itasc.contact_analysis.quantifiers.contacts

Cell-cell contacts quantifier — the registry adapter over the contacts code.

Wraps itasc.contact_analysis.contacts so the studio can build and read contacts through the generic Quantifier interface. Its chosen persistence is the contact_analysis.h5 schema, unchanged from before the rename.

Classes

ContactsQuantifier()

Quantifies cell-cell contacts: edges, T1 events, NLS classes.
class itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier[source]

Bases: Quantifier

Quantifies cell-cell contacts: edges, T1 events, NLS classes.

quantity_id: ClassVar[str] = 'contacts'

Stable key; an empty value marks an intermediate (non-registered) base.

display_name: ClassVar[str] = 'Cell–cell contacts'

Human-readable label shown wherever a quantity is selected.

requires: ClassVar[tuple[str, ...]] = ('cell_labels_path',)

PositionInputs field names this quantifier needs to build.

produces: ClassVar[str] = 'contact_analysis_path'

The contacts artifact is the input the contacts-derived quantifiers (neighbor count / enrichment / z-score / density / signed contact length) consume.

default_output_name: ClassVar[str] = 'contact_analysis.h5'

Default artifact name when a position does not dictate one.

build(inputs, output_path, *, params=None, progress_cb=None)[source]
Return type:

Path

Parameters:
default_output(inputs)[source]

The contacts .h5 lives in the position base folder, beside the committed cell_labels.tif / nucleus_labels.tif — not under the shared OUTPUT_SUBDIR that the other (dynamics) quantifiers persist into. One homogeneous per-position layout for the downstream-stable inputs and this derived-from-them graph.

Return type:

Path

Parameters:

inputs (PositionInputs)

read(output_path)[source]
Return type:

Any

Parameters:

output_path (Path)

object_table(output_path)[source]

The per-cell cells table (frame · cell_id · morphometry).

The subpopulation label is no longer carried here — it lives in the NLS sidecar CSV and is joined by cell_id at pool time.

Return type:

Mapping[str, ndarray]

Parameters:

output_path (Path)