This Section defines the Modules that are common to all Composite Image IODs.
The following Patient IE Module is common to all Composite Image IODs that reference the Patient IE.
Table C.7-1 specifies the Attributes of the Patient that describe and identify the Patient who is the subject of a Study. This Module contains Attributes of the patient that are needed for interpretation of the Composite Instances and are common for all studies performed on the patient. It contains Attributes that are also included in the Patient Modules in Section C.2.
Table C.7-1. Patient Module Attributes
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Primary identifier for the patient. NoteIn the case of imaging a group of small animals simultaneously, the single value of this identifier corresponds to the identification of the entire group. See also Section C.7.1.4.1.1. |
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Date of birth of the named patient in the Alternative Calendar (0010,0035). |
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Date of death of the named patient in the Alternative Calendar (0010,0035). |
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The Alternative Calendar used for Patient's Birth Date in Alternative Calendar (0010,0033) and Patient's Death Date in Alternative Calendar (0010,0034). See Section C.7.1.5 for Defined Terms. Required if either Patient's Birth Date in Alternative Calendar (0010,0033) or Patient's Alternative Death Date in Calendar (0010,0034) is present. |
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A photo to confirm the identity of a patient. Only a single Item is permitted in this Sequence. See C.2.2.1.1. |
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>Include Table 10-3b “Referenced Instances and Access Macro Attributes” |
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Indicates whether or not the subject is a quality control phantom. If this Attribute is absent, then the subject may or may not be a phantom. This attribute describes a characteristic of the Imaging Subject. It is distinct from Quality Control Image (0028,0300) in the General Image Module, which is used to describe an image acquired. |
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A sequence that provides reference to a Patient SOP Class/Instance pair. |
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>Include Table 10-11 “SOP Instance Reference Macro Attributes” |
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Other identification numbers or codes used to identify the patient. |
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A sequence of identification numbers or codes used to identify the patient, which may or may not be human readable, and may or may not have been obtained from an implanted or attached device such as an RFID or barcode. |
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An identifier for the patient. NoteIn the case of imaging a group of small animals simultaneously, the single value of this identifier corresponds to the identification of the entire group. See also Section C.7.1.4.1.1. |
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>Include Table 10-18 “Issuer of Patient ID Macro Attributes” |
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The taxonomic rank value (e.g., genus, subgenus, species or subspecies) of the patient. See Section C.7.1.1.1.3. Required if the patient is an animal and if Patient Species Code Sequence (0010,2202) is not present. May be present otherwise. |
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The taxonomic rank value (e.g., genus, subgenus, species or subspecies) of the patient. See Section C.7.1.1.1.3. Only a single Item shall be included in this Sequence. Required if the patient is an animal and if Patient Species Description (0010,2201) is not present. May be present otherwise. |
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The breed of the patient. See Section C.7.1.1.1.1. Required if the patient is an animal and if Patient Breed Code Sequence (0010,2293) is empty. May be present otherwise. |
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The breed of the patient. See Section C.7.1.1.1.1. |
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Defined CID 7480 “Breed”. |
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Information identifying an animal within a breed registry. |
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Identification of the organization with which an animal is registered. |
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Defined CID 7481 “Breed Registry”. |
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The strain of the patient. See Section C.7.1.1.1.4. |
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The nomenclature used for Strain Description (0010,0212). See Section C.7.1.1.1.4. |
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A coded identification of the strain of the patient. See Section C.7.1.1.1.4. One or more Items are permitted in this sequence. If more than one item is present, each item represents the same information but encoded using a different coding scheme (rather than post-coordinated modifiers). |
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Additional information about the strain of the patient that is not encoded in the formal nomenclature used in Strain Description (0010,0212). See Section C.7.1.1.1.4. |
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The stock number of the strain of the patient issued by the organization identified by Strain Source (0010,0217). See Section C.7.1.1.1.4. |
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Identification of the organization that is the source of the animal, issued by the registry identified by Strain Source Registry Code Sequence (0010,0215). See Section C.7.1.1.1.4. |
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Identification of the organization that is the registry of sources of animals. See Section C.7.1.1.1.4. |
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Name of person with medical or welfare decision making authority for the patient. Required if the patient is an animal. May be present otherwise. |
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Relationship of Responsible Person to the patient. See Section C.7.1.1.1.2 for Defined Terms. |
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Name of organization with medical or welfare decision making authority for the patient. |
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The true identity of the patient has been removed from the Attributes and the Pixel Data |
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A description or label of the mechanism or method use to remove the patient's identity. May be multi-valued if successive de-identification steps have been performed. Note
Required if Patient Identity Removed (0012,0062) is present and has a value of YES and De-identification Method Code Sequence (0012,0064) is not present. May be present otherwise. |
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A code describing the mechanism or method use to remove the patient's identity. One or more Items shall be included in this Sequence. Multiple items are used if successive de-identification steps have been performed or to describe options of a defined profile. Required if Patient Identity Removed (0012,0062) is present and has a value of YES and De-identification Method (0012,0063) is not present. May be present otherwise. |
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Defined CID 7050 “De-identification Method”. |
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The breed of an animal, if known, shall be encoded in either Patient Breed Description (0010,2292) or Patient Breed Code Sequence (0010,2293) or both.
