Annex NN Specimen Identification and Management

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.

Typical anatomic pathology cases represent the analysis of (all) tissue and/or non-biologic material (e.g., orthopedic hardware) removed in a single collection procedure (e.g., surgical operation/event, biopsy, scrape, aspiration etc.). A case is usually called an “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 analysis. 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 makes up the Part into labeled containers (cassettes). After some processing, all the tissue in each cassette is embedded in a paraffin 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” is by far the most common workflow in pathology, it is important to note that there can be numerous variations on this basic theme. In particular, laser capture microdissection and other slide sampling approaches for molecular pathology are in increasing use. Such new workflows require a generic approach in the Standard to identifying and managing specimen identification 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.

It is worthwhile to expand on this very basic, high level definition because it contains implications that are important to the development 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”).

  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 defintion 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 descripton 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 histotechs 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 CONTAINER

Specimen containers (or just “containers”) play an important role in laboratory (diagnostic) processes. In most, but not all, process steps, specimens are held in containers, and a container often carries its specimen’s ID. Sometimes the container becomes intimately involved with the specimen (e.g., a paraffin block), and in some situations (such as examining tissue under the microscope) the container (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 cover slip 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 when said specimens are the subject of a DICOM image. The Module is focused on the specimen and laboratory attributes necessary 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 specimens in laboratory processes, often “carry” a specimen’s identity, and sometimes are intimately part of the imaging process, as when a glass slide and cover slip are in the optical path in microscope imaging.

  3. Attributes that describe specimen collection, sampling and processing. Knowing how a specimen was collected, 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 proceNN.

  4. Attributes that describe the specimen or its ancestors (see Section NN.2.1, above) 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.

NN.3.2 Relationship with the Laboratory Information System

The Laboratory Information System (LIS) is critical to management of workflow and processes in the pathology lab. It is ultimately the source of the identifiers applied to specimens and containers, and is responsible for recording the processes that were applied to specimens.

An important purpose of the Specimen Module is to store specimen information necessary to understand and interpret an image within the image information object , as images may be displayed in contexts where the Laboratory Information System is not available. Implementation of the Specimen Module therefore requires close, dynamic integration between the LIS and imaging systems in the laboratory workflow.

It is expected that the Laboratory Information Systems will participate in the population of the Specimen Module by passing the appropriate information to a DICOM compliant imaging system in the Modality Worklist, or by processing the image objects itself and populating the Specimen Module attributes.

The nature of the LIS processing for imaging in the workflow will vary by product implementation. For example, an image of a gross specimen may be taken before a gross description is transcribed. A LIS might provide short term storage for images and update the description attributes in the module after a particular event (such as sign out). The DICOM Standard is silent on such implementation issues, and only discusses the attributes defined for the information objects exchanged between systems.

NN.3.3 Case Level Information and the Accession Number

A pathology “case” is a unit of work resulting in a report with associated codified, billable acts. Case Level attributes are generally outside the scope of the Specimen Module. However, a case is equivalent to a DICOM Requested Procedure, for which attributes are specified in the DICOM Study level modules.

DICOM has existing methods to handle most “case level” issues, including accepting cases referred for other institutions, clinical history, status codes, etc. These methods are considered sufficient to support DICOM imaging in Pathology.

The concept of an “Accession Number” in Pathology has been determined to be sufficiently equivalent to an “Accession Number” in Radiology that the DICOM data element “Accession Number” at the Study level at the DICOM information model may be used for the Pathology Accession Number with essentially the existing definition.

It is understood that the value of the laboratory accession number is often incorporated as part of a Specimen ID. However, there is no presumption that this is always true, and the Specimen ID should not be parsed to determine an accession number. The accession number will always be sent in its own discrete attribute.

NN.3.4 Laboratory Workflows and Specimen Types

While created with anatomic pathology in mind, the DICOM Specimen Module is designed to support specimen identification, collection, sampling and processing attributes for a wide range of laboratory workflows. The Module is designed in a general way so not to limit the nature, scope, scale or complexity of laboratory (diagnostic) workflow that may generate DICOM images.

