CP-2082 Add acquisition codes and template for fluorescence and immunohistochemistry in microscopy <informaltable rules="all" frame="box"> <tr> <td rowspan="1" colspan="1" valign="top"><para>Status</para></td> <td rowspan="1" colspan="1" valign="top"><para>Assigned</para></td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"><para>Date of Last Update</para></td> <td rowspan="1" colspan="1" valign="top"><para>2022/04/25</para></td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"><para>Person Assigned</para></td> <td rowspan="1" colspan="1" valign="top"><para>David Clunie</para><para><link xl:href="mailto:dclunie@dclunie.com"/></para></td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"><para>Submitter Name</para></td> <td rowspan="1" colspan="1" valign="top"><para>IDC</para><para><link xl:href="mailto:dclunie@dclunie.com"/></para></td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"><para>Submission Date</para></td> <td rowspan="1" colspan="1" valign="top"><para>2020/09/28</para></td> </tr> </informaltable> <informaltable rules="all" frame="box"> <tr> <td rowspan="1" colspan="1" valign="top"><para>Correction Number CP-2082</para></td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"><para>Log Summary: Add acquisition codes and template for fluorescence and immunohistochemistry in microscopy</para></td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"> <para>Name of Standard</para> <para>PS3.6, PS3.16, PS3.17</para> </td> </tr> <tr> <td rowspan="1" colspan="1" valign="top"><para>Rationale for Correction:</para> <para>Immunohistochemistry involves a process similar to conventional staining but does not use traditional staining agents. Instead it uses a substance (such as a monoclonal antibody) that is taken up by a receptor, to which is attached some means of visualizing that substance (e.g., a chromogen, a substance, itself without definite color, which may be transformed into a pigment, or a fluorophore, a fluorescent chemical compound that can re-emit light upon light excitation).</para> <para>Accordingly, a new "Processing Type" of "Immunohistochemistry procedure" is added, with a corresponding templates and context groups to describe the "Component investigated" and the chromogen or fluorophore, as well as various other related attributes.</para> <para>Also, it has become apparent that not all stains are valid substances, staining methods may involve complex processes and multiple substances, and SNOMED is invalidating these concepts, so DICOM needs to describe these by their technique code instead of a substance (that does not exist in the real world, e.g., an "acid-fast stain substance").</para> <para>Also, when an excitation wavelength is not know, but it is known that fluorescence was performed, add a generic "narrow" (spectrum) value to use for the (required) illuminant.</para> <para>Also, change all templates to make order not significant, since the interpretation of the content items is not dependent on their order.</para> <para><emphasis role="italic">[Ed.Note: Using SCT:246094008 "Component investigated" rather than C25702,NCIt,"Target" .]</emphasis></para> <para><emphasis role="italic">[Ed.Note: ? use 406858009,SCT,"Fluorescent staining" rather than 117617002, SCT, "Immunohistochemistry", since not all fluorescent stains use antibodies (e.g., phalloidin (a toxin) for staining actin).]</emphasis></para> <para><emphasis role="italic">[Ed.Note: Channel is allowed to be 1-n, but what does this mean (same step used for multiple optical paths, e.g., DAPI process repeated multiple times?) - should probably just repeat it.]</emphasis></para> <para><emphasis role="italic">[Ed.Note: GH: Defined for IHE APSR; re-use codes (for DICOM Specimen Preparation Sequence Content Item) as TID 8001: Row 3: DCM:111701 "Processing Type" = SCT:117617002 "Immunohistochemistry procedure"; New Row: SCT:246094008 "Component investigated" (no children) (? SCT:259943009 "Cellular analyte" or SCT:259776003 "Immunology analyte" or SCT:259777007 "Immunochemistry analyte", or SCT:116647005 "Receptor" (which is parent of things like ER)) = SCT:23307004 "Estrogen receptor" (etc.). Need to make list of SCT components for receptors etc.]</emphasis></para> <para><emphasis role="italic">[Ed.Note: CRS Request ID #nnnnnn to add to subset 703857004, 708056006, 246094008, 406858009, 117617002, 406979008 - sync with changes in SNOMED to technique (qualifier value).]