> ## 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

> The protein markers Lattice predicts from H&E on the public panel, with genes and curated biology notes.

Strand AI predicts spatial protein marker channels directly from an H\&E
whole-slide image using **Lattice**, our spatial-proteomics imputation model.
Each marker 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.

## Public panel

The public panel is the validated 8-channel set below: a nuclear counterstain
plus seven biological markers spanning the T cell, B cell, macrophage,
epithelial, proliferation, and checkpoint compartments. It is the panel we
publish public cohorts and accuracy claims against.

| Marker | Gene  | Category                | Predicts                                         |
| ------ | ----- | ----------------------- | ------------------------------------------------ |
| DAPI   | DAPI  | Nuclear                 | Nuclear counterstain (sanity-check channel).     |
| PanCK  | KRT   | Epithelial & tumor      | Pan-cytokeratin; epithelial / tumor compartment. |
| CD3e   | CD3E  | Immune lineage          | Pan-T cell marker.                               |
| CD8    | CD8A  | Immune lineage          | Cytotoxic T cells.                               |
| CD20   | MS4A1 | Immune lineage          | Mature B cells.                                  |
| CD68   | CD68  | Immune lineage          | Pan-macrophage.                                  |
| Ki67   | MKI67 | Nuclear & proliferation | Proliferation marker.                            |
| PDL1   | CD274 | Activation & checkpoint | Tumor and immune PD-L1 expression.               |

Additional markers are available to contracted partners under agreement. The
expanded panel changes as checkpoints are validated, so we do not publish a
fixed count: [`GET /markers`](/api-reference/endpoint/listMarkers) is the
authoritative list for your account. Contact
[support@strandai.com](mailto:support@strandai.com) to discuss an expanded panel
for your cohort.

## Discovering markers programmatically

The [`GET /markers`](/api-reference/endpoint/listMarkers) endpoint returns the
exact set your account may request, so agents and scripts can discover valid
names upfront instead of guessing. The list matches what a prediction will
accept: a self-signup account sees the public panel; a contracted account sees
its expanded panel.

<CodeGroup>
  ```bash cURL theme={"dark"}
  curl https://app.strandai.com/api/v1/markers \
    -H "Authorization: Bearer $STRAND_API_KEY"
  ```

  ```python Python theme={"dark"}
  client.markers.list().names
  ```

  ```r R theme={"dark"}
  strand_markers_list(client)$markers
  ```

  ```bash CLI theme={"dark"}
  strand markers
  ```
</CodeGroup>

The MCP server exposes the same list as the `list_markers` tool.

## 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 work with it using your existing multiplex tooling.

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, CD8) generally calibrate better than functional / activation
  markers (e.g. PDL1).
* We do not yet publish per-tissue or per-organ accuracy numbers. Those
  will be added as benchmarks become available.

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