PS-2020a / part17

JJSurfaceMeshRepresentation(Informative)​

For a general introduction into the underlying principles used in the Section C.27.1 “Surface Mesh Module” in PS3.3 see:​

Foley & van Dam [et al], Computer Graphics: Principles and Practice, Second Edition, Addison-Wesley, 1990.​

JJ.1 Multi-Dimensional Vectors​

The dimensionality of the Vectors Macro (Section C.27.3 in PS3.3) is not restricted to accommodate broader use of this macro in the​ future. Usage beyond 3-dimensional Euclidean geometry is possible The Vectors Macro may be used to represent any multi-dimen-​ sional numerical entity, like a set of parameters that are assigned to a voxel in an image or a primitive in a surface mesh.​

Examples:​

In electroanatomical mapping, one or more tracked catheters are used to sample the electrophysiological parameters of the inner​ surface of the heart. Using magnetic tracking information, a set of vertices is generated according to the positions the catheter was​ moved to during the examination. In addition to its 3D spatial position each vertex is loaded with a 7D-Vector containing the time it​ was measured at, the direction the catheter pointed to, the maximal potential measured in that point, the duration of that potential​ and the point in time (relative to the heart cycle) the potential was measured.​

For biomechanical simulation the mechanical properties of a vertex or voxel can be represented with a n-dimensional vector.​

JJ.2 Encoding Examples​

The following example demonstrates the usage of the Surface Mesh Module for a tetrahedron.​

Figure JJ.2-1. Surface Mesh Tetrahedron​

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Note​

When the actual values are binary a text string is shown.​

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KK Use Cases For The Composite Instance​ Root Retrieval Classes (Informative)​

The use cases fall into five broad groups:​

KK.1 Clinical Review​

KK.1.1 Retrieval Based On Report References​

AreferringphysicianreceivesradiologicaldiagnosticreportsonCTorMRIexaminations.Thesereportscontainreferencestospecific​ images. He chooses to review these specific images himself and/or show the patient. The references in the report point to particular​ slices. If the slices are individual images, then they may be obtained individually. If the slices are part of an enhanced multi-frame​ CT/MRobject,thenretrievalofthewholemulti-frameobjectmighttaketoolong.TheCompositeInstanceRootRetrieveServiceallows​ retrieval of only the selected frames.​

The source of the image and frame references in the report could be KOS, CDA, SR, presentation states or other sources.​

Selective retrieval can also be used to retrieve 2 or more arbitrary frames, as may be used for digital subtraction (masking), and may​ be used with any multi-frame objects, including multi-frame ultrasound, XR etc.​

Features of interest in many long "video" examinations (e.g., endoscopy) are commonly referenced as times from the start of the ex-​ amination. The same benefits of reduced WAN bandwidth use could be obtained by shortening the MPEG-2, MPEG-4 AVC/H.264,​ HEVC/H.265 or JPEG 2000 Part 2 Multi-component based stream prior to transmission.​

KK.1.2 Selective Retrieval Without References to Specific Slices​

Retrieval using the Composite Instance Retrieve Without Bulk Data Retrieve Service allows determination and retrieval of a suitable​ subset of frames. This could for instance be used to retrieve only the slices with particular imaging characteristics (e.g., T2 weighting​ from an enhanced MR object).​

KK.2 Local Use - "Relevant Priors"​

KK.2.1 Anatomic Sub-region​

A multi-frame CT or MR may cover a larger area of anatomy than is required for use as a relevant prior. How the SCU determines​ which frames are relevant is outside the scope of the Standard.​

KK.2.2 Worklists​

Relevant priors may be specified by instance and frame references in a worklist and benefit from the same facilities.​

KK.3 Attribute Based Retrieval​

There are times when it would be useful to retrieve from a Multi-frame Image only those frames satisfying certain dimensionality cri-​ teria, such as those CT slices fitting within a chosen volume. Initial retrieval of the image using the Composite Instance Retrieve​ Without Bulk Data Retrieve Service allows determination and retrieval of a suitable sub-set of frames.​