To provide specificity on the general process, the Module provides extendable lists of Container Types, Container Component Types, Specimen Types, Specimen Collection Types, Specimen Process Types and Staining Types. It is expected that the value sets for these “types” can be specialized to describe a wide range of laboratory procedures.

In typical anatomic pathology practice, and in Laboratory Information Systems, there are conventionally three identified levels of specimen preparation – part, block, and slide. These terms are actually conflations of the concepts of specimen and container. Not all processing can be described by only these three levels.

A part is the uniquely identified tissue or material collected from the patient and delivered to the pathology department for examination. Examples of parts would include a lung resection, colon biopsy at 20 cm, colon biopsy at 30 cm, peripheral blood sample, cervical cells obtained via scraping or brush, etc. A part can be delivered in a wide range of containers, usually labeled with the patients name, medical record number, and a short description of the specimen such as “colon biopsy at 20 cm”. At accession, the lab creates a part identifier and writes it on the container. The container therefore conveys the part’s identifier in the lab.

A block is a uniquely identified container, typically a cassette, containing one or more pieces of tissue dissected from the part (tissue dice). The tissue pieces may be considered, by some laboratories, as separate specimens. However in most labs, all the tissue pieces in a block are considered a single specimen.

A slide is a uniquely identified container, typically a glass microscope slide, containing tissue or other material. Common slide preparations include:

NN.3.5 Relationship Between Specimens and Containers

Virtually all specimens in a clinical laboratory are associated with a container, and specimens and containers are both important in imaging (see “Definitions”, above). In most clinical laboratory situations there is a one to one relationship between specimens and containers. In fact, pathologists and LIS systems routinely consider a specimen and its container as single entity; e.g. the slide (a container) and the tissue sections (the specimen) are considered a single unit.

However, there are legitimate use cases in which a laboratory may place two or more specimens in the same container (see Section NN.4 for examples). Therefore, the DICOM Specimen Module distinguishes between a Specimen ID and a Container ID. However, in situations where there is only one specimen per container, the value of the Specimen ID and Container ID may be the same (as assigned by the LIS).

Some Laboratory Information System may, in fact, not support multiple specimens in a container, i.e., they manage only a single identifier used for the combination of specimen and container. This is not contrary to the DICOM Standard; images produced under such a system will simply always assert that there is only one specimen in each container. However, a pathology image display application that shows images from a variety of sources must be able to distinguish between container and specimen IDs, and handle the 1:N relationship.

In allowing for one container to have multiple specimens, the Specimen Module asserts that it is the Container, not the Specimen, that is the unique target of the image. In other words, one Container ID is required in the Specimen Module, and multiple Specimen IDs are allowed in the Specimen Sequence. See Figure NN.3-1.

[pic]

Figure NN.3-1 Extension of DICOM E-R Model for Specimens

If there is more than one specimen in a container, there must be a mechanism to identify and locate each specimen. When there is more than one specimen in a container, the Module allows various approaches to specify their locations. The Specimen Localization Content Item Sequence (0040,0620), through its associated Template 8004, allows the specimen to be localized by a distance in three dimensions from a reference point on the container, by a textual description of a location or physical attribute such as a colored ink, or by its location as shown in a referenced image of the container. The referenced image may use an overlay, burned-in annotation, or an associated Presentation State SOP Instance to specify the location of the specimen.

NN.3.6 Relationship Between Specimens and Images

Because the Module supports one container with multiple specimens, the Module can be used with an image of:

However the Module is not designed for use with an image of:

Such images may be included in the Study, but would not use the Specimen Module; they would, for instance, be general Visible Light Photographic images. Note, however, that the LIS might identify a “virtual container” that contains such multiple real containers, and manage that virtual container in the laboratory workflow.

NN.4 SPECIMEN IDENTIFICATION Examples

NN.4.1 One Specimen Per Container

In normal clinical practice, when there is one specimen per container, the value of the specimen identifier and the value of the container identifier will be the same. In Figure NN.4-1, each slide is prepared from a single tissue sample from a single block (cassette).

