Correct code for microscope slide and add staining codes to example Status Final Text Date of Last Update 2022/01/15 Person Assigned David Clunie Submitter Name IDC Submission Date 2021/06/01 Correction Number CP-2143 Log Summary: Correct code for microscope slide and add staining codes to example Name of Standard PS3.16, PS3.17 2021e Rationale for Correction: Different codes are used for "slide" in CID 8101 and the PS3.17 Annex NN example. At first sight these appear to be duplicate concepts, but they are differently placed in the SNOMED CT hierarchy - one is a specimen and the other is a physical object: SCT: 258661006 Slide (specimen) SCT: 433466003 Microscope slide (physical object). Note that in HL7, slides are modeled as "containers". A "slide" (258661006) that contains tissue is different from the physical object that is the piece of glass (433466003) itself +/- the specimen component +/- the coverslip (433472003) +/- the mounting media (430862008). Since all the other concepts in the Container Types Context Group are physical objects, continue to use 433466003, and update the example. UMLS regards 258661006 and 433466003 as the same (C1705201). This use is distinct from the use in CID 8103, which is for specimen types. where the use of the inactivated 258661006 concept needs to be replaced with the new 1179252003. Also, add staining codes rather than using plain text in the example, which is poor practice. [Ed.Note: SNOMED CRS Request ID#761891 regarding potentially duplicate codes for slides - SNOMED response "Upon review we made a few changes associated with this request. We have inactivated 258661006 |Slide (specimen)| and referred to a new concept 1179252003 |Slide submitted as specimen (specimen)|. There are cases where a slide (e.g., adhesive slide with specimen) are submitted as the specimen. This is certainly distinct from the plain device itself (e.g., 433466003 Microscope slide (physical object)), which does not imply inclusion of any tissue, coverslip, etc. 1179252003 |Slide submitted as specimen (specimen)| could be used to represent a slide submitted as a specimen which may contain any number of tissues, cells, organisms, media, etc."] Correction Wording:

Amend DICOM PS3.16 as follows:

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Container Types

Coding Scheme Designator	Code Value	Code Meaning	SNOMED-RT ID	UMLS Concept Unique ID
SCT	434464009	Tissue cassette	A-0101E	C0183953
SCT	434708008	Tissue microarray cassette	A-01022	C2315967
SCT	434746001	Specimen vial	A-01024	C2316421
SCT	433466003	Microscope slide	A-0101B	C0026017
SCT	434711009	Specimen container	A-01023	C0183391
SCT	434533009	Electron microscopy grid	A-01021	C2316945
SCT	434822004	Specimen well	A-01025	C2316030

The SNOMED CT concepts for physical objects rather than corresponding concepts for specimens are used in this Context Group. I.e., (433466003, SCT, "Microscope slide (physical object)") is used rather than (258661006, SCT, "Slide (specimen)") (now inactivated) or (1179252003, SCT, "Slide submitted as specimen (specimen)". (C0026017, UMLS, "Slide") does not make the distinction.

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Container Component Types

Coding Scheme Designator	Code Value	Code Meaning	SNOMED-RT ID	UMLS Concept Unique ID
Include
SCT	433472003	Microscope slide cover slip	A-0101D	C0492717
SCT	430862008	Microscope slide mounting media	F-62219	C2316989
SCT	434473001	Specimen container lid	A-0101F	C2316420

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Anatomic Pathology Specimen Types

Coding Scheme Designator	Code Value	Code Meaning	SNOMED-RT ID	UMLS Concept Unique ID
SCT	38266002	Entire body	T-D0010	C0229960
SCT	309050000	Body substance sample	G-80A5	C0586522
SCT	309051001	Body fluid sample	G-80A6	C1292527
SCT	119376003	Tissue specimen	G-8300	C1292533
SCT	430861001	Gross specimen	G-843A	C2316367
SCT	430856003	Tissue section	G-8439	C2316368
SCT	430970004	Core sample of tissue block	G-843B	C2316369
SCT	431196006	Tissue spot	G-843C	C2316370
SCT	258661006	Slide	G-81EA	C0444330
SCT	1179252003	Slide
SCT	258433009	Smear sample	G-803C	C0444086
SCT	430855004	Touch preparation cytologic material	T-1A404	C2316942
SCT	430346005	Liquid based cytologic material	T-1A403	C2315942
SCT	119295008	Aspirate	G-8003	C0370199
SCT	258562007	Genetic sample	G-81A0	C0444241
Include

The SNOMED CT concepts for specimens rather than corresponding concepts for physical objects are used in this Context Group. (258661006, SCT, "Slide (specimen)") has been inactivated by SNOMED and replaced with (1179252003, SCT, "Slide submitted as specimen (specimen)".

SNOMED Codes Retired from DICOM Use

Retired Code Value	Code Meaning	Replacement Code	Notes
258661006	Slide	1179252003	Replacement code has meaning of "Slide submitted as specimen (specimen)". Retired code is inactive in SNOMED CT.