In the case of a mixed breed, it shall be either:
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described in plain text in Patient Breed Description (0010,2292), e.g., "Border Collie American Bulldog mix", or just "Mixed", or
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coded as multiple specific breeds by composing the mix as multiple items of Patient Breed Code Sequence (0010,2293), e.g., (L-809A2, SRT, "Border Collie dog breed") followed by (L-80974, SRT, "American Bulldog breed"), or
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encoded non-specifically with a code that means "mixed breed" of the appropriate species, as defined in CID 7486 “Mixed Breeds”, which is included in CID 7480 “Breed”, e.g., (L-809DF, SRT, "Mixed breed dog").
If the species is not known then the Patient Species Description (0010,2201) or Patient Species Code Sequence (0010,2202) may describe a more general taxonomic rank value, such as a genus or subgenus, family or subfamily.
If the subspecies is known then the Patient Species Description (0010,2201) or Patient Species Code Sequence (0010,2202) may describe the subspecies.
The strain of an animal (group of animals that is genetically uniform), if known, may be encoded in Strain Description (0010,0212). The nomenclature used may be encoded in Strain Nomenclature (0010,0213). A precoordinated code identifying the strain may be encoded in Strain Code Sequence (0010,0219).
Defined Terms for Strain Nomenclature (0010,0213):
- MGI_2013
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International Committee on Standardized Genetic Nomenclature for Mice, Rat Genome and Nomenclature Committee. MGI-Guidelines for Nomenclature of Mouse and Rat Strains. 2013/10. Available from: http://www.informatics.jax.org/mgihome/nomen/strains.shtml
Note
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A pair of text and nomenclature Attributes are used, since standard nomenclatures typically define values that are constructed from multiple components, and do not distinguish between value and meaning. These are distinct from the precoordinated codes used in Stain Code Sequence (0010,0219).
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Some strain nomenclatures make use of superscripts. To encode these superscripts consistently in an unformatted string, the convention of enclosing the superscript text in "<" and ">" pairs may be used. E.g., "D2.B6-Ahrb-1/J" would be encoded as "D2.B6-Ahr<b-1>/J".
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Relevant information that is not encoded in the formal description of the strain (i.e., not defined in the nomenclature used), such as the number of transgenes, may be encoded as plain text in Strain Additional Information (0010,0218).
The strain of an animal may be more specifically identified by the Attributes within Strain Stock Sequence (0010,0216).
Note
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The MGI-Guidelines for Nomenclature of Mouse and Rat Strains recommends the use of the laboratory codes assigned by the Institute of Laboratory Animal Research (ILAR). See the International Laboratory Code Registry (ILCR) http://dels.nas.edu/global/ilar/lab-codes.
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Because allele names are closely tied to gene names/symbols it is necessary to have a unique and permanent code for any allele that is part of a genotype of interest. For mice, MGI is the authoritative source of the nomenclature for genes and alleles and maintains unique, permanent codes for these entities. The MGI provides a report of all precoordinated MGI codes that are assigned to specific strains at ftp://ftp.informatics.jax.org/pub/reports/MGI_Strain.rpt. These may be used in Strain Code Sequence (0010,0219) with a coding scheme of "MGI".
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Another source of pre-coordinated codes for strains is the NCI Thesaurus, which includes a snapshot of strains from the International Mouse Strain Resource (IMSR), as children of (C14421, NCIt, "Inbred Mouse Strains"). See http://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&code=C14421.
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For example, a C57BL/6J mouse strain from The Jackson Laboratory might be identified as:
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>Strain Source Registry Code Sequence (0010,0215) = (126850, DCM, "ILCR")
Retired. See PS3.3-2008.
Note
The functionality of the Specimen Identification Modulehas been replaced by the Specimen Module. See Section C.7.6.22.
Table C.7-2b contains attributes that identify a Patient as a clinical trial or research Subject.