KK.4 CAD & Data Mining Applications​

Given the massively enhanced amount of dimensional information in the new CT/MR objects, applications could be developed that​ would use this for statistical purposes without needing to fetch the whole (correspondingly large) pixel data. The Composite Instance​ Retrieve Without Bulk Data Retrieve Service permits this.​

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KK.5 Independent WADO Server​

A hospital has a large PACS (that supports multi-frame objects) that does not support WADO. The hospital installs a separate WADO​ server that obtains images from the PACS using DICOM. WADO has the means to request individual frames, supporting many of the​ above use cases.​

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LL Example SCU Use of The Composite​

InstanceRootRetrievalClasses(Informative)​

LL.1 Retrieval of Entire Composite Instances​

There are many modules in DICOM that use the Image SOP Instance Reference Macro (Table 10-3 “Image SOP Instance Reference​ Macro Attributes” in PS3.3), which includes the SOP Instance UID and SOP class UID, but not the Series Instance UID and Study​ InstanceUID.UsingtheCompositeInstanceRootRetrievalClasseshowever,retrievalofsuchinstancesissimple,asadirectretrieval​ may be requested, including only the SOP Instance UID in the Identifier of the C-GET request.​

LL.2RetrievalofSelectedFrameCompositeInstancesFromMulti-frameObjects​

Where the frames to be retrieved and viewed are known in advance, - e.g., when they are referenced by an Image Reference Macro​ in a structured report, then they may be retrieved directly using either of the Composite Instance Root Retrieval Classes.​

LL.3 Retrieval of Selected Frame Composite Instances From MPEG-2, MPEG-4​ AVC/H.264 or HEVC/H.265 Video​

If the image has been stored in MPEG-2, MPEG-4 AVC/H.264 or HEVC/H.265 format, and if the SCU has knowledge independent​ of DICOM as to which section of a "video" is required for viewing (e.g., perhaps notes from an endoscopy) then the SCU can perform​ the following steps:​

1.​Use known configuration information to identify the available transfer syntaxes.​

2.​If MPEG-2, MPEG-4 AVC/H.264, HEVC/H.265 or JPEG 2000 Part 2 Multi-component transfer syntaxes are available, then issue​ a request to retrieve the required section.​

The data received may be slightly longer than that requested, depending on the position of key frames in the data.​

3.​If only other transfer syntaxes are available, then the SCU may need to retrieve most of the object using Composite Instance​ RetrieveWithoutBulkDataRetrieveServicetofindtheframerateorframetimevector,andthencalculatealistofframestoretrieve​ as in the previous sections.​

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MMConsiderationsForApplicationsCreating​

New Images From Multi-frame Images​

MM.1 Scope​

The purpose of this annex is to aid those developing SCPs of the Composite Instance Root Retrieve Service Class. The behavior of​ the application when making any of the changes discussed in this annex should be documented in the conformance statement of the​ application.​

MM.2 Frame Extraction Issues​

There are many different aspects to consider when extracting frames to make a new object, to ensure that the new image remains a​ fully valid SOP Instance, and the following is a non-exhaustive list of important issues​

MM.2.1 Number of Frames​

The Number of Frames (0028,0008) Attribute will need to be updated.​

MM.2.2 Start and End Times​

Any Attributes that refer to start and end times such as Acquisition Time (0008,0032) and Content Time (0008,0033) must be updated​ to reflect the new start time if the first frame is not the same as the original. This is typically the case where the multi-frame object is​ a "video" and where the first frame is not included. Likewise, Image Trigger Delay (0018,1067) may need to be updated.​

MM.2.3 Time Interval versus Frame Increment Vector​

The Frame Time (0018,1063) may need to be modified if frames in the new image are not a simple contiguous sequence from the​ original, and if they are irregular, then the Frame Time Vector (0018,1065) will need to be used in its place, with a corresponding​ change to the Frame Increment Pointer (0028,0009). This also needs careful consideration if non-consecutive frames are requested​ from an image with non-linearly spaced frames.​

