute is under consideration
for removal from the OME-XML schema.
Size of the font. Units are set by FontSizeUnit.
The units used for the font size.
The style and weight applied to the text. [enumeration]
This is a simplified combination of the HTML/CSS
attributes font-style AND font-weight.
Controls whether the shape is locked and read only,
true is locked, false is editable.
The z-section the ROI applies to. If not specified then
the ROI applies to all the z-sections of the image. [units:none]
This is numbered from 0.
The timepoint the ROI applies to. If not specified then
the ROI applies to all the timepoints of the image. [units:none]
This is numbered from 0.
The channel the ROI applies to. If not specified then
the ROI applies to all the channels of the image. [units:none]
This is numbered from 0.
Rectangles
A simple rectangle object. If rotation is required apply a
transformation at the Shape level.
The X value of the left edge or the rectangle. [units pixels]
The y value of the top edge or the rectangle. [units pixels]
The width of the rectangle. [units pixels]
The height of the rectangle. [units pixels]
Masks
The Mask ROI shape is a link to a BinData object that is
a BIT mask drawn on top of the image as an ROI. It is applied
at the same scale, pixel to pixel, as the Image the ROI is
applied to, unless a transform is applied at the shape level.
The X coordinate of the left side of the image. [units pixels]
The Y coordinate of the top side of the image. [units pixels]
The width of the mask. [units pixels]
The height of the mask. [units pixels]
Points
The X coordinate of the point. [units pixels]
The Y coordinate of the point. [units pixels]
Ellipses
A simple ellipse object. If rotation is required apply a
transformation at the Shape level.
The X coordinate of the center of the ellipse. [units pixels]
The Y coordinate of the center of the ellipse. [units pixels]
The horizontal radius of the ellipse. [units pixels]
The vertical radius of the ellipse. [units pixels]
Lines
A straight line defined by it's end points.
The X coordinate of the start of the line. [units pixels]
The Y coordinate of the start of the line. [units pixels]
The X coordinate of the end of the line. [units pixels]
The Y coordinate of the end of the line. [units pixels]
Polylines
The Polyline defines open shapes formed of straight
lines. Note: Polyline uses counterclockwise winding (this is the
default OpenGL behavior)
The points of the polyline are defined as a list of comma
separated x,y coordinates seperated by spaces like "x1,y1 x2,y2 x3,y3" e.g.
"0,0 1,2 3,5" Polygons
The Polygon defines closed shapes formed of straight
lines. Note: Polygon uses counterclockwise winding (this is the
default OpenGL behavior)
The points of the Polygon are defined as a list of comma
separated x,y coordinates seperated by spaces like "x1,y1 x2,y2 x3,y3" e.g.
"0,0 1,2 3,5" Labels
The text label. Any transformation should be applied at the
shape level.
This defines the X coordinate of the current text position
of the first character in the string. [units pixels] This defines the Y coordinate of the current text position
of the first character in the string. [units pixels]
A matrix used to transform the shape.
⎡ A00, A01, A02 ⎤
⎢ A10, A11, A12 ⎥
⎣ 0, 0, 1 ⎦
Markers
Shape of marker on the end of a line. [enumeration]
Plates
This element identifies microtiter plates within a screen.
A plate can belong to more than one screen.
The Screen(s) that a plate belongs to are specified by the ScreenRef element.
The Plate ID and Name attributes are required.
The Wells in a plate are numbers from the top-left corner in a grid starting at zero.
i.e. The top-left well of a plate is index (0,0)
A description for the plate.
The Name identifies the plate to the user.
It is used much like the ID, and so must be
unique within the document.
If a plate name is not available when one is needed
it will be constructed in the following order:
1. If name is available use it.
2. If not use "Start time - End time"
(NOTE: Not a subtraction! A string representation
of the two times separated by a dash.)
3. If these times are not available use the Plate ID.
A textual annotation of the current state of the plate with respect to the
experiment work-flow; e.g.
1. Seed cell: done; 2. Transfection: done; 3. Gel doc: todo.
The ExternalIdentifier attribute may contain a reference to an external database.
The ColumnNamingConvention
The RowNamingConvention
This defines the X position to use for the origin of the
fields (individual images) taken in a well. It is used
with the X in the WellSample to display the fields
in the correct position relative to each other. Each Well
in the plate has the same well origin. Units are set by WellOriginXUnit.
In the OMERO clients by convention we display the WellOrigin
in the center of the view.
The units of the well origin in X - default:reference frame.
This defines the Y position to use for the origin of the
fields (individual images) taken in a well. It is used
with the Y in the WellSample to display the fields
in the correct position relative to each other. Each Well
in the plate has the same well origin. Units are set by WellOriginYUnit.
