Материал: part17

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VVV Segmentation of Images of Groups of​ Animals (Informative)​

Imaging of small animals used for preclinical research may involve acquiring images of multiple animals simultaneously (i.e., more​ than one animal is present in the same image).​

This Annex describes methods of cross-referencing image and other composite SOP instances produced in the acquisition and seg-​ mentation process and how the provenance of each may be recorded.​

Onlybackwardreferencesaredescribed,allowingforasequentialworkflowwithprocessingperformedbysuccessivedevices,without​ modification of earlier instances.​

VVV.1 Use Case​

The relevant Attributes are described in Section C.7.6.1.1.3 “Derivation Description” in PS3.3 and Section C.7.6.1.1.4 “Source Image​ Sequence” in PS3.3 of the General Image Module. The same principles apply if the General Image Module is not used (e.g., for En-​ hanced Multi-frame Images, in which the same Attributes are present, but nested in the appropriate Functional Group Macros).​

For the purpose of illustration, three successive steps are assumed:​

1.​acquisition of an image of several animals​

2.​processing of that image to detect (manually or automatically) the regions containing each animal, and storing the region as an​ appropriate composite instance​

3.​creation of derived images for each animal using as input the acquired image and the stored regions for each animal​

Various DICOM composite objects could be used to encode the segmented region. If the form of the segmented region is a​

•​rasterized (bitmap), then the Segmentation Storage SOP Class is appropriate​

Note​

A bitmap overlay in a Grayscale or Color Softcopy Presentation State Storage SOP Class could also be used, though​ there are no defined semantics for this unintended use of bitmap overlays.​

•​surface (mesh), then the Surface Storage SOP Class is appropriate​

•​set of isocontours, then:​

•​for 3D patient-relative coordinates, the RT Structure Set Storage SOP Class is appropriate​

•​for 2D or 3D coordinates (and geometric shapes), a Structured Report Storage SOP Class may be appropriate, if a template with​ the appropriate semantics (what the contours "mean") is defined​

•​for2Dcoordinates(andgeometricshapes),aGrayscaleorColorSoftcopyPresentationStateStorageSOPClassmaybeappro-​ priate, though there are no defined semantics for recognizing what to do with which graphic objects​

Forillustrativepurposes,theuseoftheSegmentationStorageSOPClassisassumed,andaconsistentFrameofReferenceisassumed.​

Note​

If images from different modalities are acquired, on separate devices, but with the same physical arrangement of animals,​ a more complex workflow might involve the use of one segmentation derived from one modality applied to images from a​ different modality with a different Frame of Reference, in which case use of the Spatial Registration Storage SOP Class or​ DeformableSpatialRegistrationStorageaspersistentobjectmightbeappropriate,andappropriatereferencestoitincluded.​ The same might apply if registration were necessary between images acquired on the same device, but given that research​ small animals are normally anesthetized, this is usually not required.​

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VVV.1.1 Reference Attributes​

VVV.1.1.1 Acquired Images of Multiple Animals​

No references are present, since forward references are not used.​

The Frame of Reference UID is present for cross-sectional modalities.​

Iftheanimalsarenotallalignedinthesamedirection,PatientPosition(0018,5100)foreachanimalispresentwithinGroupofPatients​ Identification Sequence (0010,0027) and a nominal Patient Position (0018,5100) is present in the General Series Module, and the​ coordinate system dependent position and orientation Attributes of the Image Plane Module Attributes (or corresponding Functional​ Groups) are relative to the nominal Patient Position (0018,5100) present in the General Series Module.​

VVV.1.1.2 Segmentation Instances​

Segmentations are Enhanced Multi-frame Images, so the Derivation Image Functional Group (Section C.7.6.16.2.6 in PS3.3) is used.​

As required by the Segmentation IOD (Section A.51.5.1 in PS3.3):​

•​the value of Purpose of Reference Sequence (0040,A170) within the Source Image Sequence (0008,2112) within Derivation Image​ Sequence (0008,9124) is (121322, DCM, "Source Image for Image Processing Operation")​

•​the value of Derivation Code Sequence (0008,9215) within Derivation Image Sequence (0008,9124) is (113076, DCM, "Segment-​ ation")​

•​though not required, the value of Derivation Description (0008, 2111) may contain additional detail describing the image processing​ operation​

The Frame of Reference UID is the same as that for the images from which the segmentation was derived.​

There is no requirement that application of the Segmentation be restricted to the image referenced in the Derivation Image Functional​ GroupMacro,whichdescribestheimagesthatthesegmentationwasderivedfrom,nottheimagestowhichitisapplicable(potentially​ all of the images in the same Frame of Reference).​

The Common Instance Reference Module is required to be present, which provides Study and Series Instance UIDs for all referenced​ instances.​