MM.2.4 MPEG-2, MPEG-4 AVC/H.264 or HEVC/H.265​

Identifying the location of the requested frames within an MPEG-2, MPEG-4 AVC/H.264 or HEVC/H.265 data stream is non-trivial,​ but if achieved, then little else other than changes to the starting times are likely to be required for MPEG-2, MPEG-4 AVC/H.264 or​ HEVC/H.265 encoded data, as the use-cases for such encoded data (e.g., endoscopy) are unlikely to include explicit frame related​ data. See the note below however for comments on "single-frame" results.​

An application holding data in MPEG-2, MPEG-4 AVC/H.264 or HEVC/H.265 format is unlikely to be able to create a range with a​ frame increment of greater than one (a calculated frame list with a 3rd value greater than one), and if such a request is made, it might​ return a status of AA02: Unable to extract Frames.​

The approximation feature of the Time Range form of request is especially suitable for data held in MPEG-2, MPEG-4 AVC/H.264 or​ HEVC/H.265form,asitallowstheapplicationtofindthenearestsurroundingkeyframes,whichgreatlysimplifieseditingandimproves​ quality.​

MM.2.5 JPEG 2000 Part 2 Multi-Component Transform​

Similar issues exist as for MPEG-2, MPEG-4 AVC/H.264 and HEVC/H.265 data and similar solutions apply.​

MM.2.6 Functional Groups For Enhanced CT, MR, etc.​

It is very important that functional groups for enhanced image objects are properly re-created to reflect the reduced set of frames, as​ they include important clinical information. The requirement in the Standard that the resulting object be a valid SOP instance does​ make such re-creations mandatory.​

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MM.2.7 Nuclear Medicine Images​

Images of the Nuclear Medicine SOP class are described by the Frame Increment Pointer (0028,0009), which in turn references a​ numberofdifferent"Vectors"asdefinedinTable"NMMulti-frameModule"inPS3.3.LiketheFunctionalGroupsabove,theseVectors​ are required to contain one value for each frame in the Image, and so their contents must be modified to match the list of frames ex-​ tracted, ensuring that the values retained are those corresponding to the extracted frames.​

MM.2.8 A "Single Frame" Multi-frame Image​

The requirement that the newly created image object generated in response to a Frame level retrieve request must be the same as​ the SOP class will frequently result in the need to create a single frame instance of an object that is more commonly a multi-frame​ object, but this should not cause any problems with the IOD rules, as all such objects may quite legally have Number of Frames = 1.​

However, a single frame may well cause problems for a transfer syntax based on "video" such as those using MPEG-2, MPEG-4​ AVC/H.264orHEVC/H.265,andthereforetheSCUwhennegotiatingaC-GETshouldconsiderthisproblem,andincludeoneormore​ transfer syntaxes suitable for holding single or non-contiguous frames where such a retrieval request is being made.​

MM.3 Frame Numbers​

Frame numbers are indexes, not identifiers for frames. In every object, the frame numbers always start at 1 and increment by 1, and​ therefore they will not be the same after extraction into a new SOP Instance.​

A SOP Instance may contain internal references to its own frames such as mask frames. These may need to be corrected.​

MM.4 Consistency​

There is no requirement in the Frame Level Retrieve Service for the SCP to cache or otherwise retain any of the information it uses​ tocreatethenewSOPInstance,andtherefore,anSCUsubmittingmultiplerequestsforthesameinformationcannotexpecttoreceive​ the "same" object with the same Instance and Series UIDs each time. However, an SCP may choose to cache such instances, and​ if returning an instance identical to one previously created, then the same Instance and Series UIDs may be used. The newly created​ object is however guaranteed to be a valid SOP instance and an SCU may therefore choose to send such an instance to an SCP​ using C-STORE, in which case it should be handled exactly as any other Composite Instance of that SOP class.​

MM.5 Time Synchronization​

The time base for the new composite instance should be the same as for the source image and should use the same time synchron-​ ization frame of reference. This allows the object to retain synchronization to any simultaneously acquired waveform data​