[pic]

Figure NN.4-1 Sampling for one specimen per container

NN.4.2 Multiple Items From Same Block

Figure NN.4-2 shows more than one tissue item on the same slide coming from the same block (but cut from different levels). The laboratory information system considers two tissue sections (on the same slide) to be separate specimens.

Two Specimen IDs will be assigned, different from the Container (Slide) ID. The specimens may be localized, for example, by descriptive text “Left” and “Right”.

If the slide is imaged, a single image with more than one specimen may be created. In this case, both specimens must be identified in the Specimen Sequence of the Specimen Module. If only one specimen is imaged, only its Specimen ID must be included in the Specimen Sequence; however, both IDs may be included (e.g., if the image acquisition system cannot determine which specimens in/on the container are in the field of view).

[pic]

Figure NN.4-2 Container with two specimens from same parent

NN.4.3 Items From Different Parts in the Same Block

Figure NN.4-3 shows processing where more than one tissue item is embedded in the same block within the same Cassette, but coming from different clinical specimens (parts). This may represent different lymph nodes embedded into one cassette, or different tissue dice coming from different parts in a frozen section examination, or tissue from the proximal margin and from the distal margin, and both were placed in the same cassette. Because the laboratory wanted to maintain the sample as separate specimens (to maintain their identity), the LIS gave them different IDs and the tissue from Part A was inked blue and the tissue from Part B was inked red.

The specimen IDs must be different from each other and from the container (cassette) ID. The specimens may be localized, for example, by descriptive text “Red” and “Blue” for Visual Coding of Specimen.

If a section is made from the block, each tissue section will include fragments from two specimens (red and blue). The slide (container) ID will be different from the section id (which will be different form each other).

If the slide is imaged, a single image with more than one specimen may be created but the different specimens must be identified and unambiguously localized within the container.

[pic]

Figure NN.4-3 Sampling for two specimens from different ancestors

NN.4.4 Items From Different Parts on the Same Slide

Figure NN.4-4 shows the result of two tissue collections placed on the same slide by the surgeon. E.g., in gynecological smears the different directions of smears might represent different parts (portio, cervix).

The specimen IDs must be different from each other and from the container (slide) ID. The specimens may be localized, for example, by descriptive text “Short direction smear” and “Long direction smear”.

[pic]

Figure NN.4-4 Two specimens smears on one slide

NN.4.5 Tissue Micro Array

Slides created from a TMA block have small fragments of many different tissues coming from different patients, all of which may be processed at the same time, under the same conditions by a desired technique. These are typically utilized in research. See Figure NN.4-5. Tissue items (spots) on the TMA slide come from different tissue items (cores) in TMA blocks (from different donor blocks, different parts and different patients).

Each Specimen (spot) must have its own ID. The specimens may be localized, for example, by X-Y coordinates, or by a textual column-row identifier for the spot (e.g., “E3” for fifth column, third row).

If the TMA slide is imaged as a whole, e.g., at low resolution as an index, it must be given a “pseudo-patient” identifier (since it does not relate to a single patient). Images created for each spot should be assigned to the real patients.

[pic]

Figure NN.4-5 Sampling for TMA Slide

NN.5 STRUCTURE OF THE SPECIMEN MODULE

The Specimen Module content is specified as a Macro as an editorial convention to facilitate its use in both Composite IODs and in the Modality Worklist Information Model.

The Module has two main sections. The first deals with the specimen container. The second deals with the specimens within that container. Because more than one specimen may reside in single container, the specimen section is set up as a sequence.

The Container section is divided two “sub-sections”:

The Specimen Description Sequence contains five “sub-sections”

NN.6 EXAMPLES OF SPECIMEN MODULE USE

This section includes examples of the use of the SPECIMEN MODULE. EACH EXAMPLE HAS two tables.

The first table contains the majority of the container and specimen elements of the Specimen Module. The second includes the Specimen Preparation Sequence (which documents the sampling, processing and staining steps).

