The algorithm plane

Serve functions to the biopb agent over the biopb.image Ops protocol, from one file or a Docker image.

Serve functions over Ops

One file, no packaging. A parameter annotated Tensor(axes) is a tensor argument; every other parameter is a kwarg, advertised with its default.

# /// script
# requires-python = ">=3.11"
# dependencies = ["biopb-image-base[lazy]", "scikit-image"]
# ///
from biopb_image_base import Tensor, op, serve

@op(description="Mean intensity and area per label", labels=["measurement"])
def label_stats(image: Tensor("YX"), labels: Tensor("YX")) -> dict:
    from skimage.measure import regionprops_table
    return regionprops_table(labels, image, properties=["label", "area", "mean_intensity"])

@op(description="Gaussian denoise", labels=["denoising"], input="blocks", overlap=16)
def gaussian(image: Tensor("YX"), sigma: float = 2.0):
    from skimage.filters import gaussian as g
    return g(image, sigma=sigma, preserve_range=True)

if __name__ == "__main__":
    serve()

uv run server.py --port 50051 serves it; --describe prints the op list and exits.

• input="eager" (default) hands the function numpy arrays, "lazy" dask arrays, and "blocks" maps a pixelwise function over blocks with block_shape and overlap, iterating the axes not in axes.
• A single return value is the output result, a tuple 0, 1, .... Arrays are tensors; anything else is JSON. A generator yields progress strings and per-item outputs, and what it returns is the final event's outputs.
• Large results go to the embedded tensor server under --cache-dir, else to the plane named by BIOPB_TENSOR_URL/BIOPB_TENSOR_TOKEN, else inline.
• The core install serves inline pixels only; [lazy] adds lazy input and the plane sink. The server checks $BIOPB_ALGORITHM_TOKEN when set; bound off loopback without one, it mints one and prints it.

Register a server with biopb-mcp

A server file copied to ~/.config/biopb/algorithms/<name>.py is run by the control in an environment of its own. A server running elsewhere is named with a <name>.json file there:

{"url": "grpc://your_ip_address:50051"}

The control probes it and the kernel binds its ops into ops. A server that does not implement Ops -- one still speaking the retired ProcessImage protocol, say -- is listed as an error.

The Docker base image

biopb-image-base carries biopb, the tensor server and this package, for a server whose model is easier to ship as an image. It defines no entrypoint: a derived image adds its model's packages and a server file.

# Dockerfile
FROM biopb-image-base

RUN pip install --no-cache-dir cellpose
COPY server.py /opt/biopb/server.py

ENTRYPOINT ["python", "/opt/biopb/server.py", "--host", "0.0.0.0"]
CMD ["--cache-dir", "/data/cache"]

docker run --rm -p 50051:50051 -p 8817:8817 -v tensor-cache:/data/cache \
  my-biopb-server \
    --cache-dir /data/cache --cache-size 32GB \
    --tensor-external-location grpc://$(hostname):8817

Bound off loopback, the server mints a token and prints it unless BIOPB_ALGORITHM_TOKEN is set. --cache-dir returns large results through an embedded tensor server (port 8817), and --tensor-external-location is the address clients reach it at: localhost works only for clients on the same host.

Development

Build the base image

Run from repo root:

./biopb-image-runtime/scripts/build.sh            # from the latest tags
./biopb-image-runtime/scripts/build.sh --no-cache

Or build the wheels yourself:

pip wheel . --no-deps -w wheels/
pip wheel biopb-tensor-server/ --no-deps -w wheels/
docker build -t biopb-image-base -f biopb-image-runtime/Dockerfile .

docker compose -f biopb-image-runtime/docker-compose.yaml up runs echo_server.py, an Ops server that echoes its input, with the embedded cache.

Tests

pip install -e "biopb-image-runtime[test]"
pytest biopb-image-runtime/tests/

The server tests run an Ops server file as a subprocess; no Docker or GPU.

Environment Variables

Files

biopb-image-runtime/
├── Dockerfile              # Base image for derived services
├── docker-compose.yaml     # Development setup
├── echo_server.py          # The compose file's Ops server
├── pyproject.toml          # Python package
├── requirements.txt        # The image's dependencies
├── src/biopb_image_base/
│   ├── __init__.py
│   ├── ops.py              # @op, serve(): the Ops server
│   ├── server.py           # Embedded tensor cache
│   ├── common.py           # Token interceptor, error translation
│   ├── health.py           # gRPC health check
│   ├── logging_config.py   # Logging setup
│   ├── stitch.py           # Stitching tiled segmentations
│   └── dynamics_local.py   # Flow dynamics for stitching
├── tests/
├── scripts/
│   └── build.sh            # Build script
└── README.md