In the OMERO clients by convention we display the WellOrigin
in the center of the view.
The units of the well origin in Y - default:reference frame.
The number of rows in the plate
The number of columns in the plate
The index of the WellSample to display as the default Field
Predefined list of values for the well labels
While the label type 'number' has a clear meaning the 'letter'
type is more complex.
If you have less than 26 values use letters A to Z.
Once you get more than 26 values there are several different
approaches in use.
One we have see include:
Single letter, then double letter each running A to Z, right first
e.g. A, B, C, ... X, Y, Z, AA, AB, AC, ... AY, AZ, BA, BB, ...
This is the format used by Microsoft Excel so users may be familiar with it.
This is the approach we use in the OMERO client applications.
CAPITALsmall, each running A to Z, small first
e.g. Aa, Ab, Ac, ... Ax, Ay, Az, Ba, Bb, Bc, ... By, Bz, Ca, Cb, ...
This is in use by some plate manufactures.
Single letter, then double letter, then triple letter, and so on
e.g. A, B, C, ... X, Y, Z, AA, BB, CC, ... YY, ZZ, AAA, BBB, ...
This has the advantage that the first 26 are the same as the standard
but has a problem an the labels get wider and wider leading to user
interface problems.
1, 2, 3, ...
Reagents
Reagent is used to describe a chemical or some other physical experimental parameter.
A long description for the reagent.
A short name for the reagent
This is a reference to an external (to OME) representation of the Reagent.
It serves as a foreign key into an external database. - It is sometimes referred to as ExternalIdentifier.
Screens
The Screen element is a grouping for Plates.
The required attribute is the Screen's Name and ID - both must be unique within the document.
The Screen element may contain an ExternalRef attribute that refers to an external database.
A description of the screen may be specified in the Description element.
Screens may contain overlapping sets of Plates i.e. Screens and Plates have a many-to-many relationship.
Plates contain one or more ScreenRef elements to specify what screens they belong to.
A description for the screen.
The PlateRef element is a reference to a Plate element.
Screen elements may have one or more PlateRef elements to define the plates that are part of the screen.
Plates may belong to more than one screen.
A pointer to an externally defined protocol, usually in a screening database.
A description of the screen protocol; may contain very detailed information to
reproduce some of that found in a screening database.
A description of the set of reagents; may contain very detailed information to
reproduce some of that information found in a screening database.
A pointer to an externally defined set of reagents, usually in a screening
database/automation database.
A human readable identifier for the screen type; e.g. RNAi, cDNA, SiRNA, etc.
This string is likely to become an enumeration in future releases.
PlateAcquisitions
PlateAcquisition is used to describe a single acquisition run for a plate.
This object is used to record the set of images acquired in a single
acquisition run. The Images for this run are linked to PlateAcquisition
through WellSample.
A description for the PlateAcquisition.
Time when the last image of this acquisition was collected
Time when the first image of this acquisition was collected
The maximum number of fields (well samples) in any well
in this PlateAcquisition.
This is only used to speed up user interaction by stopping
the reading of every well sample.
Wells
A Well is a component of the Well/Plate/Screen construct to describe screening applications.
A Well has a number of WellSample elements that link to the Images collected in this well.
The ReagentRef links any Reagents that were used in this Well. A well is part of only one Plate.
The origin for the row and column identifiers is the top left corner of the plate starting at zero.
i.e The top left well of a plate is index (0,0)
This is the column index of the well, the origin is the top left corner of the plate
with the first column of cells being column zero. i.e top left is (0,0)
The combination of Row, Column has to be unique for each well in a plate.
This is the row index of the well, the origin is the top left corner of the plate
with the first row of wells being row zero. i.e top left is (0,0)
The combination of Row, Column has to be unique for each well in a plate.
A description of the externally defined identifier for this plate.
The ExternalIdentifier attribute may contain a reference to an external database.
A human readable identifier for the screening status.
e.g. empty, positive control, negative control, control, experimental, etc.
A marker color used to highlight the well - 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.
WellSamples
WellSample is an individual image that has been captured within a Well.
This is the main link to the core Image element
The X position of the field (image) within the well relative to
the well origin defined on the Plate. Units are set by PositionXUnit.
The units of the position in X - default:reference frame.
The Y position of the field (image) within the well relative to
the well origin defined on the Plate. Units are set by PositionYUnit.
The units of the position in Y - default:reference frame.
The time-point at which the image started to be collected
This records the order of the well samples. Each
index should be unique for a given plate but they do not
have to be sequential, there may be gaps if part of the
dataset is missing. In the user interface the displayed
value of the index will be calculated modulo the number
of PlateAcquisitions for the plate.
The WellSampleRef element is a reference to a WellSample element.
