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The OME Data Model specification
Open Microscopy Environment
OME XML Schema 1.0 RC3
Copyright (C) 2002-2011 Open Microscopy Environment
The OME element must contain one or more Image and one or more Experimenter elements.
All other elements are optional.
This element describes the actual image and its meta-data.
The elements that are references (ending in Ref) refer to elements defined outside of the Image element.
If any of the required Image attributes are missing, its guaranteed to be an invalid document.
The only required elements are the CreationDate and Data.
The Image may also contain optional elements containing vendor-specific data (#wildCard element in the diagram).
There are also provisions to include vendor-specific data on a per-wavelength, per-timepoint, per-plane or per-XYZ stack.
The GUID is a globally unique identifier assigned by OME.
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.
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.
Similarly, WaveStart and WaveIncrement are used in spectral images like FTIR. These are both positive integers.
One of these per XYZ stack in the Image (optional). A single plane Image is still technically a stack.
Note that the size of the unused dimensions is 1, not 0.
Additional elements may be present as vendor extensions.
One of these per plane in the Image (optional).
Additional elements may be present as vendor extensions.
The creation date of the Image - when the Image was acquired.
The element contains a string in the dateTime format (i.e. 1988-04-07T18:39:09)
Time in seconds since acquisition of this document began.
A floating-point (real) number.
Exposure time in seconds.
A floating point (real) number.
The Image will be unreadable if any attributes are missing.
The Pixels may be stored externally or internally.
DimensionOrder is a string enumeration which must be set to 'XYZWT', 'XYZTW', 'XYWTZ', 'XYWZT', 'XYTWZ', or 'XYTZW'.
BitsPerPixel is an integer enumeration and must be set to 1, 8 or 16.
BigEndian is a boolean ('true' or 'false'). True for essentially all CPUs other than Intel.
If an external file is used, this tag must be specified with the required href attribute.
The file pointed to is a raw binary pixel dump.
The Offset attribute specifies the number of bytes after the start of the file where the dump begins.
The SHA1 attribute is a digest (openssl sha1) of the file pointed to by href.
Compression may be set to 'gzip' or 'bzip2'.
If the external file is compressed, and the Compression attribute is set,
the SHA1 and href attribute refer to the compressed file.
The file must contain enough pixels to satisfy the dimension extents and bits per pixel specified in Image.
If it does not, the Image is invalid.
Pixel data stored within the OME XML document is stored in this element using base64 encoding.
This is a stage position in the microscope's reference frame.
The Stats element is used in several places.
It is usually optional, but if used, it must be empty and at least set the Min, Max, and Mean attributes.
Excitation wavelength in nm.
The emission wavelength in nm.
A neutral-density filter value between 0.0 and 1.0
There must be one per wavelength in the Image.
Even a single-plane Image has to have one.
Either the Fluor or the excitation and emission wavelengths (in nm) or both must be specified.
Currently, these are all optional, which is an incorrect schema specification (FIXME?).
Either WavelengthInfo element or the WaveStart and WaveIncrement Image attributes must be used.
This is also not correctly specified in the schema (FIXME?).
An optional FilterRef element with a required FilterID attribute may be used to refer to a complete filter specification.
The Filter element is defined under Instrument within OME.
If a FilterRef is used, an InstrumentRef element must also exist within Image.
The WaveNumber is the wavenumber in the raw pixel dump that this information pertains to.
The optional FilterID, LightSourceID, CameraID and OTFID attributes refer to a Filter, LightSource Camera and OTF
elements defined within the OME element.
There is optionally one of these per Image.
This specifies mapping of image wavelengths to RGB or greyscale colorspace with one byte per pixel per RGB channel.
Elements of type WaveScaleType specify the scaling of pixel values (up to 16 bit) to colorspace values (8 bit).
These elements have three required attributes: the WaveNumber, BlackLevel, and WhiteLevel.
The fourth Gamma attribute is optional.
The WaveNumber specifies the wave number in the pixel dump. Waves are numbered from 0.
Pixel values between BlackLevel and WhiteLevel will be assigned values 0-255, respectively.
Values below BlackLevel or above WhiteLevel will be assigned 0 and 255 respectively.
Either the GreyWave or one or more of RedWave, GreenWave, BlueWave must be specified.
The Projection element specifies that the display is a maximum intensity projection.
The range of Z-sections for the projection is specified with the Zstart and Zstop attributes.
Presence of the Movie element indicates that the display should be a movie.
