Catalog Setup

Catalog-backed commands use PyIceberg catalogs.

Commands that require catalog configuration:

• register

• ingest

• publish-chunks

• export-cytomining-catalog

Catalog Name vs Catalog Object

You can pass either:

• a catalog name string, such as "default" (resolved by PyIceberg configuration)

• a catalog object instance

Example with a catalog object:

from pyiceberg.catalog import load_catalog

from iceberg_bioimage import register_store

catalog = load_catalog("default")
result = register_store(
    "data/experiment.zarr",
    catalog,
    "bioimage.cytotable",
)
print(result.to_dict())

Recommended Namespace

For new projects, use:

• bioimage.cytotable

The library also supports fallback to legacy layouts where canonical tables already exist directly under bioimage.

Verify Catalog Access

Test catalog-backed listing with:

from iceberg_bioimage import list_catalog_tables

tables = list_catalog_tables("default", "bioimage.cytotable")
print(tables)

If this fails, validate your PyIceberg catalog settings and backend credentials before running publish/export commands.