</emphasis></para> <para><emphasis role="italic">[Ed.Note: CRS Request ID #769287 to add "Narrow spectrum" to use in place of generic qualifier value 134223000 "Narrow"]</emphasis></para> <para><emphasis role="italic">[Ed.Note: TBD. PS3.17 examples of DAPI-AT, Alexa 647 KI-67, HRP DAB KI-67, Alexa Fluor 350 Phalloidin, or similar]</emphasis></para> <para><emphasis role="italic">[Ed.Note: CRS Request ID #769280 - inactivate 406976001|Acid fast stain (substance) - SNOMED has also inactivated 67122001 | Acid fast stain method (procedure) and replaced it with 708056006 | Acid fast stain technique (qualifier value)</emphasis></para> <para><emphasis role="italic">[Ed.Note: Will need new technique (qualifier value) for Z-N (currently a procedure) (CRS#769280)]</emphasis></para> <para><emphasis role="italic">[Ed.Note: Is there going to be a technique (qualifier value) replacement for 104210008 Hematoxylin and eosin stain method (CRS#769280)]</emphasis></para> <para><emphasis role="italic">[Ed.Note: Will SNOMED retire 127790008 Staining method (procedure) (CRS#769280)? Replace with 703857004 | Staining technique (qualifier value) in template and context groups for now, to illustrate the impact of this upcoming SNOMED change.]</emphasis></para> <para><emphasis role="italic">[Ed.Note; Should just remove "staining" entry from CID 8130 Staining Protocols (rather than replacing 127790008 with 703857004), since otherwise just results in staining = staining, which is meaningless.]</emphasis></para> <para><emphasis role="italic">[Ed.Note: Should the removal/replacement of stain substances that are not real substances like 406976001 Acid fast stain (substance) (CRS ID#769280) be done in a separate CP?]</emphasis></para> <para><emphasis role="italic">[Ed.Note: TBD. Replace other uses of DCM codes for ER etc. with SCT.? separate CP]</emphasis></para> </td> </tr> <tr> <td rowspan="1" colspan="1" valign="top">Correction Wording:</td> </tr> </informaltable> </chapter> <chapter> <title/> <informaltable rules="all" frame="box"> <tr> <td> <para><emphasis role="italic">Amend DICOM PS3.16 as follows (changes to existing text are bold and <emphasis role="bold"><emphasis role="underline">underlined</emphasis></emphasis> for additions and <emphasis role="bold"><emphasis role="strikethrough">struckthrough</emphasis></emphasis> for removals):</emphasis></para> </td> </tr> </informaltable> <section label="TID 8001" status="3" xml:id="sect_TID_8001"> <title>Specimen Preparation This Template describes a single specimen preparation step. Type: Extensible Order: Non-Significant Root: No
Specimen Preparation
VT Concept Name VM Req Type Condition Value Set Constraint
1 TEXT EV (121041, DCM, "Specimen Identifier") 1 M
2 TEXT EV (111724, DCM, "Issuer of Specimen Identifier") 1 U
3 CODE EV (111701, DCM, "Processing type") 1 M D
4 DATETIME DT (111702, DCM, "DateTime of processing") 1 U
5 TEXT DT (111703, DCM, "Processing step description") 1 U
6 CODE DT (111703, DCM, "Processing step description") 1 U D
6b TEXT EV (255592004, SCT, "Channel") 1-n U
6c TEXT EV (C25472, NCIt, "Cycle") 1 U
6d TEXT EV (ddd003, DCM, "Subcycle") 1 U
7 CODE DT (17636008, SCT, "Specimen Collection") 1 MC IFF Row 3 Processing Type value is (17636008, SCT, "Specimen Collection") B
8 INCLUDE D 1 MC IFF Row 3 Processing Type value is (433465004, SCT, "Specimen Sampling")
9 INCLUDE D 1 MC IFF Row 3 Processing type value is (127790008, SCT, "Staining") (703857004, SCT, "Staining")
9b INCLUDE D 1 MC IFF Row 3 Processing type value is (117617002, SCT, "Immunohistochemistry")
10 CODE DT (430864009, SCT, "Tissue Fixative") 1 U B
11 CODE DT (430863003, SCT, "Embedding medium") 1 U B
Content Item Descriptions ... Row 6b May be used to indicate which Optical Path Identifier (0048,0106) value(s) in the image corresponds to this processing step, such as when different substances with different fluorescent characteristics are used simultaneously. Rows 6c, 6d May be used to describe in which cycle or sub-cycle of a multi-cycle procedure (e.g., successive cycle of clearing and staining) this step was performed. Rows 3, 9 Previously, (127790008, SCT, "Staining method (procedure)") was used with the meaning "Staining", but has been replaced by (703857004, SCT, "Staining technique (qualifier value)").