The range of timepoints to display in the movie is specified by the Tstart and Tstop attributes.
The MIME type of the desired video format is specified by Movie's MIMEtype attribute.
The ROI element describes a 3-D region of interest. It is up to the viewer to either display the ROI only,
or to simply mark it somehow.
The wave number, black level, white level and optional gamma for the red channel of an RGB image.
The wave number, black level, white level and optional gamma for the green channel of an RGB image.
The wave number, black level, white level and optional gamma for the blue channel of an RGB image.
The wave number, black level, white level and optional gamma for a greyscale image.
The GreyWave element may contain an optional ColorMap attribute, which can be set to ''
The presence of this element indicates the user wants to view the Image as a maximum intensity projection.
The Zstart and Zstop attributes are optional. If they are not specified, then the entire Z stack will be projected.
Presence of this element indicates the user wants to view the Image as a movie.
The range of timepoints to be displayed are indicated by the optional Tstart and Tstop attributes.
If they are not specified, the movie is to include all timepoints.
The desired movie format (MIME type) is specified by the required MIMEtype attribute.
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, Camera, Objective and Filters components.
Additionally, one or more OTF elements may be specified, describing the optical transfer function under different conditions.
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.
The OTF element contains an optical transfer function.
The same OTF can be used for all wavelengths, or there may be one per wavelength.
There may be multiple light sources, cameras and filters on a microscope.
Each of these has their own ID attribute, which can be refered to from WavelengthInfo.
It is understood that the light path configuration can be different for each wavelength,
but cannot be different for each timepoint or each plane of an XYZ stack.
The StageLabel is simply a string to describe a particular stage position.
This is usefull for experiments involving visiting several points on a slide over a timecourse.
The PlateInfo element associates the image with a microtiter plate.
This element must contain a Well element to to specify what well this image belongs to.
When several images are acquired within a single well, they are differentiated by using the optional Sample element.
The ExperimenterID attribute is required, and the presence of at least one Experimenter element is required within OME.
The required elements are the same as for the ContactInfo type, but include the OMEname element,
which is the experimenters login or username in OME.
Interestingly, Experimenters don't have a group affiliation.\
This is because this is an image-centric document, so the image itself is affiliated with an experimenter and a group.
We can infer that at the time of acquisition, the experimenter who acquired the image belonged to that group,
but that may no longer be the case.
This is the username of the experimenter (in a 'unix' or 'database' sense).
First name, optionally containing a middle initial.
A person's last or surname.
A person's email address.
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 elemnts to specify what screens they belong to.
The ScreenRef element is a reference to a Screen element.
Plate elements may have one or more ScreenRef elements to define the screen that a plate belongs to.
Plates may belong to more than one screen.
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 EternRef attribute may contain a reference to an external database.
The PlateID and Name attributes are required.
The Name identifies the plate to the user. It is used much like the PlateID, and so must be unique within the document.
This is a sample number within a well.
It has an optional ExternRef attribute which may specify a link to an external database.
Standard well designation (A12, B01, etc) goes in the Address attribute.
This attribute is checked against the regular expression '^[A-Z]+[0-9]+$'.
The contents of this element may contain descriptive information.
A description of the microscope's objective lens.
Required tags include the lens numerical aperture, and the magnification, both of which a floating point (real) numbers.
Filters may be separate excitation dichroic mirror and emission filters specified by the
ExFilter, Dichroic and EmFilter tags respectively.
Alternatively all three components may be specified by a single filter set.
There should be one filter element specified per wavelength in the image.
The wave number associated with a filter set is specified in WavelengthInfo's required WaveNumber attribute.
All elements are ManufactSpec type, so they have the required attributes Manufacturer, Model, and SerialNumber.
The ExFilter an EmFilter elements may also contain a Type attribute which may be set to
'LongPass', 'ShortPass', 'BandPass', or 'MultiPass'.
The magnification of the lens - i.e. '60.0' is a 60X lens.
The numerical aperture of the lens expressed as a ploating point (real) number.
Excitation filter manufacturer specification.
The optional Type attribute may contain 'LongPass', 'ShortPass', 'BandPass', or 'MultiPass'.
Emission filter manufacturer specification.
The optional Type attribute may contain 'LongPass', 'ShortPass', 'BandPass', or 'MultiPass'.
Filter set manufacturer specification
The type of camera used to capture the image.
The optional CameraID allows specifying several cameras on the same microscope.
The CameraID can be used as a reference within the WavelengthInfo element in the Image element.