MM.6 Audio​

Where the original object is MPEG-2, MPEG-4 AVC/H.264 or HEVC/H.265 with interleaved audio data in the MPEG-2 System, and​ where the retrieved object is also MPEG-2, MPEG-4 AVC/H.264 or HEVC/H.265 encoded, then audio could normally be preserved​ and maintain synchronization, but in other cases, the audio may be lost.​

MM.7 Private Attributes​

AswithallmodificationstoexistingSOPinstances,anapplicationshouldremoveanydatathatitcannotguaranteetomakeconsistent​ withthemodificationsitismaking.Therefore,anapplicationcreatingnewimagesfromMulti-frameImagesshouldremoveanyPrivate​ Attributes about which it lacks sufficient information to allow safe and consistent modification. This behavior should be documented​ in the conformance statement.​

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NNSpecimenIdentificationandManagement​

This annex explains the use of the Specimen Module for pathology or laboratory specimen imaging.​

NN.1 Pathology Workflow​

The concept of a specimen is deeply connected to analysis (lab) workflow, the decisions made during analysis, and the "containers"​ used within the workflow.​

Typicalanatomicpathologycasesrepresenttheanalysisof(all)tissueand/ornon-biologicmaterial(e.g.,orthopedichardware)removed​ inasinglecollectionprocedure(e.g.,surgicaloperation/event,biopsy,scrape,aspirationetc.).Acaseisusuallycalledan"Accession"​ and is given a single accession number in the Laboratory Information System.​

During an operation, the surgeon may label and send one or more discrete collections of material (specimens) to pathology for ana-​ lysis. By sending discrete, labeled collections of tissue in separate containers, the surgeon is requesting that each discrete labeled​ collection (specimen) be analyzed and reported independently - as a separate "Part" of the overall case. Therefore, each Part is an​ important, logical component of the laboratory workflow. Within each Accession, each Part is managed separately from the others​ and is identified uniquely in the workflow and in the Laboratory Information System.​

During the initial gross (or "eyeball") examination of a Part, the pathologist may determine that some or all of the tissue in a Part​ should be analyzed further (usually through histology). The pathologist will place all or selected sub-samples of the material that​ makesupthePartintolabeledcontainers(cassettes).Aftersomeprocessing,allthetissueineachcassetteisembeddedinaparaffin​ block (or epoxy resin for electron microscopy); at the end of the process, the block is physically attached to the cassette and has the​ same label. Therefore, each "Block" is an important, logical component of the laboratory workflow, which corresponds to physical​ material in a container for handling, separating and identifying material managed in the workflow. Within the workflow and Laboratory​ Information System, each Block is identified uniquely and managed separately from all others.​

From a Block, technicians can slice very thin sections. One or more of these sections is placed on one or more slides. (Note, material​ from a Part can also be placed directly on a slide bypassing the block). A slide can be stained and then examined by the pathologists.​ Each "Slide", therefore, is an important, logical component of the laboratory workflow, which corresponds to physical material in a​ container for handling, separating and identifying material managed in the workflow. Within the workflow and within the Laboratory​ Information Systems, each Slide is identified uniquely and managed separately from all others.​

While"Parts"to"Blocks"to"Slides"isbyfarthemostcommonworkflowinpathology,itisimportanttonotethattherecanbenumerous​ variationsonthisbasictheme.Inparticular,lasercapturemicrodissectionandotherslidesamplingapproachesformolecularpathology​ are in increasing use. Such new workflows require a generic approach in the Standard to identifying and managing specimen identi-​ fication and processing, not one limited only to "Parts", "Blocks", and "Slides". Therefore, the Standard adopts a generic approach of​ describing uniquely identified Specimens in Containers.​

NN.2 Basic Concepts and Definitions​

NN.2.1 Specimen​

A physical object (or a collection of objects) is a specimen when the laboratory considers it a single discrete, uniquely identified unit​ that is the subject of one or more steps in the laboratory (diagnostic) workflow.​

To say the same thing in a slightly different way: "Specimen" is defined as a role played by a physical entity (one or more physical​ objects considered as single unit) when the entity is identified uniquely by the laboratory and is the direct subject of more steps in a​ laboratory (diagnostic) workflow.​