Specimen Sampling Type: Extensible Order: Non-Significant Root: No
Specimen Sampling
VT Concept Name VM Req Type Condition Value Set Constraint
1 ...
Specimen Staining Type: Extensible Order: Non-Significant Root: No
Specimen Staining
VT Concept Name VM Req Type Condition Value Set Constraint
1 CODE DT (424361007, SCT, "Using substance") 1-n MC IF Rows 2, 3, 4 not present D
2 TEXT DT (424361007, SCT, "Using substance") 1 MC IF Rows 1, 3, 4 not present
3 CODE DT (703857004, SCT, "Staining") 1 MC IF Rows 1, 2, 4 not present D
4 TEXT DT (703857004, SCT, "Staining") 1 MC IF Rows 1, 2, 3 not present
Specimen Localization Type: Extensible Order: Non-Significant Root: No
Specimen Localization
VT Concept Name VM Req Type Condition Value Set Constraint
1 ...
Add new templates to DICOM PS3.16:
Immunohistochemistry Type: Extensible Order: Non-Significant Root: No
Immunohistochemistry
VT Concept Name VM Req Type Condition Value Set Constraint
1 CODE EV (246094008, SCT, "Component investigated") 1 MC IF Row 2 not present D
2 TEXT EV (246094008, SCT, "Component investigated") 1 MC IF Row 1 not present
3 CODE EV (C2480, NCIt, "Tracer") 1 U D
4 INCLUDE 1 MC IFF Row 3 Tracer value is (ddd001, DCM, "Chromogen")
5 INCLUDE 1 MC IFF Row 3 Tracer value is (C0598447, UMLS, "Fluorophore")
6 CODE EV (424361007, SCT, "Using substance") 1-n U
7 TEXT EV (424361007, SCT, "Using substance") 1 U
8 CODE DT (703857004, SCT, "Staining technique") 1 U D
9 TEXT DT (703857004, SCT, "Staining technique") 1 U
10 TEXT EV (C37925, NCIt, "Clone") 1 U
11 TEXT EV (C0947322, UMLS, "Manufacturer Name") 1 U
12 TEXT EV (111529, DCM, "Brand Name") 1 U
13 NUMERIC EV (C4281604, UMLS, "Dilution") 1 U UNITS = EV (1, UCUM, "No units")
14 NUMERIC EV (255592004, SCT, "Exposure Time") 1 U UNITS = DT (s, UCUM, "s")
Content Item Descriptions Rows 1, 2 Describes the target of the process. Either a CODE or TEXT or both may be present.
Color Immunohistochemistry Type: Extensible Order: Non-Significant Root: No
Color Immunohistochemistry
VT Concept Name VM Req Type Condition Value Set Constraint
1 CODE EV (ddd001, DCM, "Chromogen") 1 UC IF Row 2 not present D
2 TEXT EV (DCM_ddd001, DCM, "Chromogen") 1 UC IF Row 1 not present
3 CODE EV (ddd002, DCM, "Reporter enzyme") 1 UC IF Row 4 not present D
4 TEXT EV (DCM_ddd002, DCM, "Reporter enzyme") 1 UC IF Row 3 not present
Content Item Descriptions Rows 1, 2 Either a CODE or TEXT or both may be present. Rows 3, 4 Either a CODE or TEXT or both may be present.
Fluorescence Immunohistochemistry Type: Extensible Order: Non-Significant Root: No
Fluorescence Immunohistochemistry
VT Concept Name VM Req Type Condition Value Set Constraint
1 CODE EV (C0598447, UMLS, "Fluorophore") 1 UC IF Row 1 not present D
2 TEXT EV (C0598447, UMLS, "Fluorophore") 1 UC IF Row 2 not present
Content Item Descriptions Rows 1, 2 Either a CODE or TEXT or both may be present.
