> ## Documentation Index
> Fetch the complete documentation index at: https://docs.strandai.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Supported markers

> Browse the 52 protein markers Lattice predicts from H&E today, grouped by immune lineage, checkpoint, stromal, and tumor biology, with model versions.

Strand AI predicts protein markers directly from an H\&E whole-slide image
using **Lattice**, our spatial-proteomics imputation model. Each marker
listed below has a model checkpoint trained against paired multiplex
ground truth, predominantly from tumor biology. Predictions outside an
oncology context are exploratory; see the [intro page](/introduction)
for what this means for non-cancer tissue.

To request a marker not on this list, email
[support@strandai.com](mailto:support@strandai.com). We add markers as
ground-truth training data becomes available.

<Note>
  Per-marker model cards with calibration plots, per-tissue accuracy, and
  held-out benchmarks are coming soon. The table below is a snapshot of
  what's predictable today.
</Note>

## Marker panel

All 52 markers below are served by Lattice. Grouped by biology; expand any
group to see the full list.

<AccordionGroup>
  <Accordion title="Immune lineage (18)" defaultOpen={true}>
    | Marker     | Predicts                                                  |
    | ---------- | --------------------------------------------------------- |
    | **CD3e**   | Pan-T cell marker.                                        |
    | **CD4**    | Helper T cells.                                           |
    | **CD8**    | Cytotoxic T cells.                                        |
    | **CD45**   | Pan-leukocyte.                                            |
    | **CD45RA** | Naive T cells (PTPRC isoform).                            |
    | **CD45RO** | Memory T cells (PTPRC isoform).                           |
    | **CD20**   | Mature B cells.                                           |
    | **CD21**   | Mature B cells and follicular dendritic cells.            |
    | **CD79**   | B cell receptor signaling.                                |
    | **CD11b**  | Myeloid / neutrophils / monocytes.                        |
    | **CD11c**  | Dendritic cell / myeloid lineage marker.                  |
    | **CD14**   | Monocytes and tissue macrophages.                         |
    | **CD68**   | Pan-macrophage.                                           |
    | **CD163**  | M2-polarised macrophages.                                 |
    | **CD141**  | Endothelial and BDCA-3 dendritic cell subset.             |
    | **CD66**   | Granulocytes and select epithelial cells (CEACAM family). |
    | **MPO**    | Neutrophil granule enzyme.                                |
    | **FoxP3**  | Regulatory T cells.                                       |
  </Accordion>

  <Accordion title="Activation, checkpoint & function (15)">
    | Marker        | Predicts                                                |
    | ------------- | ------------------------------------------------------- |
    | **PD1**       | T-cell exhaustion / checkpoint.                         |
    | **PDL1**      | Tumor and immune PD-L1 expression.                      |
    | **LAG3**      | T cell exhaustion / checkpoint.                         |
    | **VISTA**     | T cell suppression / checkpoint.                        |
    | **ICOS**      | T cell costimulation.                                   |
    | **CD38**      | B, T, and plasma cell activation.                       |
    | **CD39**      | T-regulatory / endothelial ectonucleotidase.            |
    | **CD40**      | B cell activation and antigen-presenting cells.         |
    | **CD44**      | Hyaluronan receptor; broad immune and tumor expression. |
    | **IDO1**      | Immunosuppressive enzyme.                               |
    | **GranzymeB** | Cytotoxic effector function.                            |
    | **IFNg**      | Interferon-γ; activated T and NK cells.                 |
    | **HLA-DR**    | MHC class II; antigen-presenting cells.                 |
    | **HLA-ABC**   | Classical MHC class I.                                  |
    | **HLA-E**     | Non-classical MHC class I; NK cell inhibition.          |
  </Accordion>

  <Accordion title="Nuclear & proliferation (3)">
    | Marker   | Predicts                                     |
    | -------- | -------------------------------------------- |
    | **DAPI** | Nuclear counterstain (sanity-check channel). |
    | **Ki67** | Proliferation marker.                        |
    | **PCNA** | Proliferation marker (DNA replication).      |
  </Accordion>

  <Accordion title="Epithelial & tumor (6)">
    | Marker          | Predicts                                         |
    | --------------- | ------------------------------------------------ |
    | **PanCK**       | Pan-cytokeratin; epithelial / tumor compartment. |
    | **EpCAM**       | Pan-epithelial adhesion marker.                  |
    | **ECad**        | E-cadherin; epithelial cell-cell adhesion.       |
    | **Keratin8/18** | Simple epithelial cytokeratins.                  |
    | **TP63**        | Squamous and basal epithelial cells.             |
    | **GATA3**       | TH2 / luminal epithelial transcription factor.   |
  </Accordion>

  <Accordion title="Stromal, vascular & structural (7)">
    | Marker         | Predicts                                                       |
    | -------------- | -------------------------------------------------------------- |
    | **aSMA**       | α-smooth muscle actin; stromal myofibroblasts and vasculature. |
    | **Vimentin**   | Mesenchymal marker; stromal and EMT-state cells.               |
    | **Caveolin1**  | Caveolae scaffold; stromal and tumor compartments.             |
    | **CD31**       | PECAM-1; endothelium and microvasculature.                     |
    | **CD34**       | Endothelial and hematopoietic stem / progenitor cells.         |
    | **CollagenIV** | Basement membrane.                                             |
    | **Podoplanin** | Lymphatic endothelium and cancer-associated stroma.            |
  </Accordion>

  <Accordion title="Other (3)">
    | Marker     | Predicts                                   |
    | ---------- | ------------------------------------------ |
    | **BCL2**   | Apoptosis regulator.                       |
    | **Gal3**   | Galectin-3; immune and stromal modulation. |
    | **PGP9.5** | Pan-neuronal / nerve fibers.               |
  </Accordion>
</AccordionGroup>

## Reading the predictions

Predictions are returned as a multi-channel OME-Zarr aligned to the slide's
pixel grid. Each requested marker becomes a separate channel; the SDK
helpers convert it to `AnnData` (Python) or `SpatialExperiment` (R) so
you can treat it like real multiplex data.

See the [Quickstart](/quickstart) for an end-to-end example and the
[Python](/sdks/python) / [R](/sdks/r) SDK reference for the conversion
helpers.

## Accuracy caveats

* Predictions are **model outputs**, not ground truth. Use them as a
  hypothesis-generation surface, particularly on cohorts that look
  out-of-distribution to the training data.
* Per-marker confidence varies. Lineage and structural markers (e.g.
  PanCK, CD31, aSMA) generally calibrate better than functional /
  activation markers (e.g. GranzymeB, PD1).
* We do not yet publish per-tissue or per-organ accuracy numbers. Those
  ship with the per-marker model cards.

Reach out at [support@strandai.com](mailto:support@strandai.com) if you
want pre-publication benchmarks on a specific tissue or marker.