Itisworthwhiletoexpandonthisverybasic,highleveldefinitionbecauseitcontainsimplicationsthatareimportanttothedevelopment​ and implementation of the DICOM Specimen Module. In particular:​

1.​A single discrete physical object or a collection of several physical objects can act as a single specimen as long as the collection​ is considered a unit during the laboratory (diagnostic) process step involved. In other words, a specimen may include multiple​ physical pieces, as long as they are considered a single unit in the workflow. For example, when multiple fragments of tissue are​ placed in a cassette, most laboratories would consider that collection of fragments as one specimen (one "block").​

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2.​A specimen must be identified. It must have an ID that identifies it as a unique subject in the laboratory workflow. An entity that​ does not have an identifier is not a specimen.​

3.​Specimens are sampled and processed during a laboratory's (diagnostic) workflow. Sampling can create new (child) specimens.​ These child specimens are full specimens in their own right (they have unique identifiers and are direct subjects in one or more​ steps in the laboratory's (diagnostic) workflow. This property of specimens (that can be created from existing specimens by​ sampling) extends a common definition of specimen, which limits the word to the original object received for examination (e.g.,​ from surgery).​

4.​However, child specimens can and do carry some Attributes from ancestors. For example, a tissue section cut from a formalin​ fixed block remains formalin fixed, and a tissue section cut from a block dissected from the proximal margin of a colon resection​ is still made up of tissue from the proximal margin. A description of a specimen therefore, may require description of its parent​ specimens.​

5.​A specimen is defined by decisions in the laboratory workflow. For example, in a typical laboratory, multiple tissue sections cut​ from a single block and placed on the same slide are considered a single specimen (as single unit identified by the slide number).​ However, if the histotechnologists had placed each tissue section on its own slide (and given each slide a unique number), each​ tissue section would be a specimen in its own right .​

NN.2.2 Containers​

Specimen containers (or just "containers") play an important role in laboratory (diagnostic) processes. In most, but not all, process​ steps,specimensareheldincontainers,andacontaineroftencarriesitsspecimen'sID.Sometimesthecontainerbecomesintimately​ involved with the specimen (e.g., a paraffin block), and in some situations (such as examining tissue under the microscope) the con-​ tainer (the slide and coverslip) become part of the optical path.​

Containers have identifiers that are important in laboratory operations and in some imaging processes (such as whole slide imaging).​ The DICOM Specimen Module distinguishes the Container ID and the Specimen ID, making them different data elements. In many​ laboratories where there is one specimen per container, the value of the specimen ID and container ID will be same. However, there​ are use cases in which there are more than one specimen in a container. In those situations, the value of the container ID and the​ specimen IDs will be different (see Section NN.3.5).​

Containers are often made up of components. For example, a "slide" is container that is made up of the glass slide, the coverslip and​ the "glue" the binds them together. The Module allows each component to be described in detail.​

NN.3 Specimen Module​

NN.3.1 Scope​

The Specimen Module (see PS3.3) defines formal DICOM Attributes for the identification and description of laboratory specimens​ whensaidspecimensarethesubjectofaDICOMimage.TheModuleisfocusedonthespecimenandlaboratoryAttributesnecessary​ to understand and interpret the image. These include:​

1.​Attributes that identify (specify) the specimen (within a given institution and across institutions).​

2.​Attributes that identify and describe the container in which the specimen resides. Containers are intimately associated with spe-​ cimens in laboratory processes, often "carry" a specimen's identity, and sometimes are intimately part of the imaging process,​ as when a glass slide and coverslip are in the optical path in microscope imaging.​

3.​Attributesthatdescribespecimencollection,samplingandprocessing.Knowinghowaspecimenwascollected,sampled,processed​ and stained is vital in interpreting an image of a specimen. One can make a strong case that those laboratory steps are part of​ the imaging process.​

4.​Attributes that describe the specimen or its ancestors (see Section NN.2.1) when these descriptions help with the interpretation​ of the image.​

Attributes that convey diagnostic opinions or interpretations are not within the scope of the Specimen Module. The DICOM Specimen​ Module does not seek to replace or mirror the pathologist's report.​

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