Add new context groups to DICOM PS3.16:
Specimen Components Investigated Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: yyyymmdd UID: uuux8116
Specimen Components Investigated
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 23307004 Estrogen receptor F-B8520 C0034804
SCT 61078009 Progesterone receptor F-B8550 C0034833
SCT 44368005 Oncogene protein HER-2/neu F-E3260 C0069515
NCIt C17675 KI-67 Antigen C0208804
NCIt C94697 PDCD1 C0135710
UMLS C2744928 Adenine-Thymine C2744928
Immunohistochemistry Tracer Type Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: yyyymmdd UID: uuux8117
Immunohistochemistry Tracer Type
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
DCM ddd001 Chromogen
UMLS C0598447 Fluorophore C0598447
Chromogens for Immunohistochemistry Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: yyyymmdd UID: uuux8118
Chromogens for Immunohistochemistry
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
PUBCHEM_CID 8588 Aminoethyl carbazole
PUBCHEM_CID 7071 Diaminobenzidine
PUBCHEM_CID 41206 Tetramethylbenzidine
PUBCHEM_CID 11787 Chloronaphthol
Reporter Enzymes for Immunohistochemistry Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: yyyymmdd UID: uuux8119
Reporter Enzymes for Immunohistochemistry
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 64652000 Horseradish peroxidase C-30781 C0019941
SCT 57056007 Alkaline phosphatase F-6A2F8 C0002059
Fluorophores for Immunohistochemistry Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: yyyymmdd UID: uuux8129
Fluorophores for Immunohistochemistry
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
C122989 NCIt DAPI C0057142
C0062907 UMLS Hoechst 33342 C0062907
Alexa Fluor 488
C4278267 UMLS Alexa Fluor 555 C4278267
C3489916 UMLS Alexa Fluor 647 C3489916
Amend DICOM PS3.16 as follows (changes to existing text are bold and underlined for additions and struckthrough for removals):
Specimen Preparation Procedure Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20080626yyyymmdd UID: 1.2.840.10008.6.1.1049
Specimen Preparation Procedure
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID HL7 v3 ActClass equivalent
SCT 17636008 Specimen collection P3-02000 C0200345 SPECCOLLECT
SCT 428995007 Specimen receiving P3-05013 C1997702 CONTREG
SCT 433465004 Sampling of tissue specimen P3-4000A C2316400 PROC
SCT 127790008 703857004 Staining P3-00003 R-FBDF9 C0487602 C3839348 SPCTRT
SCT 9265001 Specimen processing P3-05000 C0037793 SPCTRT
DCM 111729 Specimen storage STORE
SCT 117617002 Immunohistochemistry P3-44150 C0021044
Previously, (127790008, SCT, "Staining method (procedure)") was used with the meaning "Staining", but has been replaced by (703857004, SCT, "Staining technique (qualifier value)").
Specimen Stains Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20190817yyyymmdd UID: 1.2.840.10008.6.1.1050
Specimen Stains
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 406976001 acid fast stain C-22860 C1318720
SCT 255792001 acid phosphatase stain C-2280A C0440036
SCT 255793006 Albert's stain C-2280B C0440037
SCT 4656000 alcian blue 8GX stain C-22963 C0001933
SCT 47995002 alcohol soluble nigrosine stain C-22932 C0303908
SCT 406981005 aldehyde fuchsin stain C-2286D C0491984
SCT 54432009 alizarin blue S stain C-22961 C0303917
SCT 21951008 alizarin cyanine green stain C-22959 C0303916
SCT 65580004 alizarin red S stain C-22953 C0051165
SCT 27016007 alizarin yellow GG stain C-22813 C0303861
SCT 28622002 alizarin yellow R stain C-22814 C0619792
SCT 406971006 alkaline phosphatase stain C-2285B C1318717
SCT 406990003 aniline blue stain C-2287E C1321796
SCT 255794000 auramine stain C-2280C C0440038
SCT 85066006 azo black stain C-22873 C0058437
SCT 76048000 azocarmine G (GX) stain C-22929 C0303907
SCT 35609001 azophloxin stain C-22842 C0073022
SCT 2159007 azorubin S stain C-22831 C0002406
SCT 16836001 azure A stain C-22945 C0052826
SCT 8926000 azure B stain C-22946 C0052827
SCT 11069001 azure C stain C-22944 C0052828
