Staining mapping
Two mapping modes exist for staining in mappers.xlsx. Which one to use depends on the staining type.
→ For the mapper row structure and column layout, see mappers.xlsx.
Choosing a mapping mode
| Staining type | Mapper row Type |
Notes |
|---|---|---|
| Standalone chemical stain | procedure |
Entire stain mapped as one entity |
| IHC antibody stain | list |
Each component mapped separately |
| In-situ hybridisation (ISH; CISH = chromogenic ISH) | list |
Each component mapped separately |
| Immunofluorescence (IF) | list |
Each component mapped separately |
When a chemical stain is used as a counterstain within an IHC panel, it must follow the list mode — not procedure — so it can be listed alongside the antibody components.
Chemical stains
Use Type: procedure. Map the entire staining procedure to its SNOMED CT Concept ID (International Edition).
Common SNOMED CT codes
| Stain | Concept ID | Fully Specified Name (FSN) |
|---|---|---|
| Hematoxylin & Eosin (H&E) | 104210008 | Hematoxylin and eosin stain method (procedure) |
| Alcian blue / PAS | 117224009 | Alcian blue with Periodic acid Schiff stain method (procedure) |
| Congo red | 117055006 | Congo red stain method (procedure) |
| Giemsa | 104208006 | Giemsa stain method (procedure) |
| Gomori | 117236003 | Gomori stain method (procedure) |
| Masson trichrome | 117018006 | Masson trichrome stain method (procedure) |
| Periodic acid Schiff (PAS) | 104216002 | Periodic acid Schiff stain method (procedure) |
Finding a missing code
Use the SNOMED CT Browser (International Edition). Search for the staining method name, select the result with semantic type procedure, and copy the Concept ID. Use only Active concepts.
If no SNOMED CT code exists for a staining method, do not leave the field empty. Provide a consistent free-text string as the value instead — the same consistency rule that applies to IHC antibody names (see Antibody naming): choose one string for the method and reuse it across every dataset your site submits. Reach support if you are unsure whether a code exists.
Targeted stains (IHC, ISH, IF)
Use Type: list. Each individual staining component — each antibody or probe, and the counterstain — must be a separate row that shares the same Mapping Key.
There are no SNOMED CT codes for IHC antibodies. Use a consistent free-text string for the Target field (see Antibody naming below).
Counterstain rule
Every targeted staining must include its counterstain as an additional list row with Stain Type: chemical, mapped to that counterstain’s SNOMED CT substance code.
The counterstain is usually hematoxylin in IHC — but it can be a different counterstain in some cases, and in ISH / CISH it is not necessarily hematoxylin. Map whichever counterstain was actually used. The hematoxylin case (the most common) looks like this:
| Mapping Key | Type | Stain Type | Code | Scheme | Meaning |
|---|---|---|---|---|---|
| (any IHC key) | list |
chemical |
12710003 | SNOMED CT | Hematoxylin stain (substance) |
Omitting the counterstain does not block export, but leaves the staining record incomplete in BigPicture.
Antibody naming
Use a short string that pathologists and researchers would recognise from routine practice. Apply the same string consistently across all datasets your site submits — inconsistent naming for the same antibody across datasets reduces searchability in the BigPicture Discovery service.
The same consistency rule applies to ISH / CISH probe strings: use a single, consistent value for a given probe across all datasets your site submits.
| Preferred | Avoid |
|---|---|
CD3 |
CD3 antibody, Anti-CD3 |
PD-L1 |
Programmed Death Ligand 1, Anti-PD-L1 |
PD-L1 (SP142) |
Anti-PD-L1 (SP142), SP142 alone |
A recognised clone designation is acceptable when used consistently.
Controlled vocabulary
Valid values for the controlled fields in staining mapper rows.
Stain Type (list rows only)
| Value | Use for |
|---|---|
chemical |
Chemical compounds (including counterstains) |
immunostaining |
Antibody-based stains (IHC, IF); legacy immunogenic still accepted |
in_situ_hybridisation or ish |
In-situ hybridisation (ISH / CISH) |
Values are matched case-insensitively.
Compound (list rows only)
| Value | Use for |
|---|---|
ANTIBODY |
IHC or IF antibody |
Double-stranded DNA |
ISH / CISH probe (dsDNA) |
Single-stranded DNA |
ISH / CISH probe (ssDNA) |
RNA |
RNA FISH probe |
Synthetic oligonucleotide |
Synthetic probe |
Reporter Type
| Value |
|---|
chromogen |
fluorochrome |
Reporter Color
| Value |
|---|
brown |
red |
black |
teal |
purple |
green |
yellow |
Acknowledgements
The staining domain guidance on this page — mapping-mode choice, the counterstain rule, and antibody/probe naming conventions — was contributed and reviewed by Yossra H. Selma Zidi-Mouaffak, Pathologist