Project objects¶

open_export() creates these reader-bound objects. Use their lookup and navigation methods rather than constructing them directly.

ProjectExport ¶

An open, validated NeuroQP project export.

member ¶

member(path: str) -> FileArtifact

Get a raw archive member as a file artifact.

find_stainings ¶

find_stainings(
    name: str | None = None,
) -> tuple[Staining, ...]

Find canonical staining names using a case/punctuation-insensitive alias.

Animal ¶

An animal and its slices.

Slice ¶

A project slice with navigation to related objects.

image ¶

image(image_id: str) -> Image

Get this slice's uniquely identified image.

find_images ¶

find_images(
    *,
    staining: Staining | Staining | str | None = None,
    magnification: str | None = None,
    filename: str | None = None,
) -> tuple[Image, ...]

Find images using any combination of common metadata fields.

Image ¶

An exported image artifact.

size_bytes `property` ¶

size_bytes: int

Encoded image-file size in bytes.

open ¶

open() -> BinaryIO

Open the exact archived image member.

as_path ¶

as_path(
    *, directory: str | Path | None = None
) -> AbstractContextManager[Path]

Provide the image as a filesystem path within a context manager.

Staining ¶

A project staining.

FileArtifact ¶

A file contained in an open export.

size_bytes `property` ¶

size_bytes: int

Encoded artifact size in bytes.

This is the stored file size, not the memory required for decoded image pixels.

open ¶

open() -> BinaryIO

Open the artifact as a binary stream.

Returns:

Type	Description
`BinaryIO`	A native file stream for an extracted export or a streaming ZIP member.

Notes

Close the stream before closing its parent export.

as_path ¶

as_path(
    *, directory: str | Path | None = None
) -> Iterator[Path]

Provide a filesystem path for the artifact.

Parameters:

Name	Type	Description	Default
`directory`	`str \| Path \| None`	Scratch directory used when a ZIP member must be copied.	`None`

Returns:

Type	Description
`AbstractContextManager[Path]`	A context manager yielding the original path for a directory export or a temporary copy for a ZIP export.

Notes

Use the path only inside this context and while the parent export is open. Temporary ZIP copies are removed when the context exits.

Registration ¶

Registration module access.

for_slice ¶

for_slice(
    slice_: Slice | Slice | str,
) -> SliceRegistration | None

Return available registration data for one slice.

SliceRegistration `dataclass` ¶

Available registration data for one slice.

ClassificationModule ¶

Provide the classifications and cell matches included in an export.

Attributes:

Name	Type	Description
`classifications`		Selected classifications, one per included staining.
`matches`		Included staining-pair cell matches.

for_staining ¶

for_staining(
    staining: Staining | Staining | str,
) -> Classification

Get the selected classification for a staining.

Parameters:

Name	Type	Description	Default
`staining`	`Staining \| Staining \| str`	Staining object, metadata record, exact name, or ID.	required

Returns:

Type	Description
`Classification`	Selected classifier and available results.

Raises:

Type	Description
`ObjectNotFoundError`	If the export has no classification for the staining.
`AmbiguousNameError`	If the staining name is not unique.

match ¶

match(pair_key: str) -> Match

Get a staining-pair match by its exported key.

Parameters:

Name	Type	Description	Default
`pair_key`	`str`	Key discovered from :attr:`matches`.	required

Returns:

Type	Description
`Match`	Match metadata and available slice results.

Raises:

Type	Description
`ObjectNotFoundError`	If the pair key is not present.

Classification ¶

Provide classifier metadata and results for one staining.

Attributes:

Name	Type	Description
`staining`		Classified project staining.
`classifier`		Selected classifier metadata.
`training_summary`		Training summary current at export time.
`training_samples`		Exported positive and negative training samples.
`result_index`		Slice-level result metadata available for lazy loading.
`omitted_slices`		Documented slices without a result.

find_training_samples ¶

find_training_samples(
    *,
    slice: Slice | Slice | str | None = None,
    label: str | None = None,
    cell_id: int | None = None,
) -> tuple[TrainingSample, ...]

Filter exported training samples.

Parameters:

Name	Type	Description	Default
`slice`	`Slice \| Slice \| str \| None`	Slice object, metadata record, or ID to include.	`None`
`label`	`str \| None`	Exported label, normally `"on"` or `"off"`.	`None`
`cell_id`	`int \| None`	Cell label to include.	`None`

Returns:

Type	Description
`tuple of TrainingSample`	Samples matching every supplied filter.

find_omitted_slices ¶

find_omitted_slices(
    *,
    slice: Slice | Slice | str | None = None,
    reason_code: str | None = None,
) -> tuple[SliceExclusion, ...]

Filter slices that have no classification result.