SCT 406982003 bauer's chromic acid leucofuchsin stain C-2286E C1318723
SCT 27844007 benzo fast scarlet stain C-22872 C0303882
SCT 255795004 beta-glucuronidase stain C-2280D C0440039
SCT 76605005 biebrich scarlet stain C-22866 C0303878
SCT 44488008 bismark brown R stain C-22849 C0303872
SCT 85190005 bismark brown Y stain C-22848 C0303871
SCT 1346008 blue shade eosin stain C-22921 C0303904
SCT 41750006 brazilin stain C-22965 C0054031
SCT 8342001 brilliant cresyl blue stain C-22934 C0054052
SCT 86541009 brilliant crocein stain C-22869 C0303880
SCT 8429000 brilliant orange stain C-22865 C0303877
SCT 57753006 brilliant yellow stain C-22857 C0058441
SCT 406955006 butyrate esterase stain C-2283C C1321545
SCT 764166003 carbol fuchsin stain C0054697
SCT 73892005 carmine stain C-22971 C0007250
SCT 432003 carminic acid stain C-22972 C0054801
SCT 37575004 carmoisine A stain C-22822 C0052799
SCT 38707008 celestine blue B stain C-22936 C0055019
SCT 255796003 chloroacetate esterase stain C-2280E C0440040
SCT 406986000 chromic acid stain C-2287B C1321562
SCT 85981002 chromotrope 2R stain C-22838 C0109683
SCT 10247008 chrysoidine R stain C-22806 C0109694
SCT 16943008 chrysoidine Y stain C-22805 C0055663
SCT 91606004 cochineal stain C-22973 C0110382
SCT 406952009 colloidal iron stain C-22837 C1318877
SCT 45106005 Congo red stain C-22851 C0009742
SCT 406960005 cresyl echt violet stain C-22847 C1318879
SCT 406959000 cresyl violet stain C-22840 C0056484
SCT 68459007 crystal ponceau stain C-22833 C0303867
SCT 89028002 curcumin stain C-22966 C0010467
SCT 72572003 diamond black stain C-22826 C0303866
SCT 11780008 durazol red stain C-22871 C0303881
SCT 40076005 erie garnet stain C-22852 C0303873
SCT 58631000 eriochrome blue black SE stain C-22839 C0059526
SCT 7434003 erythrosin B stain C-22924 C0014824
SCT 5043000 erythrosin Y stain C-22923 C0303905
SCT 22931006 Evans blue stain C-22854 C0015205
SCT 34700000 fast blue B salt stain C-22883 C0303888
SCT 91295002 fast blue BB salt stain C-22881 C0060085
SCT 64112001 fast blue RR salt stain C-22878 C0303885
SCT 89148006 fast garnet GBC salt stain C-22882 C0303887
SCT 24167004 fast green FCF stain C-22886 C0060087
SCT 40718007 fast red B salt stain C-22876 C0303883
SCT 47486002 fast red ITR stain C-22877 C0303884
SCT 76633005 fast red TR salt stain C-22875 C0950478
SCT 88660000 fast sulfon black F stain C-22867 C0303879
SCT 72371006 fast violet B salt stain C-22879 C0303886
SCT 76439002 fat red 7B stain C-22859 C0117300
SCT 255797007 Feulgen reaction stain C-2280F C0440041
SCT 255798002 field's stain C-22810 C0440042
SCT 255799005 Flagellar stain C-22816 C0440043
SCT 35352008 fluorescent stain C-22A00 C0303920
SCT 406980006 fouchet stain C-2286C C1318722
SCT 60920007 fuchsin acid stain C-22902 C0252873
SCT 50062004 fuchsin basic stain C-22889 C0073578
SCT 8836009 gallocyanine stain C-22935 C0061013
SCT 373646006 giemsa stain F-61968 C0017542
SCT 385484003 gram stain C-22830 C0061856
SCT 406983008 hansel stain C-2286F C1318724
SCT 75956008 hematein stain C-22967 C0062204
SCT 12710003 hematoxylin stain C-22968 C0018964
SCT 255800009 immunofluorescent stain C-22817 C0183489
SCT 406972004 India ink stain C-2285C C0123471
SCT 45475000 indigo carmine stain C-22962 C0021219
SCT 11727009 indophenol from naphthol stain C-22927 C0303906
SCT 47030008 insoluble berlin blue stain C-22974 C0303918
SCT 68263003 janus green B stain C-22804 C0064136
SCT 255801008 Jenner-Giemsa stain C-22818 C0440044
SCT 29342009 kenacid blue R stain C-22899 C0303892
SCT 35724001 lacmoid stain C-22942 C0303910
SCT 255802001 Leishman stain C-22819 C0440052
SCT 89139001 light green SF stain C-22887 C0064970
SCT 6701008 lissamine fast red B stain C-22841 C0303868
SCT 25079009 lissamine fast yellow stain C-22843 C0303869
SCT 38543004 lissamine green B stain C-22914 C0061890
SCT 111102009 lissamine rhodamine stain C-22917 C0303900
SCT 406958008 luxol fast blue stain C-2283F C0065274
