M-Optimus tile embedding - Bioptimus Documentation

POST

api

embed

m-optimus

M-Optimus tile embedding

curl --request POST \
  --url http://localhost:8080/api/embed/m-optimus \
  --header 'Content-Type: application/json' \
  --data '
{
  "image_data": "<base64-png-224x224>",
  "slide_name": "slide_A",
  "x": 0,
  "y": 0,
  "width": 224,
  "height": 224,
  "tissue_ratio": 0.8,
  "patch_idx": 0,
  "resolution": 0.5
}
'

{
  "output": [
    123
  ],
  "slide_name": "<string>",
  "x": 123,
  "y": 123,
  "width": 123,
  "height": 123,
  "tissue_ratio": 123,
  "patch_idx": 123,
  "resolution": 123
}

Body

application/json

image_data

string

required

Base64-encoded PNG tile. (The SDK also accepts a PIL Image or raw bytes.)

slide_name

string

required

Stem of the source slide filename.

integer

required

Tile x-coordinate in the slide.

integer

required

Tile y-coordinate in the slide.

width

integer

required

Tile width in pixels.

height

integer

required

Tile height in pixels.

patch_idx

integer

required

Index of this tile in the extraction plan.

bulk_rna

number[] | null

Optional bulk RNA counts vector (M-Optimus prediction only).

tissue_ratio

number | null

Fraction of tissue in the tile.

resolution

number | null

Extraction resolution in microns per pixel.

Response

Embedding result

output

number[]

Model output vector: embeddings (1536), gene predictions, or a flattened mask.

slide_name

string

integer

width

integer

height

integer

tissue_ratio

number | null

patch_idx

integer

resolution

number | null

M-Optimus spatial gene expression predictionPredict spatial gene expression from a tile and optional bulk RNA counts. Input: a 224×224 tile at 0.5 MPP, plus an optional `bulk_rna` vector aligned to the model's input gene set (see GET /api/metadata/m-optimus). When `bulk_rna` is omitted, a zero vector is used (H&E-only mode). Output: predicted expression for each output gene in `output`.

⌘I

M-Optimus tile embedding

curl --request POST \
  --url http://localhost:8080/api/embed/m-optimus \
  --header 'Content-Type: application/json' \
  --data '
{
  "image_data": "<base64-png-224x224>",
  "slide_name": "slide_A",
  "x": 0,
  "y": 0,
  "width": 224,
  "height": 224,
  "tissue_ratio": 0.8,
  "patch_idx": 0,
  "resolution": 0.5
}
'

{
  "output": [
    123
  ],
  "slide_name": "<string>",
  "x": 123,
  "y": 123,
  "width": 123,
  "height": 123,
  "tissue_ratio": 123,
  "patch_idx": 123,
  "resolution": 123
}