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)