SCT 27120008 malachite green stain C-22890 C0065555
SCT 406953004 Mallory bleach stain C-2283A C1318878
SCT 46139004 martius yellow stain C-22802 C0303860
SCT 255803006 may-Grunwald giemsa stain C-2281A C0065757
SCT 24516006 meldola blue stain C-22937 C0065912
SCT 54791001 metanil yellow stain C-22811 C0066052
SCT 9010006 methyl blue stain C-22907 C0303897
SCT 255804000 methyl green pyronin stain C-2281B C0440045
SCT 42248000 methyl orange stain C-22809 C0066274
SCT 13744001 methyl red stain C-22808 C0066279
SCT 387239001 methyl violet stain F-61A76 C0017440
SCT 6725000 methylene blue stain C-22947 C0025746
SCT 406961009 methylene violet stain C-2284A C0492805
SCT 31260003 methylene violet stain (Bernthsen) C-22952 C0303911
SCT 406991004 modified trichrome stain C-2287F C1318726
SCT 406964001 mucicarmine stain C-2284B C0066912
SCT 255805004 myeloperoxidase stain C-2281C C0440053
SCT 16788000 naphthalene black 12B stain C-22846 C0303870
SCT 14958002 naphthol green B stain C-22801 C0303859
SCT 111101002 naphthol yellow S stain C-22803 C0068424
SCT 406973009 naphthol-AS-D-chloracetate esterase stain C-2285D C1318718
SCT 67956008 neutral red stain C-22928 C0027941
SCT 255806003 neutrophil alkaline phosphatase stain C-2281D C0440046
SCT 31714001 new fuchsin stain C-22891 C0068661
SCT 406965000 night blue stain C-2284C C0068751
SCT 77073008 nile blue stain C-22941 C0068765
SCT 86750008 nitrazine yellow stain C-22823 C0068806
SCT 255807007 nonspecific esterase stain C-2281E C0440047
SCT 78869007 nuclear fast red stain C-22955 C0303913
SCT 40808006 oil red O stain C-22863 C0069388
SCT 54221006 orange G stain C-22832 C0069591
SCT 25941002 orange II stain C-22824 C0069592
SCT 406966004 orcein stain C-2284D C0069596
SCT 5442001 page blue 83 stain C-22901 C0303893
SCT 2088005 page blue G-90 stain C-22898 C0056270
SCT 48540004 patent blue V sodium salt stain C-22885 C0116465
SCT 255808002 periodic acid Schiff stain C-2281F C0440048
SCT 333111009 permethrin stain R-F748A C1446695
SCT 406974003 peroxidase stain C-2285E C1318719
SCT 71957009 phloxin B stain C-22922 C0031567
SCT 406967008 phosphotungstic acid-hematoxylin stain C-2284E C0491956
SCT 65730007 ponceau 3R stain C-22829 C0071718
SCT 89856006 ponceau S stain C-22868 C0071720
SCT 70520000 ponceau xylidine stain C-22828 C0950345
SCT 89577003 pontamine sky blue 5BX stain C-22855 C0303874
SCT 80305003 pontamine sky blue 6BX stain C-22856 C0303875
SCT 34763001 potassium hydroxide stain C-10330 C0071767
SCT 24900003 procion brilliant blue MRS stain C-22956 C0303914
SCT 406993001 protargol S stain C-2288A C0492806
SCT 406452004 Prussian blue stain C-13036 C0060234
SCT 406968003 quinacrine fluorescent stain C-2284F C1318715
SCT 406977005 rhodamine stain C-2286A C0600322
SCT 255810000 Romanowsky stain C-2282A C0440055
SCT 408742009 rose bengal stain R-10223 C0035857
SCT 15529003 rosolic acid sodium salt stain C-22908 C0303898
SCT 38271009 saffron stain C-22964 C0162753
SCT 406988004 safranin stain F-61DA5 C0073949
SCT 406985001 silver nitrate stain C-2287A C1321600
SCT 406951002 silver stain C-22836 C1318876
SCT 51567006 sirius red F3B stain C-22874 C0071047
SCT 43549000 solochrome azurine (BS) stain C-22912 C0303899
SCT 11201005 solochrome black 6B stain C-22821 C0303864
SCT 25091000 solochrome cyanine R stain C-22909 C0074807
SCT 38902009 solochrome dark blue stain C-22825 C0054495
SCT 64991008 soluble berlin blue stain C-22975 C0303919
SCT 11645004 spirit soluble aniline blue stain C-22906 C1260876
SCT 83600004 spirit soluble eosin stain C-22920 C0303903
SCT 255811001 spore stain C-2282B C0440049
SCT 314900004 Sudan stain C-2282D C1282434
SCT 22968009 sunset yellow FCF stain C-22827 C0060120
SCT 21592006 tartrazine stain C-22844 C0039329
SCT 406975002 terminal deoxynucleotidyl transferase stain C-2285F C0687124
SCT 406995008 thioflavine S stain C-2288D C0952039
SCT 61068006 thioflavine T stain C-22926 C0076466