Table C.7-2b. Clinical Trial Subject Module Attributes
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The name of the clinical trial or research sponsor. See Section C.7.1.3.1.1. |
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Identifier for the noted protocol. See Section C.7.1.3.1.2. |
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The name of the clinical trial or research protocol. See Section C.7.1.3.1.3. |
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The identifier of the site responsible for submitting clinical trial or research data. See Section C.7.1.3.1.4. |
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Name of the site responsible for submitting clinical trial or research data. See Section C.7.1.3.1.5 |
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The assigned identifier for the clinical trial or research subject. See Section C.7.1.3.1.6. Shall be present if Clinical Trial Subject Reading ID (0012,0042) is absent. May be present otherwise. |
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Identifies the subject for blinded evaluations. Shall be present if Clinical Trial Subject ID (0012,0040) is absent. May be present otherwise. See Section C.7.1.3.1.7. |
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Name of the Ethics Committee or Institutional Review Board (IRB) or Institutional Animal Care and Use Committees (IACUC) responsible for approval of the Clinical Trial or research. Required if Clinical Trial Protocol Ethics Committee Approval Number (0012,0082) is present. |
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Approval number issued by committee described in Clinical Trial Protocol Ethics Committee Name (0012,0081). |
Identification of subjects in clinical trials or research generally requires a combination of the following four attributes:
For trials in which subject identifiers are unique within the scope of the Clinical Trial Protocol (e.g., if subject identifiers are centrally assigned or contain the site identifier) the Clinical Trial Site ID (0012,0030) is not required to identify subjects.
The Clinical Trial Sponsor Name (0012,0010) identifies the entity responsible for conducting the clinical trial or research and for defining the Clinical Trial Protocol ID (0012,0020).
The Clinical Trial Protocol ID (0012,0020) is the number or character sequence used by the Clinical Trial Sponsor to uniquely identify the investigational protocol in which the subject has been enrolled.
The Clinical Trial Protocol Name (0012,0021) contains the title of the investigational protocol in which the subject has been enrolled.
The Clinical Trial Site ID (0012,0030) is the identification number or character string (issued by the entity identified by the Clinical Trial Sponsor Name (0012,0010)) used to identify the site responsible for submitting clinical trial or research data.
The Clinical Trial Site Name (0012,0031) is a character string used to identify the site responsible for submitting clinical trial or research data.
Table C.7.1.4-1 specifies the Attributes of the Patient Group Macro that describe multiple imaging subjects (such as small animals for pre-clinical research) imaged at the same time as a group. This macro may be included in the Section C.2.2 Patient Identification Module and the Section C.7.1.1 Patient Module.
Table C.7.1.4-1. Patient Group Macro Attributes
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A sequence containing the value used for Patient ID (0010,0020) and related Attributes in the source composite instances that contained a group of subjects whose data was acquired at the same time, from which this composite instance was extracted. See Section C.7.1.4.1.1. |
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>Include Table 10-18 “Issuer of Patient ID Macro Attributes” |
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A sequence containing the identifiers and locations of the individual subjects whose data was acquired at the same time (as a group) and encoded in this composite instance. See Section C.7.1.4.1.1. |
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>Include Table 10-18 “Issuer of Patient ID Macro Attributes” |
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The position in the image pixel data of the individual subject identified in this sequence relative to the other subjects. See Section C.7.1.4.1.1.1. |
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Patient position descriptor relative to the equipment. See Section C.7.1.4.1.1.1. See Section C.7.3.1.1.2 for Defined Terms and further explanation. |
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It is common to image multiple small animals for pre-clinical research as a group at the same time.
In such cases, the single value of Patient ID (0010,0020) corresponds to the identification of the entire group. The same applies to related attributes, if present, such as Issuer of Patient ID (0010,0021). Other Attributes of the Patient Module that are present shall be those shared by the entire group of animals, otherwise they shall be absent or empty (e.g., Patient's Sex (0010,0040)). Any acquisition-related Attributes that are patient-specific (e.g., injected contrast or radiopharmaceutical dose) shall also be absent or empty (and the information may be communicated in separate acquisition context instances).
The Group of Patients Identification Sequence (0010,0027) provides a means of describing the identifiers and locations of the individual subjects, if known at the time of acquisition, regardless of whether or not the group images are later segmented into individual images.
It is also common to segment the acquired images of the group of animals and extract the image pixel data for each animal into separate images.
The Source Patient Group Identification Sequence (0010,0026) provides a "backward reference" within the segmented (individual subject) images to the Patient ID (0010,0020) used to identify the whole group.
Note
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Individual derived SOP Instances may reference the source image explicitly by its SOP Instance UID. Additional objects, such as Segmentations, may be created to encode the regions segmented for individual animals, and referenced from the derived images. See also Annex VVV “Segmentation of Images of Groups of Animals (Informative)” in PS3.17.
