Eyck

Eyck is a standalone FastAPI application for hierarchical and overlapping single-cell annotation. It discovers source-owned eyck.toml files and never imports code from those source projects or mutates their H5AD inputs.

Run a local server with:

eyck annotations serve real_datasets

Manifest v1

schema_version = 1

[[projects]]
id = "example"
title = "Example cells"
dataset_id = "example-v1"
source_owner = "source"
h5ad = "data/cells.h5ad"
labels = "annotations/example/labels.json"
output = "output/annotation_projects/example"
embeddings = [{ id = "umap", obsm = "X_umap" }]
metadata_columns = ["sample"]
modalities = [{ id = "crispr", obsm = "X_crispr" }]
initial_memberships = "output/annotation_projects/example/generated_initial.parquet"

All paths are relative to and confined within the directory containing the manifest. labels.json has schema_version and a labels array. Each label has an id, name, optional description, optional ontology_ids, and parent_ids.

Annotated matrix exchange

Eyck can declaratively export annotated count matrices without importing the producer's code or changing its H5AD and membership inputs. Each eyck.annotated_matrix.v1 export is a self-validating directory containing string feature and observation axes and a canonical int32 CSR count matrix. The format is task-neutral and records member integrity, ordered-axis and matrix semantics, the normalized export selection, and selection outcomes.

Materialize a TOML plan and validate an export with:

eyck annotated-matrix materialize export-plan.toml exports --timeout-seconds 300
eyck annotated-matrix validate exports/example