SCT 406969006 thionin stain C-22850 C0076494
SCT 12001002 thionine stain C-22943 C0076494
SCT 84217005 titan yellow stain C-22845 C0076731
SCT 406989007 trichrome stain C-2287D C0077066
SCT 35094004 tropaeolin O stain C-22815 C0303863
SCT 53511009 tropaeolin OO stain C-22812 C0077384
SCT 60441008 trypan blue stain C-22853 C0041213
SCT 406957003 Van Gieson stain C-2283E C0491963
SCT 406992006 verhoeff's hematoxylin stain C-22880 C1319311
SCT 20230008 vital new red stain C-22858 C0303876
SCT 88625006 water soluble aniline blue stain C-22904 C1321796
SCT 58755002 water soluble anthracene brown stain C-22954 C0303912
SCT 12119009 water soluble nigrosine stain C-22933 C0303909
SCT 60739006 waxoline blue stain C-22957 C0303915
SCT 409549005 wayson stain F-61E5A C1443889
SCT 373682001 wright stain F-619B7 C1261259
SCT 55831004 xylene cyanol FF stain C-22888 C0303889
SCT 255813003 Ziehl-Neelsen stain C-2282C C0440051
SCT 29252006 acridine orange stain C-22A08 C0001185
SCT 17693003 acriflavine stain C-22A07 C0001187
SCT 84656005 atebrin FS stain C-22A03 C0303922
SCT 73251007 auramine G stain C-22A02 C0303921
SCT 81397005 auramine O stain C-22A01 C0878260
SCT 49687009 coriphosphine stain C-22A11 C0056341
SCT 85596006 fluorescein stain C-22A05 C0060520
SCT 108880002 fluorexon stain C-22AA1 C0060549
SCT 27671009 rhodamine B stain C-22A04 C0073194
SCT 25351006 Fluorescein sodium stain C-22A06 C0147866
SCT 36572009 Sudan black B stain C-22864 C0075489
SCT 310805002 Sudan black stain C-2282E C0588374
SCT 10740006 Sudan blue stain C-22958 C0075490
SCT 12030009 Sudan II stain C-22807 C0075492
SCT 39777001 Sudan III stain C-22861 C0075491
SCT 69133007 Sudan IV stain C-22862 C0074127
SCT 76925007 alkali blue 5B (4B) stain C-22903 C0303894
SCT 63929007 alkali blue 6B stain C-22905 C0303895
SCT 34128002 chrome azurol S stain C-22911 C0055614
SCT 17172002 dibromofluorescein stain C-22918 C0303901
SCT 65445001 ethyl violet stain C-22897 C0059784
SCT 22021002 methyl green stain C-22896 C0025701
SCT 15896008 methyl violet 2B stain C-22892 C0303890
SCT 14544006 methyl violet 6B stain C-22894 C0303891
SCT 76001002 pyronine B stain C-22916 C0072769
SCT 43106008 pyronine G stain C-22915 C0034316
SCT 29522004 toluidine blue stain C-22951 C0040380
SCT 82682000 victoria blue 4R stain C-22895 C0078233
SCT 22749001 victoria blue B stain C-22913 C0078234
SCT 36879007 water soluble eosin stain C-22919 C0303902
Microscopy Illuminator and Sensor Color Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20100824yyyymmdd UID: 1.2.840.10008.6.1.899
Microscopy Illuminator and Sensor Color
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 414298005 Full Spectrum R-102C0 C1532530
SCT 134223000 Narrow R-41727 C0333164
SCT 414497003 Infrared R-102BE C1532326
SCT 371240000 Red G-A11A C1260956
SCT 371246006 Green G-A11E C0332583
SCT 405738005 Blue G-A12F C1260957
SCT 415770004 Ultraviolet R-102BF C1532472
Staining Protocols This Context Group is intended for use in the Scheduled Protocol Code Sequence (0040,0008) and the Performed Protocol Code Sequence (0040,0260) attributes for an automated slide stainer. When so used, an Item with value (127790008, SCT, "Staining") (703857004, SCT, "Staining") will also include a Protocol Context Sequence (0040,0440) usingwhich may use to identify the specific stain substance or specify a more specific stain method. Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20111028yyyymmdd UID: 1.2.840.10008.6.1.944
Staining Protocols
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 127790008 703857004 Staining P3-00003 R-FBDF9 C0487602 C3839348
SCT 104210008 Hematoxylin and eosin stain method P3-50495 C0523207
SCT 708056006 Acid fast stain technique R-FF04E C0200974
SCT 406979008 Ziehl-Neelsen stain method P3-00068 C1318721
Previously, (127790008, SCT, "Staining method (procedure)") was used with the meaning "Staining", but has been replaced by (703857004, SCT, "Staining technique (qualifier value)").