In the first table, invocations of Macros have been expanded to their constituent attributes. The Table does not include Type 3 (optional) attributes that are not used for the example case.

The second table shows the Items of the Specimen Preparation Sequence and its subsidiary Specimen Preparation Step Content Item Sequence. That latter sequence itself has subsidiary Code Sequence Items, but these are shown in the canonical DICOM “triplet” format (see PS3.16), e.g., (T-28600, SRT, “Left Upper Lobe of Lung”). In the table, inclusions of subsidiary templates have been expanded to their constituent Content Items. The Table does not include Type U (optional) Content Items that are not used for the example case.

Values in the colored columns of the two tables actually appear in the image object.

NN.6.1 Gross Specimen

This is an example of how the SPECIMEN MODULE can be populated for a gross specimen (a lung lobe resection received from surgery). The associated image would be a gross image taken in gross room.

Table NN.6-1 Specimen Module for Gross Specimen

Attribute Name Tag Attribute Description Example Value Comments
Container Identifier (0040,0512) The identifier for the container that contains the specimen(s) being imaged. S07-100 A Note that the container ID is required, even though the container itself does not figure in the image.
Issuer of the Container Identifier Sequence (0040,0513) Organization that assigned the Container Identifier  
>Local Namespace Entity ID (0040,0031) Identifies an entity within the local namespace or domain. Case Medical Center
Container Type Code Sequence (0040,0518) Type of container that contains the specimen(s) being imaged. Zero or one items shall be permitted in this sequence This would likely be a default container value for all gross specimens. The LIS does not keep information on the gross container type, so this is an empty sequence.
Specimen Description Sequence (0040,0560)  Sequence of identifiers and detailed description of the specimen(s) being imaged. One or more Items shall be included in this Sequence.  
>Specimen Identifier (0040,0551)  A departmental information system identifier for the Specimen. S07-100 A Specimen and Container have same ID
>Issuer of the Specimen Identifier Sequence (0040,0562) The name or code for the institution that has assigned the Specimen Identifier.  
>> Local Namespace Entity ID (0040,0031) Identifies an entity within the local namespace or domain. Case Medical Center
>Specimen UID (0040,0554) Unique Identifier for Specimen 1.2.840.99790.986.33.1677.1.1.17.1  
>Specimen Short Description (0040,0600) Short textual specimen description Part A: LEFT UPPER LOBE The LIS "Specimen Received" field is mapped to this DICOM field
>Specimen Detailed Description (0040,0602) Detailed textual specimen description A: Received fresh for intraoperative consultation, labeled with the patient's name, number and "left upper lobe," is a pink-tan, wedge-shaped segment of soft tissue, 6.9 x 4.2 x 1.0 cm. The pleural surface is pink-tan and glistening with a stapled line measuring 12.0 cm. in length. The pleural surface shows a 0.5 cm. area of puckering. The pleural surface is inked black. The cut surface reveals a 1.2 x 1.1 cm, white-gray, irregular mass abutting the pleural surface and deep to the puckered area. The remainder of the cut surface is red-brown and congested. No other lesions are identified. Representative sections are submitted. This is a mapping from the LIS “Gross Description” field. Note that in Case S07-100 there were six parts. This means the LIS gross description field will have six sections (A - F). We would have to parse the gross description field into those parts (A-F) and then only incorporate section "A" into this attribute. NOTE: One could consider listing all the Blocks associated with Part A. It would be easy to do and might give useful information.
>Specimen Preparation Sequence (0040,0610) Sequence of Items identifying the process steps used to prepare the specimen for image acquisition. One or more Items may be present. This Sequence includes description of the specimen sampling step from a parent specimen, potentially back to the original part collection. (see Table NN.6-2)  
>>Specimen Preparation Step Content Item Sequence (0040,0612) Sequence of Content Items identifying the processes used in one preparation step to prepare the specimen for image acquisition. One or more Items may be present.
>Primary Anatomic Structure Sequence (0008,2228) Original anatomic location in patient of specimen. This location may be inherited from the parent specimen, or further refined by modifiers depending on the sampling procedure for this specimen. 
>>Code Value (0008,0100) T-28600 This is a code sequence item
>>Coding Scheme Designator (0008,0102) SRT
>>Code Meaning (0008,0104) Left Upper Lobe of Lung

