Scientific results

Classification and match loaders return these containers. Their arrays align by row and are documented with shapes, dtypes, units, and side semantics below.

ClassificationResult dataclass

Store aligned classification arrays for one slice.

Attributes:

Name	Type	Description
metadata	ClassificationResultInfo	Slice, staining, classifier, lineage, and timestamp metadata.
cell_ids	Array	(N,) int32 labels from the source detection mask.
centroids	Array	(N, 2) float32 pixel coordinates in (x, y) order. The origin is the top-left of the source detection image or mask; x increases right and y increases down.
probabilities	Array	(N,) float32 classifier probabilities.
is_positive	Array	(N,) boolean mask. It is the authoritative exported classification and equals probabilities >= threshold.
threshold	float	Probability threshold used for this slice.

Notes

Every row index refers to the same detected cell across all arrays. Coordinates are image pixels, not micrometres or atlas coordinates.

positive_centroids property

positive_centroids: Array

Return centroids rows classified as positive.

ClassificationResults dataclass

Store aligned classification arrays concatenated across slices.

Attributes:

Name	Type	Description
cell_ids	Array	(N,) int32 cell labels. Labels are unique only within a slice.
slice_ids	Array	(N,) slice identifiers aligned with every other array.
centroids	Array	(N, 2) float32 source-image pixel coordinates in (x, y) order.
probabilities	Array	(N,) float32 classifier probabilities.
is_positive	Array	(N,) authoritative boolean classification mask.
by_slice	MappingProxyType[str, ClassificationResult]	Read-only mapping from slice ID to its :class:ClassificationResult.

Notes

Use (slice_id, cell_id) as a cell key. Thresholds can differ by slice and remain available through :attr:by_slice.

positive_centroids property

positive_centroids: Array

Return centroids rows classified as positive.

MatchResult dataclass

Store aligned one-to-one cell matches for one slice.

Attributes:

Name	Type	Description
metadata	MatchResultInfo	Slice metadata and the actual staining and detection run assigned to each side.
cell_ids_a, cell_ids_b		(M,) int32 cell labels for sides A and B.
centroids_a, centroids_b		(M, 2) float32 source-mask pixel coordinates in (x, y) order for the corresponding side.
intersection_area	Array	(M,) int32 overlap area in pixels.
area_a, area_b		(M,) int32 cell-mask areas in pixels for each side.
overlap_fraction_a, overlap_fraction_b		Intersection area divided by the corresponding side's area.
overlap_fraction_min	Array	Smaller of the two side-specific overlap fractions.
iou	Array	Intersection over union: intersection / (area_a + area_b - intersection).
algorithm_version	str	Matching algorithm version.
overlap_threshold	float	Minimum overlap_fraction_min retained by the matching algorithm.

Notes

Every row index describes one matched pair. Read side identities from metadata.side_a and metadata.side_b; do not infer them from the pair key.

MatchResults dataclass

Store aligned cell-match arrays concatenated across slices.

Attributes:

Name	Type	Description
slice_ids	Array	(M,) slice identifiers aligned with every other array.
cell_ids_a, cell_ids_b		(M,) int32 cell labels for sides A and B. Labels are unique only within a slice.
centroids_a, centroids_b		(M, 2) float32 source-mask pixel coordinates in (x, y) order.
intersection_area, area_a, area_b		(M,) pixel-area arrays.
overlap_fraction_a, overlap_fraction_b		(M,) side-specific intersection fractions.
overlap_fraction_min	Array	(M,) smaller side-specific overlap fraction.
iou	Array	(M,) intersection-over-union values.
by_slice	MappingProxyType[str, MatchResult]	Read-only mapping from slice ID to its :class:MatchResult.

Notes

Use (slice_id, cell_id) to identify cells. Side identities and thresholds remain available through :attr:by_slice.