A segmentation instance may contain multiple segments, thus multiple animals could be described in a single segmentation instance,​ or each animal could be described in one of multiple segments within a single segmentation instance. The manner in which each​ segment is numbered, labeled and categorized is thus important. Each segment may be described as follows:​

•​Segment Number (0062,0004) from 1 to the number of animals (since the Attribute definition requires starting at 1, incrementing​ by 1)​

•​SegmentLabel(0062,0005)usingahuman-readablelabelthatappropriatelyidentifieseachanimalinthecontextoftheexperiment,​ e.g., it may have the same value as the Patient ID (0010,0020) used for each separate animal.​

•​Segmented Property Category Code Sequence (0062,0003) value of (309825002, SCT, "Spatial and Relational Concept")​

•​Segmented Property Type Code Sequence (0062,000F) value of (113132, DCM, "Single subject selected from group")​

Note​

The properties of (309825002, SCT, "Spatial and Relational Concept") and (113132, DCM, "Single subject selected from​ group") are suggested instead of a more generic description, such as (123037004, SCT, "Anatomical Structure") and​ (38266002, SCT, "Entire Body"), since though the latter would be accurate, it would not convey the additional implication of​ selectionofonefrommany.Further,insomecases,theentirebodymaynotactuallybeimaged(e.g.,justtheheadofmultiple​ subjects may be imaged simultaneously for brain studies).​

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VVV.1.1.3 Derived Images of Single Animals​

It is recommended that the source image(s) be referenced using Source Image Sequence (0008,2112), either in the top level Data​ Set or within the Derivation Image Functional Group (Section C.7.6.16.2.6 in PS3.3) as appropriate for the IOD, with:​

•​the value of Purpose of Reference Sequence (0040,A170) within the Source Image Sequence (0008,2112) being (113130, DCM,​ "Predecessor containing group of imaging subjects")​

•​the value of Derivation Code Sequence (0008,9215) being (113131, DCM, "Extraction of individual subject from group")​

•​the value of Derivation Description (0008,2111) containing additional detail describing the image processing operation​

It is recommended that the segmentation used be referenced using Referenced Image Sequence (0008,1140), either in the top level​ Data Set or within the Referenced Image Functional Group (Section C.7.6.16.2.5 in PS3.3) as appropriate for the IOD, with:​

•​the value of Purpose of Reference Sequence (0040,A170) within Referenced Image Sequence (0008,1140) being (121321, DCM,​ "Mask image for image processing operation")​

Note​

If instead of a segmentation (which is a form of image), a non-image object were used to encode the segmented regions,​ then use of Referenced Instance Sequence (0008,114A) instead of Referenced Image Sequence (0008,1140) would be​ appropriate.​

The Frame of Reference UID is the same as the source images and the segmentation.​

Ifalltheanimalsarenotalignedinthesamedirection(i.e.,donothavethesamevalueforPatientPosition(0018,5100)),thecoordinate​ system dependent position and orientation Attributes of the Image Plane Module Attributes (or corresponding Functional Groups)​ may have been recomputed. If the animals are aligned in different directions, and Patient Position (0018,5100) from within Group of​ Patients Identification Sequence (0010,0027) in the source images is compared against Patient Position (0018,5100) from the Gen-​ eral Series Module in the source images, the difference may be used to recompute (rotate, flip and translate) new patient-relative​ vectors and offsets within the same Frame of Reference. The value in the Patient Position (0018,5100) from the General Series​ Module in the derived images are appropriate for the selected animal.​

It is recommended that the Common Instance Reference Module be present even if it is not required by the IOD, to provide Study​ and Series Instance UIDs for all referenced instances.​

VVV.1.2 Propagation of Composite Context​

Propagation and replacement of the appropriate patient-level and study-level identifying and descriptive Attributes is also required.​

The issues related to the identification of the "patient" in such cases are addressed in Section C.7.1.4.1.1 “Groups of Subjects” in​ PS3.3.​

New studies are required if the patient identifiers have changed.​

New series are required for each of the derived (types) of objects, since they are created by different equipment and have different​ values for Modality.​

VVV.1.3 Propagation of History​

The history of operations applied to a composite instance and its predecessors may be recorded in multiple items of Derivation Code​ Sequence (0008,9215). It is preferable, when creating a new derived object, to add to the end of the existing sequence of items,​ rather than to completely replace them. It is also common to add to the plain text that is contained in Derivation Description (0008,​ 2111), rather than replacing it (maximum length permitting).​

The history of which devices (and human operators) have operated on a composite instance and its predecessors may be recorded​ in Contributing Equipment Sequence (0018,A001). Again, it is preferable that the existing sequence of items be extended rather than​ replaced, if possible.​

For both Derivation Code Sequence (0008,9215) and Contributing Equipment Sequence (0018,A001), if multiple predecessors are​ applicable (e.g., the source image and a segmentation mask), then the sequence of items of both predecessors may be merged.​

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