Table NN.6-2 Specimen Preparation Sequence for Gross Specimen

Specimen Preparation Sequence - Item # Specimen Prep. Step Content Item Sequence - Item # Template / Row Value Type (0040,A040) Concept Name Code Sequence (0040,A043)
Container Identifier (0040,0512) The identifier for the container that contains the specimen(s) being imaged. S07-100 A 5 1
Issuer of the Container Identifier Sequence (0040,0513) Organization that assigned the Container Identifier  
>Local Namespace Entity ID (0040,0031) Identifies an entity within the local namespace or domain. Case Medical Center
Container Type Code Sequence (0040,0518) Type of container that contains the specimen(s) being imaged. Only a single item shall be permitted in this sequence This would likely be a default container value for all slide specimens.
>Code Value (0008,0100) G-81EA This is a code sequence item
>Coding Scheme Designator (0008,0102) SRT
>Code Meaning (0008,0104) Slide
Container Component Sequence (0040,0520) Description of one or more components of the container (e.g., description of the slide and of the coverslip). One or more Items may be included in this Sequence.  
>Container Component Type Code Sequence (0050,0012) Type of container component. One Item shall be included in this Sequence.
>>Code Value (0008,0100) A-0101D This is a code sequence item
>>Coding Scheme Designator (0008,0102) SRT
>>Code Meaning (0008,0104) Microscope slide cover slip
>Container Component Material (0050,001A) Material of container component. GLASS
Specimen Description Sequence (0040,0560)  Sequence of identifiers and detailed description of the specimen(s) being imaged. One or more Items shall be included in this Sequence.
>Specimen Identifier (0040,0551)  A departmental information system identifier for the Specimen. S07-100 A 5 1 Specimen and Container have same ID
>Issuer of the Specimen Identifier Sequence (0040,0562) The name or code for the institution that has assigned the Specimen Identifier.  
>>Local Namespace Entity ID (0040,0031) Identifies an entity within the local namespace or domain. Case Medical Center
>Specimen UID (0040,0554) Unique Identifier for Specimen 1.2.840.99790.986.33.1677.1.1.19.5  
>Specimen Short Description (0040,0600) Short textual specimen description Part A: LEFT UPPER LOBE, Block 5: Mass (2 pc), Slide 1: H&E This attribute concatenates four LIS fields: 1. Specimen Received, 2. Cassette Summary, 3. Number of Pieces in Block, 4. Staining. This does not always work this nicely. Often one or more of fields is empty or confusing. Note this field is limited to 64 characters
>Specimen Detailed Description (0040,0602) Detailed textual specimen description A: Received fresh for intraoperative consultation, labeled with the patient's name, number and "left upper lobe," is a pink-tan, wedge-shaped segment of soft tissue, 6.9 x 4.2 x 1.0 cm. The pleural surface is pink-tan and glistening with a stapled line measuring 12.0 cm. in length. The pleural surface shows a 0.5 cm. area of puckering. The pleural surface is inked black. The cut surface reveals a 1.2 x 1.1 cm, white-gray, irregular mass abutting the pleural surface and deep to the puckered area. The remainder of the cut surface is red-brown and congested. No other lesions are identified. Representative sections are submitted. Block 5: "Mass" (2 pieces) This is a mapping from the LIS Gross Description Field and the Block Summary. Note that in Case S07-100, there were six parts. This means the LIS gross description field will have six sections (A - F). We would have to parse the gross description field into those parts (A-F) and then only incorporate section "A" into this attribute. The same would be true of the Blocks. NOTE: One could consider listing all the Blocks associated with Part A. It would be easy to do and might give useful information.
>Specimen Preparation Sequence (0040,0610) Sequence of Items identifying the process steps used to prepare the specimen for image acquisition. One or more Items may be present. This Sequence includes description of the specimen sampling step from a parent specimen, potentially back to the original part collection. (see Table NN.6-4)  
>>Specimen Preparation Step Content Item Sequence (0040,0612) Sequence of Content Items identifying the processes used in one preparation step to prepare the specimen for image acquisition. One or more Items may be present.
>Primary Anatomic Structure Sequence (0008,2228) Original anatomic location in patient of specimen. This location may be inherited from the parent specimen, or further refined by modifiers depending on the sampling procedure for this specimen. 
>>Code Value (0008,0100) T-28600 This is a code sequence item
>>Coding Scheme Designator (0008,0102) SRT
>>Code Meaning (0008,0104) Left Upper Lobe of Lung