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For example, an image of a group of 6 mice in a 3 column, 2 row single longitudinal plane array might be described as:
In this example, the optional Issuer of Patient ID (0010,0021) is shown to emphasize that if it is needed, it should be repeated; i.e., there is no "inheritance" of the issuer from the data set enclosing the sequence.
The naming of the group and the individual animals in the identifier is purely illustrative; it is not meant to imply preference for one local convention or another, or for using a discrete identifier for the group as opposed to, say, a concatenated list of individual animal identifiers used as the group identifier.
See Figure C.7.1.4-1.
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For example, segmented images of an individual animal derived from the group image might be described as:
Subject Relative Position in Image (0010,0028) shall be encoded as a 3D ordinal position in machine-relative orthogonal dimensions, such that when facing the front of the machine (gantry):
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the first value starts at one for the left most subject holder and monotonically increases by one for each successive subject holder towards the right,
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the second value starts at one for the top most subject holder and monotonically increases by one for each successively lower subject holder,
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the third value starts at one for the outer most subject holder and monotonically increases by one for each successive subject holder inwards (i.e., increasing values from the front to the back of the gantry along the direction orthogonal to the first two dimensions, usually the long axis of the table).
Note
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The order and sign of the machine-relative directions is consistent with the Axis Definition in ACR-NEMA 300 1985.
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Image-relative positions are not used, since there may be multiple acquisitions in different orientations. The machine-relative positions are applicable regardless of whether acquired images are cross-sections or projections.
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Patient-relative positions are not used, since the animals may not be arranged in the same direction (e.g., a pair of animals may be arranged head-to-head).
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There is no requirement that there be the same number of animals in each dimension. E.g., one in the top "row"and two below, in one longitudinal plane, would be represented as 1\1\1, 1\2\1, 2\1\1.
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The goal is to describe only the relative locations of animals in any form of multiple animal holder ("mouse hotel"), without attempting to specify the exact physical dimensions or absolute locations, regardless of whether the holder is regular or symmetric in any particular dimension or not (e.g., to include "revolver-like" and hexagonal arrangements). Nor is the "distance" between each animal described.
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The position is defined in terms of subject holders rather than subjects, since some holders may be empty or unused but still partially or completely visible in some of the images. In such cases the relative positions need to be consistently encoded by the acquisition device and recognized by automated segmentation algorithms. E.g., if the top row of in a two row holder is unoccupied, then the animals in the bottom row will be identified with a row position of 2, not 1.
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Due to field of view and anatomical region of interest considerations, adjacent animals may sometimes be partially overlapped (e.g., Cheng TE et al. A rat head holder for simultaneous scanning of two rats in small animal PET scanners: Design, construction, feasibility testing and kinetic validation. Journal of Neuroscience Methods. 2009 Jan 15;176(1):24–33. http://dx.doi.org/10.1016/j.jneumeth.2008.08.031 and Xu S et al. In vivo multiple-mouse imaging at 1.5 T. Magnetic Resonance in Medicine. 2003;49(3):551–7. http://dx.doi.org/10.1002/mrm.10397); such cases may be described as a either a single plane or two planes of animals, as long as there is sufficient information to identify which animal is which.
See Figure C.7.1.4-3.
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The description of the physical relative locations of the animals does not account for any spatial distortion that may occur in the images due to the acquisition technique used (e.g., aliasing in MRI).
Patient Position (0018,5100) may be used to describe the machine-relative position of each animal when the animals are not all arranged in the same direction.
Note
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Patient Position (0018,5100) is used rather than Patient Orientation Code Sequence (0054,0410) because Patient Position (0018,5100) is present in the IODs for those modalities most commonly used for small animal imaging in preclinical research.
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For example, a pair of prone animals arranged head-to-head longitudinally along the bore of the machine would be described as:
See Figure C.7.1.4-2.
The presence of Subject Relative Position in Image (0010,0028) and Patient Position (0018,5100) within Group of Patients Identification Sequence (0010,0027) within the Patient Module implies that the relative locations and orientations of multiple animals within a group cannot change over time. I.e., a "group", identified by a particular Patient ID (0010,0021) (the unique key of the Patient entity in the Information Model), is defined not only by the animals that comprise it but also their relative locations and positioning. If the same animals are imaged together but in a different arrangement, a different Patient ID (0010,0021) for the group shall be used.
Figure C.7.1.4-1. Example of Subject Relative Position in Image for group of 6 mice in a 3 column, 2 row single longitudinal plane array, all feet first prone
Figure C.7.1.4-2. Example of Subject Relative Position in Image and differing Patient Position for group of 2 mice head-to-head
Figure C.7.1.4-3. Example of Subject Relative Position in Image and overlapping narrow field of view group of 2 mice head-to-head