Just some free-form text to describe Images, Screens and Projects.
The content model is ANY, which means that en entire XML sub-document can be placed here.
The microscope's manufacturer specification.
The thumbnail may be an external URI reference specified by the href attribute, or it may contain an SVG sub-document
(denoted by the #wildCard 'element').
The MIMEtype is a required attribute, and must be set to 'SVG' if the tag's contents are an SVG document.
Any of the common fluors, i.e. 'FITC', 'Texas Red', etc.
There is presently no restriction of what kind of string to put here.
That is up to the user, or the application program that generates OME XML.
The 'center of mass' of the XYZ stack.
The ProjectID and Name attributes are 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 ProjectIDs.
Projects do not directly contain images - only by virtue of containing datasets, which themselves contain images.
An element type specifying a floating point (real) three dimensional (X, Y, Z) coordinate.
There may be one or more of these in a Dataset.
This empty element has a required ProjectID attribute that refers to Projects defined within the OME element.
This empty element has a required ExperimenterID attribute which refers to one of the Experimenters defined within OME.
The GroupID and Name attributes are required.
Contact information should be specified for the leader of the group and a contact person.
The Leader and/or Contact may themselves be experimenters defined in OME,
in which case they can refer to Experimenters defined within OME using their ExperimenterRef elements.
Contact information for a Group leader.
The contact info may be specified within this element using FirstName, LastName, email and Institution elements,
or the contact information may be specified using the ExperimenterRef element if the group leader is defined as an Experimenter.
An element type to specify an Experimenter under OME.
It consists of a Person element group and a login name specified under OMEname.
The Contact element describes the contact person for a group of experimenters - typically a project leader or lab manager.
This person may be specified as a reference to an OME experimenter, or the full contact information can be specified
within the element using the FIrstName, LastName, email and Institution elements.
This empty element has a reference (the GroupID attribute) to a Group defined within OME.
An element type to specify a group of people.
This is an element type to describe contact information for a person.
The person may be an OME Experimenter, in which case the element contains an ExperimenterRef element only,
or if the contact is not an OME experimenter, the contact information can be described within the element using the
FirstName, LastName, email and Institution elements (the Person element group).
This empty element can be used (via the required InstrumentID attribute) to refer to an Instrument defined within OME.
The organizing structure that people belong to other than groups. A university, or company, etc.
We do not specify people belonging to groups.
While Images belong to a person and a group, the relationship between people and groups is not up to OME.
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.
The dichroic mirror used for this filter combination.
A three dimensional 'Region of Interest'. The Z coordinates are optional.
If they are not used, and the Image has more than one plane,
the enire set of planes is assumed to be included in the ROI.
An element type specifying a filter specification.
It extends the ManufactSpec element type to include the filter type specified in the Type attribute.
The lightsource for the instrument. An instrument may have several light sources.
The type of lightsource is specified by the Type attribute, which is currently unrestricted.
If several lightsources are specified for an instrument, the LightSourceID must be specified for each,
and the individual lightsources can be refered to through their LightSourceIDs.
The optical transfer function. FilterID refers to the set of filters used in computing the OTF.
BitsPerPixel is an integer '1', '8', '16'.
The OpticalAxisAvg is a boolean specifying wether or not optical axis averaging was done.
SizeX, SizeY specify the width and height of the OTF.
This element must contain either an External element or a BinData element.
Both of these work the same way as they do for the Data element within Image.
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.
Wether or not the list of Images in this dataset can be altered is specified by the Locked attribute.
The ExperimenterRef and GroupRef 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 ProjectRef elements within the Dataset element.
The DatasetRef element refers to a Dataset by specifying the DatasetID attribute.
One or more DatasetRef elements may be listed within the Image element to specify what Datasets
the Image belongs to.
This element allows the grouping of several OME XML documents into one group.
This is useful for specifying many documents and Images belonging to a single Screen, or Project or Dataset.
All of the element IDs (i.e. ProjectID, InstrumentID, ExperimenterID, etc) become valid across the entire document group,
meaning references are valid across documents, and not only within a document. This also means that the element IDs
must be unique across the entire group, and not only within a single document.
The documents in the group are specified using one or more DocumentRef elements.
Each of the documents in the group must have the same documents listed in their respective DocumentGroup element.
It is not necessary (or even possible, due to the SHA1 attribute) to make self-references in this list.
The DocumentRef element referes to an external OME XML document using the href and SHA1 attributes.