The example Specimen Preparation Sequence first describes the most recent processing of the slide (staining), then goes back to show its provenance. Notice that there is no sampling process for the slide described here; the LIS did not record the step of slicing of blocks into slides.

Table NN.6-4 Specimen Preparation Sequence for Slide

Specimen Preparation Sequence - Item # Specimen Prep. Step Content Item Sequence - Item # Template / Row Value Type (0040,A040) Concept Name Code Sequence (0040,A043) Example Value
1 TISSUE_INTENSITY NA Identity None NA
2 TISSUE_INTENSITY RGB1 = grayscale TISSUE_INTENSITY Grayscale Output = RGB1 Weight 1 = 1.0 (constant)
Weight 2 = 0.0 (constant)
3 TISSUE_INTENSITY RGB1 = f(TISSUE_INTENSITY) Colorized Output = RGB1 Weight 1 = 1.0 (constant)
Weight 2 = 0.0 (constant)
4 TISSUE_INTENSITY RGB1 = grayscale TISSUE_INTENSITY Grayscale Output = proportional summation of RGB1 and RGB2 Weight 1 = constant
FLOW_VELOCITY RGB2 = g(FLOW_VELOCITY) Colorized Weight 2 = constant
5 TISSUE_INTENSITY RGB1 = grayscale TISSUE_INTENSITY Grayscale Threshold based on FLOW_VELOCITY Weight 1 = 1 – Alpha 2
FLOW_VELOCITY RGB2 = g(FLOW_VELOCITY) Colorized Weight 2 = constant
6 TISSUE_INTENSITY RGB1 = grayscale TISSUE_INTENSITY Grayscale Threshold based on FLOW_VELOCITY (MSB) and FLOW_VARIANCE (LSB) with 2-dimensional color mapping Weight 1 = 1 - Alpha 2
FLOW_VELOCITY RGB2 = g(FLOW_VELOCITY, FLOW_ VARIANCE) Colorized Weight 2 = Alpha 2
FLOW_ VARIANCE Colorized
7 TISSUE_INTENSITY RGB1 = f(TISSUE_INTENSITY) Colorized Combination based on all data value inputs with colorized tissue and colorized 2-dimensional color mapping of flow and variance. Weight 1 = Alpha 1
FLOW_VELOCITY RGB2 = g(FLOW_VELOCITY, FLOW_ VARIANCE) Colorized Weight 2 = Alpha 2
FLOW_ VARIANCE Colorized

In the examples below, the following attributes are referenced:

Data Type (0018,9808)

Data Path Assignment (0028,1402)

Bits Mapped to Color Lookup Table (0028,1403)

Blending LUT 1 Transfer Function (0028,1405)

Blending LUT 2 Transfer Function (0028,140D)

Blending Weight Constant (0028,1406)

RGB LUT Transfer Function (0028,140F)

Alpha LUT Transfer Function (0028,1410)

Red Palette Color Lookup Table Descriptor (0028,1101)

Red Palette Color Lookup Table Data (0028,1201)

Green Palette Color Lookup Table Descriptor (0028,1102)

Green Palette Color Lookup Table Data (0028,1202)

Blue Palette Color Lookup Table Descriptor (0028,1103)

Blue Palette Color Lookup Table Data (0028,1203)

Alpha Palette Color Lookup Table Descriptor (0028,1104)

Alpha Palette Color Lookup Table Data (0028,1204)