DICOM PS3.16 as follows for reference unchanged:
Specimen Preparation Steps Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20080626 UID: 1.2.840.10008.6.1.1051
Specimen Preparation Steps
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 433455005 Specimen microwave heating P3-40005 C2317595
SCT 433457002 Specimen steam heating P3-40009 C2316565
SCT 433456006 Protease digestion of tissue specimen P3-40006 C2316566
SCT 433470006 Specimen dehydration P3-4000B C2317330
SCT 27872000 Specimen freezing P3-05050 C0200367
SCT 433452008 Specimen clearing P3-40003 C2316366
Specimen Fixatives Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20190124 UID: 1.2.840.10008.6.1.1052
Specimen Fixatives
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 434162003 Neutral Buffered Formalin C-2141C C0492002
SCT 433474002 Bouin's fluid F-62235 C0053963
SCT 431510009 Formalin C-2141B C0949307
SCT 433338005 Carnoy's fluid F-62231 C2317379
SCT 434295000 Formol sublimate F-62238 C0621539
SCT 433471005 Helly's fluid F-62233 C2317380
SCT 430028007 Michel's medium F-6220F C1550080
SCT 433473008 Zenker's fluid F-62234 C2317478
SCT 52836003 Paraformaldehyde C-21403 C0070066
SCT 2869004 Acetic acid C-21624 C0000983
SCT 259153006 Chloroform C-20830 C0008238
SCT 430821002 Chromium trioxide C-12916 C0055630
SCT 419442005 Ethanol C-21047 C0001962
SCT 111095003 Formaldehyde C-21402 C0016564
SCT 11496005 Mercuric chloride C-13321 C0025417
SCT 259221006 Methanol C-2102B C0001963
SCT 13931001 Osmium tetroxide C-15211 C0029385
SCT 24215009 Picric acid C-21919 C0071044
SCT 19893005 Potassium dichromate C-13518 C0032829
Specimen Embedding Media Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20080626 UID: 1.2.840.10008.6.1.1053
Specimen Embedding Media
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 311731000 Paraffin wax F-616D8 C0030415
SCT 433469005 Tissue freezing medium F-62232 C2315537
SCT 61088005 Plastic C-2A000 C0032167
SCT 10249006 Agar C-84085 C0001771
SCT 65345002 Epoxy resin C-2A400 C0014631
SCT 261712009 Acrylic resin C-100EA C0444831
Add new terms to DICOM PS3.16:
DICOM Controlled Terminology Definitions (Normative)
DICOM Controlled Terminology Definitions
Code Value Code Meaning Definition Notes
ddd001 Chromogen A substance, itself without definite color, which may be transformed into a pigment. E.g., as used to visualize a monoconal antibody to a receptor for immunohistochemistry. From http://medical-dictionary.thefreedictionary.com/chromogen
ddd002 Reporter enzyme Enzyme that performs a chemical reaction that produces a color compound. E.g., as used to visualize a monoconal antibody to a receptor for immunohistochemistry.
ddd003 Subcycle A subordinate event in a sequence of subordinate events to a parent event in a sequence of events.
Add new context group UIDs to DICOM PS3.6:
Registry of DICOM Unique Identifiers (UIDs) (Normative)
Context Group UID Values
Context UID Context Identifier Context Group Name Comment
uuux8116
uuux8117
uuux8118
uuux8119
uuux8129
Amend DICOM PS3.17:
Slide ... 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 / 1 CODE (424361007, SCT, "Using substance") (12710003, SCT, "hematoxylin stain")
5 8001 / 9 8003 / 1 CODE (424361007, SCT, "Using substance") (36879007, SCT, "water soluble eosin stain")
6 8001 / 9 8003 / 3 CODE (127790008, SCT, "Staining") (104210008, SCT, "Hematoxylin and eosin stain method")