Amend DICOM PS3.17 as follows:

This is an example of how the Specimen Module can be populated for a slide (from a lung lobe resection received from surgery). The associated image would be a whole slide image.

Specimen Module for a Slide

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 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)		258661006 433466003	This is a code sequence item
>Coding Scheme Designator	(0008,0102)		SCT
>Code Meaning	(0008,0104)		Slide Microscope 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)		433472003	This is a code sequence item
>>Coding Scheme Designator	(0008,0102)		SCT
>>Code Meaning	(0008,0104)		Microscope slide coverslip
>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. 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. 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 )
>>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)		44714003	This is a code sequence item
>>Coding Scheme Designator	(0008,0102)		SCT
>>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.

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	Comments
1	1	8001 / 1	TEXT	(121041, DCM, "Specimen Identifier")	S07-100 A	Part Collection in OR.
	2	8001 / 2	TEXT	(111724, DCM, "Issuer of Specimen Identifier")	Case Medical Center
	3	8001 / 3	CODE	(111701, DCM, "Processing type")	(17636008, SCT, "Specimen collection")
	4	8001 / 4	DATETIME	(111702, DCM, "DateTime of processing")	200703230827
	5	8001 / 5	TEXT	(111703, DCM, "Processing step description")	Taken
	6	8001 / 8 8002 / 1	CODE	(111704, DCM, "Sampling Method")	(65801008, SCT, "Excision")
2	1	8001 / 1	TEXT	(121041, DCM, "Specimen Identifier")	S07-100 A	Specimen received in Pathology department
	2	8001 / 2	TEXT	(111724, DCM, "Issuer of Specimen Identifier")	Case Medical Center
	3	8001 / 3	CODE	(111701, DCM, "Processing type")	(428995007, SCT, "Specimen Receiving")
	4	8001 / 4	DATETIME	(111702, DCM, "DateTime of processing")	200703230943
3	1	8001 / 1	TEXT	(121041, DCM, "Specimen Identifier")	S07-100 A 5	Sampling to block
	2	8001 / 2	TEXT	(111724, DCM, "Issuer of Specimen Identifier")	Case Medical Center
	3	8001 / 3	CODE	(111701, DCM, "Processing type")	(433465004, SCT, "Sampling of tissue specimen")
	4	8001 / 5	TEXT	(111703, DCM, "Processing step description")	Block Creation
	5	8001 / 8 8002 / 1	CODE	(111704, DCM, "Sampling Method")	(122459003, SCT, "Dissection")
	6	8001 / 8 8002 / 2	TEXT	(111705, DCM, "Parent Specimen Identifier")	S07-100 A
	7	8001 / 8 8002 / 3	TEXT	(111706, DCM, "Issuer of Parent Specimen Identifier")	Case Medical Center
	8	8001 / 8 8002 / 4	CODE	(111707, DCM, "Parent specimen type")	(38866009, SCT, "Anatomic part")
	9	8001 / 8 8002 / 6	TEXT	(111709, DCM, "Location of sampling site")	Mass	This is coming from the summary of blocks field in the LIS
4	1	8001 / 1	TEXT	(121041, DCM, "Specimen Identifier")	S07-100 A 5	Block Processing
	2	8001 / 2	TEXT	(111724, DCM, "Issuer of Specimen Identifier")	Case Medical Center
	3	8001 / 3	CODE	(111701, DCM, "Processing type")	(9265001, SCT, "Specimen Processing")
	4	8001 / 4	DATETIME	(111702, DCM, "DateTime of processing")	200703231900
	5	8001 / 5	TEXT	(111703, DCM, "Processing step description")	Standard Block Processing (Formalin)
	6	8001 / 10	CODE	(430864009, SCT, "Tissue Fixative")	(111095003, SCT, "Formalin")
5	1	8001 / 1	TEXT	(121041, DCM, "Specimen Identifier")	S07-100 A 5	Block embedding
	2	8001 / 2	TEXT	(111724, DCM, "Issuer of Specimen Identifier")	Case Medical Center
	3	8001 / 3	CODE	(111701, DCM, "Processing type")	(9265001, SCT, "Specimen Processing")
	4	8001 / 4	DATETIME	(111702, DCM, "DateTime of processing")	200703240500
	5	8001 / 5	TEXT	(111703, DCM, "Processing step description")	Embedding (paraffin)
	6	8001 / 11	CODE	(430863003, SCT, "Embedding medium")	(255667006, SCT, "Paraffin")
6	1	8001 / 1	TEXT	(121041, DCM, "Specimen Identifier")	S07-100 A 5 1	Slide Staining
	2	8001 / 3	CODE	(111701, DCM, "Processing type")	(127790008, SCT, "Staining")
	3	8001 / 4	DATETIME	(111702, DCM, "DateTime of processing")	200703240700
	4	8001 / 9 8003 / 21	TEXTCODE	(424361007, SCT, "Using substance")	H&E (1)(12710003, SCT, "hematoxylin stain")
	5	8001 / 9 8003 / 1	CODE	(424361007, SCT, "Using substance")	(36879007, SCT, "water soluble eosin stain")