Parameters:

Name	Type	Description	Default
`slice`	`Slice \| Slice \| str \| None`	Slice object, metadata record, or ID to include.	`None`
`reason_code`	`str \| None`	Stable exporter reason code to include.	`None`

Returns:

Type	Description
`tuple of SliceExclusion`	Omissions matching every supplied filter.

result_info ¶

result_info(
    slice_: Slice | Slice | str,
) -> ClassificationResultInfo

Get result metadata for one slice without loading arrays.

Parameters:

Name	Type	Description	Default
`slice_`	`Slice \| Slice \| str`	Slice object, metadata record, or ID.	required

Returns:

Type	Description
`ClassificationResultInfo`	Slice-level result metadata.

Raises:

Type	Description
`ObjectNotFoundError`	If the slice has no classification result.

load_result ¶

load_result(
    slice_: Slice | Slice | str,
) -> ClassificationResult

Load and validate one slice's classification arrays.

Parameters:

Name	Type	Description	Default
`slice_`	`Slice \| Slice \| str`	Slice object, metadata record, or ID.	required

Returns:

Type	Description
`ClassificationResult`	Aligned cell IDs, centroids, probabilities, and classifications.

Raises:

Type	Description
`ObjectNotFoundError`	If the slice has no classification result.
`InvalidExportError`	If the stored arrays fail validation.
`ClosedExportError`	If the parent export is closed.

load_results ¶

load_results() -> ClassificationResults

Load and concatenate every available slice result.

Returns:

Type	Description
`ClassificationResults`	Aligned arrays with a slice ID for every detected cell.

Raises:

Type	Description
`InvalidExportError`	If any stored result fails validation.
`ClosedExportError`	If the parent export is closed.

Match ¶

Provide cell-match metadata and results for one staining pair.

Attributes:

Name	Type	Description
`pair_key`		Opaque exported key used to retrieve this match.
`staining_a, staining_b`		Stainings in the exported pair definition. Read each result's metadata for its actual NPZ side orientation.
`result_index`		Slice-level match metadata available for lazy loading.
`omitted_slices`		Documented slices without a match result.

find_omitted_slices ¶

find_omitted_slices(
    *,
    slice: Slice | Slice | str | None = None,
    reason_code: str | None = None,
) -> tuple[SliceExclusion, ...]

Filter slices that have no match result.

Parameters:

Name	Type	Description	Default
`slice`	`Slice \| Slice \| str \| None`	Slice object, metadata record, or ID to include.	`None`
`reason_code`	`str \| None`	Stable exporter reason code to include.	`None`

Returns:

Type	Description
`tuple of SliceExclusion`	Omissions matching every supplied filter.

result_info ¶

result_info(slice_: Slice | Slice | str) -> MatchResultInfo

Get match metadata for one slice without loading arrays.

Parameters:

Name	Type	Description	Default
`slice_`	`Slice \| Slice \| str`	Slice object, metadata record, or ID.	required

Returns:

Type	Description
`MatchResultInfo`	Slice-level match metadata, including side identities.

Raises:

Type	Description
`ObjectNotFoundError`	If the slice has no match result.

load_result ¶

load_result(slice_: Slice | Slice | str) -> MatchResult

Load and validate one slice's match arrays.

Parameters:

Name	Type	Description	Default
`slice_`	`Slice \| Slice \| str`	Slice object, metadata record, or ID.	required

Returns:

Type	Description
`MatchResult`	Aligned one-to-one cell-pair arrays.

Raises:

Type	Description
`ObjectNotFoundError`	If the slice has no match result.
`InvalidExportError`	If the stored arrays fail validation.
`ClosedExportError`	If the parent export is closed.

load_results ¶

load_results() -> MatchResults

Load and concatenate every available slice match.

Returns:

Type	Description
`MatchResults`	Aligned arrays with a slice ID for every matched pair.

Raises:

Type	Description
`InvalidExportError`	If any stored match fails validation.
`ClosedExportError`	If the parent export is closed.

Project objects¶

ProjectExport ¶

member ¶

find_stainings ¶

Animal ¶

Slice ¶

image ¶

find_images ¶

Image ¶

size_bytes property ¶

open ¶

as_path ¶

Staining ¶

FileArtifact ¶

size_bytes property ¶

open ¶

as_path ¶

Registration ¶

for_slice ¶

SliceRegistration dataclass ¶

ClassificationModule ¶

for_staining ¶

match ¶

Classification ¶

find_training_samples ¶

find_omitted_slices ¶

result_info ¶

load_result ¶

load_results ¶

Match ¶

find_omitted_slices ¶

result_info ¶

load_result ¶

load_results ¶

size_bytes `property` ¶

size_bytes `property` ¶

SliceRegistration `dataclass` ¶